GT Enzymes 2015 GGMM 2015 - 4ème Congrès du GT Enzymes
Transcription
GT Enzymes 2015 GGMM 2015 - 4ème Congrès du GT Enzymes
GT Enzymes 2015 (25-27 Mai 2015) et GGMM 2015 (26-28 Mai 2015) à SETE 1 Bienvenue ! Bonjour à toutes et tous et bienvenue à Sète. Nous sommes très heureux de vous accueillir au centre Lazaret du 25 au 28 mai 2015 pour le 4ème congrès du Groupe Thé matique "Enzymes: Structure, Fonction, Catalyse, Ingénierie et Régulation" et pour le 19 ème congrès du "Groupe de Graphism e et de Modélisation Moléculaire". Cette année, ces congrès se recouperont pour accentuer les échanges entre les deux groupes thématiques qui partagent des objectifs communs. Cet événement permettra de relier le côté expérimental de l' enzymologie aux m éthodes prédictives en passant par le graphisme structural et moléculaire. Deux dem i-journées seront consacrées à des thém atiques communes: "les enzy mes comme cibles th érapeutiques" et "Ingén ierie enzymatique et évolution dirigée". Nous rem ercions les bu reaux des deux groupes pou r avoir accepté cette mixité exceptionnelle. Le programme comprend 6 sessions, incluant 6 conférences plénières de 45 minutes et 3 7 conférences de 15 minutes dont les orateurs ont été sélectionnés à partir des résumé soumis, et croyez-nous le choix n'a pas été facile! Toutes les présentations par affiche, au nom bre de 45, donneront lieu à une présentation "Flash" d'une diapositive unique avec une m inute de présentation. Vous pourrez profit er des trois longues sessions de présentations par affiche pour discuter avec leurs auteurs et deux prix pour la m eilleure affiche seront rem is à l'issue des congrès respectifs. Vous participerez au jeu de "l'expert est dans la salle" qui permettra de profiter de savoir-faire originaux. Enfin, nous ser ons heureux d'entendre le lauréat du prix du GGMM, Isidro Cortes, dont l' excellent dossier a été retenu par le bureau du GGMM parmi l’ensemble des très bons dossiers déposés. Nous tenons à remercier les conférenciers invités, J. Blumberger, J. Cherfils, D. Douguet, D. Hilvert, T. Isenberg et T. St rick, dont certains viennent de loin. Nous espérons que vous profiterez pleinement de leur présence et que les discussions seront nom breuses et intéressantes. Nous remercions également le comité scientifiq ue pour son aide précieuse dans l' élaboration de ce programme: I. André, M. Baaden, S. Barb e, S. Boschi-Muller, N. Colloc' h, A. Kajava, C. Léger, M. Remaud-Simeon, F. Rodrigues-Lima, O. Sperandio, O. Taboureau et C. Tellier. Les rencontres se dérouleront dans un endroit c onvivial qui bénéficie d' un accès direct à la plage. Afin de profiter au m aximum de la belle Région du L anguedoc Roussillon, un apéritif Sétois et une dégustation de pr oduits régionaux seront offerts a ux participants. Et pour ceux qui veulent poursuivre les discussions, le bar sera ouvert jusqu'à tard dans la soirée! Nous vous souhaitons un excellent congrès, de enrichissantes. s échanges intéressants et des rencontres L'équipe organisatrice Rachel Cerdan Laurent Chaloin Frédéric de Lamotte Gilles Labesse Corinne Lionne 4 Le GT Enzymes Le Groupe Thématique « Enzymes : Structure, Fonction, Catalyse, Ingénierie, Régulation » a été créé en 2008 sous l’impulsion du conseil d’administration de la SFBBM, et à l’initiative du Pr Guy Branlant. Ce GT a pour but de fédérer au niveau national la communauté scientifique des enzymologistes au sens large, de participer à la formation des étudiants et de contribuer au maintien et au développement de cette discipline. Depuis 2009, le GT organise un congrès tous les deux ans. Le premier congrès était axé sur les aspects modernes de l'enzymologie en insistant sur les problèmes à l'interface de la chimie et de la biologie (Nancy, 2009), le second concernait les différentes disciplines et approches dans un contexte de biologie intégrative (Ax-les-Thermes, 2011), alors que le troisième abordait les enzymes dans leurs dimensions moléculaires et intégratives (Paris, 2013). Les congrès du GT permettent à des chercheurs de stature internationale mais aussi à de jeunes scientifiques de présenter leurs travaux, d’échanger sur de nouveaux résultats et projets, mais également d’établir de nouvelles collaborations et d’échanger informations et matériel. Ils contribuent ainsi à maintenir une dynamique de recherche nationale et une compétitivité sur le plan international. 5 Le GGMM Le GGMM est une société savante qui rassemble une grande partie de la communauté française dont l’activité́ est dédiée à, ou implique, l’utilisation de la modélisation moléculaire. Cette association loi 1901 a été créée en 1983 à l’initiative de Joël Janin, Evelyne James-Surcouf et Gérard Pepe dans le but de promouvoir le développement de la modélisation moléculaire. Le GGMM est également un groupe thématique de la Société Française de Biophysique (SFB) et de la Société Française de Biochimie et Biologie Moléculaire (SFBBM). Le GGMM regroupe aujourd’hui un très large panel de thématiques d'une grande diversité allant de la bio-informatique à la chimie théorique, avec des représentations à plusieurs échelles comme l'électron, les molécules et leurs assemblages et même la cellule avec des approches globales de type protéomique. Le but du GGMM est de promouvoir le développement de la modélisation moléculaire au sens large, par la mise en place d’actions spécifiques telles que le prix du GGMM qui est décerné, tous les deux ans, à un jeune chercheur en récompense de travaux originaux ainsi que la diffusion d’offres d’emplois, académiques et industrielles, en modélisation moléculaire. Il s'agit en priorité de permettre aux futures générations de modélisateurs de s'exprimer et s'échanger. Tous les deux ans, le GGMM organise un congrès dont l’objectif est de rassembler la communauté́ francophone pour communiquer sur les avancées dans le domaine de la modélisation et la dynamique moléculaire, les nouvelles approches et les nouveaux développements pour l’analyse des structures, les avancées en chimie théorique en drug design, etc... Le site web du GGMM http://ggmmfr.wordpress.com/ est 6 accessible à cette adresse : Nos partenaires Nous tenons à remercier chaleureusement tous nos partenaires et sponsors pour leur soutien financier et matériel, sans qui l'organisation de ce double congrès n'aurait pas été possible. Merci pour votre soutien et votre fidélité. 7 Programme Lundi 25 mai 2015 12:30 Déjeuner 14:15 Mot de Bienvenue – GT Enzymes Session 1 – Structures et mécanismes enzymatiques Modérateurs : Gilles LABESSE et Fernando RODRIGUES-LIMA 14:30 Jacqueline CHERFILS – Conférence Plénière Structure and function of bacterial FIC toxins 15:15 Jérôme SANTOLINI De quoi la NO-Synthase est elle le nom ? 15:30 Nolan CHATRON Piston-driven activation mechanism of VKORC1, the human vitamin K epoxide reductase 15:45 Bertrand CASTAING Inhibition sélective des ADN glycosylases : approches structure-fonction 16:00 16:30 Pause café Présentations Flash n°1 – Posters 1 à 7 S. BOSCHI-MULLER / N. COLLOC'H / R. DUVAL / A. KRIZNIK / C. MATHIEU / M. MERROUCH / S. RAHUEL-CLERMONT 16:45 Ewelina GUCA Structural characterization of Plasmodium falciparum CCT and fragment-based drug design approach for targeting phospholipid biosynthesis pathway 17:00 Pierre LAFITE Understanding the mechanism of UGT74B1 from Arabidopsis thaliana: S- or Oglycosyltransferase ? 17:15 Claire STINES-CHAUMEIL Monitoring the transition of apo i nto holo forms of soluble glucose dehydrogenase by stopped-flow and c rystallographic studies to decipher the mechanism of reconstitution/activation of this enzyme 17:30 Jean-Christophe LEC Mécanisme de la 3-mercaptopyruvate sulfurtransférase : une enzyme impliquée dans la production de sulfure d'hydrogène 17:45 Présentation Elsevier – Journal Biochimie Apéritif de bienvenue SESSION POSTERS 19:30 Dîner 18:00 8 Mardi 26 mai 2015 Matin Session 2 – Régulation et efficacité Modérateurs : Sandrine BOSCHI-MULLER et Charles TELLIER 09:30 Terence STRICK – Conférence Plénière Approches corrélatives en analyse molécule-unique 10:15 Hélène MUNIER-LEHMANN Régulation des IMPDHs bactériennes au travers des modules CBS 10:30 Nicolas BOSC Identification of Discriminant Conformation-Dependent Residues of Protein Kinases: a Proteometric Analysis 10:45 Jessica HADJ-SAID La Carbon Monoxide Dehydrogenase (CODH) de Desulfovibrio vulgaris 11:00 Pause café 11:30 Loic CARRIQUE Study of the regulatory behavior of Plasmodium falciparum IMP-specific 5'nucleotidase (PfISN1) 11:45 Sophie RAHUEL-CLERMONT Cellular redox signaling by thiol peroxidase : Mechanisms responsible for the specificity of the redox relay H2O2/Orp1/Yap1 in S. cerevisiae 12:00 Marc-André DELSUC Amyloid properties of a conserved domain in the N-Term domain of the Androgen Receptor - Implications for new therapeutic routes 12:15 Déjeuner 9 Mardi 26 mai 2015 Après-midi 14:00 Mot de Bienvenue – GGMM Session 3 – Ingénierie enzymatique et évolution dirigée Modérateurs : Christophe LEGER et Magali REMAUD SIMEON 14:15 Donald HILVERT – Conférence Plénière Design and optimization of artificial enzymes: nearer to nature 15:00 Présentations Flash n°2 – Posters 8 à 17 I. ANDRE / S. BARBE / A. BRAKA / M. BRUT / K. DRUART / N. FLOQUET / M. GUEROULT / S. KELLOU-TAIRI / V. MARTINY / C. RIEUX 15:15 Thomas GAILLARD Design computationnel de protéines avec une fonction d'énergie MMGBSA 15:30 Seydou TRAORE Cost Function Network Optimization: exact algorithms towards Computational Protein Design 15:45 David RINALDO Computational approach to enzyme design 16:00 Présentations Flash n°3 – Posters 18 à 26 F. BARAKAT / S. BAUD / J-B. CHERON / J. CORTES / S. CROUZY / D. DE VECCHIS / S. DOUTRELIGNE / L. VERZEAUX / D. FLATTERS 16:15 Pause café SESSION POSTERS 18:30 Apéritif Sétois 19:30 Dîner Soirée festive 16:45 10 Mercredi 27 mai 2015 Matin Session 4 – Les enzymes comme cibles thérapeutiques Modérateurs : Rachel CERDAN et Laurent CHALOIN 09:00 Dominique DOUGUET – Conférence Plénière Enzymes as target class for approved drugs The case of secretory phospholipase A2 (sPLA2) family of proteins as novel therapeutic targets 09:45 Présentations Flash n°4 – Posters 27 à 35 N. FLOQUET / C. GAGEAT / S. GRUDININ / M. KATAVA / Y. LAURIN / G. LEROUX / C. MAROT / I. MEREU / D. MIAS-LUCQUIN 10:00 Kamel DJAOUT Développement d'antibactériens dirigés contre la ThyX de Mycobacterium tuberculosis 10:15 Fanny KREBS Molecular dynamics study of ligand recognition by DXR: implications for the design of new antibiotic compounds 10:30 Jana SOPKOVA-DE OLIVEIRA SANTOS Discovery of Oligopyridyl scaffold molecules as potent Mcl-1 inhibitors 10:45 11:15 Pause café Présentations Flash n°5 – Posters 36 à 45 A-E. MOLZA / D. MONET / M. NG FUK CHONG / M-K. NGUYEN / J. REBEHMED / N. RENAULT / E. SELWA / D. STRATMANN / T. TUBIANA / S. WIENINGER 11:30 Florent BARBAULT Into the intimacy of an irreversible inhibition: SMD(QM/MM) simulations of the fibroblast growth factor receptor-1 (FGFR1) kinase domain 11:45 Inès RASOLOHERY PatchSearch: a fast method for flexible recognition of protein binding sites 12:00 Hiba ABI HUSSEIN PockDrug-Server: a new web server for predicting pocket druggability on hol o and apo proteins Prix poster GT Enzymes 12:30 Déjeuner et départ GT Enzymes 12:15 11 Mercredi 27 mai 2015 Après-midi Session 5 – Relations dynamique - fonction Modérateurs : Nathalie COLLOC'H et Andrey KAJAVA 14:00 Jochen BLUMBERGER – Conférence Plénière Combining molecular dynamics and Markov state modelling to understand ligand transport in enzymes 14:45 Jérôme EBERHARDT Structural dynamics of the retinoid X receptor ligand binding domain by accelerated molecular dynamics 15:00 Benoît DAVID Turning glycoside hydrolases into transglycosidases: an e xperimental and theoretical study of the internal water dynamics in the Thermus thermophilus βglycosidase 15:15 Julien DIHARCE Description théorique d'un phénomène de "substrate channeling" dans la biosynthèse des flavonoïdes 15:30 Maxime LOUET L'allostérie dynamique de la protéine CAP révélée par les forces inter-atomiques 15:45 Présentation du jeu "L'expert est dans la salle" 16:00 Pause café 16:30 Matthieu CHAVENT Assessing the crowding of Membrane Proteins at the Mesoscale 16:45 Kaouther BEN OUIRANE New way to fight against antibiotic resistance: reconstruction of a t hreecomponent efflux pump 17:00 Jean-Pierre DUNEAU Étude de l'assemblage des protéines membranaires par simulation de dynamique moléculaire à gros grains et méthodes de Forces de Biais Adaptatif 17:15 Christophe NARTH Tinker-HP : Dynamique moléculaire polarisable haute performance 17:30 Assemblée Générale GGMM Dégustation de produits régionaux SESSION POSTERS 19:30 Dîner 18:00 21:00 "L'expert est dans la salle" 12 Jeudi 28 mai 2015 Matin Session 6 – Visualisation et prédiction structurale Modérateurs : Marc BAADEN et Frédéric DE LAMOTTE 09:00 Tobias ISENBERG – Conférence Plénière Illustrative Molecular Visualizations 09:45 Fabrice ALLAIN Modélisation de novo de structures protéiques par contacts évolutifs 10:00 Mathias FERBER Integrating the Solvent Accessible Surface Distance with cross-links-based modeling methods improves the conformational sampling of protein assemblies 10:15 Emilie NEVEU A Detailed Data-Driven Protein-Protein Interaction Potential Accelerated By Polar Fourier Correlation 10:30 Isaure CHAUVOT DE BEAUCHENE Fragment-based modeling of ssRNA-protein complexes 10:45 Pause café 11:15 Jean-Christophe GELLY ORION : improving remote homology detection using a structural alphabet 11:30 Stéphane REDON SAMSON: Software for Adaptive Modeling and Simulation Of Nanosystems 11:45 Prix du GGMM - Isidro CORTES Integration of Chemical and B iological (’omics’) Data for the Prediction of Cancer Cell-Line Sensitivity 12:15 12:30 Prix poster GGMM Déjeuner et départ GGMM 13 Table des matières Edito 4 Le GT Enzymes 5 Le GGMM 6 Nos Partenaires 7 Programme détaillé 8 Structures et mécanismes enzymatiques 21 Structure and function of bacterial FIC toxins, Jacqueline Cherfils . . . . . . . . 22 De quoi la NO-Synthase est elle le nom ?, Jérôme Santolini . . . . . . . . . . . . 23 Piston-driven activation mechanism of VKORC1, the human vitamin K epoxide reductase, Nolan Chatron [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Inhibition sélective des ADN glycosylases : approches structure-fonction, Bertrand Castaing [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Structural characterization of Plasmodium falciparum CCT and fragment-based drug design approach for targeting phospholipid biosynthesis pathway, Ewelina Guca [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Understanding the mechanism of UGT74B1 from Arabidopsis thaliana: S- or Oglycosyltransferase ?, Pierre Lafite [et al.] . . . . . . . . . . . . . . . . . . . . . . 28 14 Monitoring the transition of apo into holo forms of soluble glucose dehydrogenase by stopped-flow and crystallographic studies to decipher the mechanism of reconstitution/activation of this enzyme., Claire Stines-Chaumeil [et al.] . . . . . 29 Mécanisme de la 3-mercaptopyruvate sulfurtransférase : une enzyme impliquée dans la production de sulfure d’hydrogène., Jean-Christophe Lec [et al.] . . . . . 30 Régulation et efficacité 31 Approches correlatives en analyse molecule-unique, Terence Strick . . . . . . . . . 32 Régulation des IMPDHs bactériennes au travers des modules CBS, Hélène MunierLehmann . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Identification of Discriminant Conformation-Dependent Residues of Protein Kinases: a Proteometric Analysis, Nicolas Bosc [et al.] . . . . . . . . . . . . . . . . 34 La Carbon Monoxide Dehydrogenase (CODH) de Desulfovibrio vulgaris., Jessica Hadj-Said [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Study of the regulatory behavior of Plasmodium falciparum IMP-specific 5’-nucleotidase (PfISN1), Loic Carrique [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Cellular redox signaling by thiol peroxidase : Mechanisms responsible for the specificity of the redox relay H2O2/Orp1/Yap1 in S. cerevisiae, Antoine Berweiler [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Amyloid properties of a conserved domain in the N-Term domain of the Androgen Receptor - Implications for new therapeutic routes -, Julia Asencio Hernández [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Ingénierie enzymatique et évolution dirigée 41 Design and optimization of artificial enzymes: nearer to nature, Donald Hilvert . 42 Design computationnel de protéines avec une fonction d’énergie MMGBSA, Thomas Gaillard [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Cost Function Network Optimization: exact algorithms towards Computational Protein Design, Seydou Traore [et al.] . . . . . . . . . . . . . . . . . . . . . . . . 45 Computational approach to enzyme design, David Rinaldo . . . . . . . . . . . . . 48 Les enzymes comme cibles thérapeutiques 15 49 Enzymes as target class for approved drugs The case of secretory phospholipase A2 (sPLA2) family of proteins as novel therapeutic targets, Dominique Douguet . 50 Développement d’antibactériens dirigés contre la ThyX de Mycobacterium tuberculosis, Kamel Djaout [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Molecular dynamics study of ligand recognition by DXR: implications for the design of new antibiotic compounds, Fanny Krebs [et al.] . . . . . . . . . . . . . . 52 Discovery of Oligopyridyl scaffold molecules as potent Mcl-1 inhibitors, Jana Sopkova-De Oliveira Santos [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Into the intimacy of an irreversible inhibition: SMD(QM/MM) simulations of the fibroblast growth factor receptor-1 (FGFR1) kinase domain., Yan Li [et al.] . . . 55 PatchSearch: a fast method for flexible recognition of protein binding sites, Inès Rasolohery [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins, Hiba Abi Hussein [et al.] . . . . . . . . . . . . . . . . . . . . . . . . 59 Relations dynamique - fonction 60 Combining molecular dynamics and Markov state modelling to understand ligand transport in enzymes, Jochen Blumberger [et al.] . . . . . . . . . . . . . . . . . . 61 Structural dynamics of the retinoid X receptor ligand binding domain by accelerated molecular dynamics, Jérôme Eberhardt [et al.] . . . . . . . . . . . . . . . . . 62 Turning glycoside hydrolases into transglycosidases: an experimental and theoretical study of the internal water dynamics in the Thermus thermophilus glycosidase, Benoît David [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Description théorique d’un phénomène de ”substrate channeling” dans la biosynthèse des flavonoïdes., Julien Diharce [et al.] . . . . . . . . . . . . . . . . . . . . . 65 L’allostérie dynamique de la protéine CAP révélée par les forces inter-atomiques, Maxime Louet . Louet . . . .[et . .al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Maxime Assessing the crowding of Membrane Proteins at the Mesoscale, Matthieu Chavent [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 New way to fight against antibiotic resistance: reconstruction of a three-component efflux pump, Kaouther Ben Ouirane [et al.] . . . . . . . . . . . . . . . . . . . . . 69 16 Étude de l’assemblage des protéines membranaires par simulation de dynamique moléculaire à gros grains et méthodes de Forces de Biais Adaptatif., Jean-Pierre Duneau [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 Tinker-HP : Dynamique moléculaire polarisable haute performance, Christophe Narth [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Visualisation et prédiction structurale 72 Illustrative Molecular Visualizations, Tobias Isenberg . . . . . . . . . . . . . . . . 73 Modélisation de novo de structures protéiques par contacts évolutifs, Fabrice Allain [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 Integrating the Solvent Accessible Surface Distance with cross-links-based modeling methods improves the conformational sampling of protein assemblies, Mathias Ferber [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 A Detailed Data-Driven Protein-Protein Interaction Potential Accelerated By Polar Fourier Correlation, Emilie Neveu [et al.] . . . . . . . . . . . . . . . . . . . . . 77 Fragment-based modeling of ssRNA-protein complexes, Isaure Chauvot De Beauchene [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 ORION : improving remote homology detection using a structural alphabet, Yassine Ghouzam [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 SAMSON: Software for Adaptive Modeling and Simulation Of Nanosystems, Nadhir Abdellatif [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Integration of Chemical and Biological (’omics’) Data for the Prediction of Cancer Cell-Line Sensitivity, Isidro Cortes [et al.] . . . . . . . . . . . . . . . . . . . . . . 85 Session poster GT Enzymes/GGMM 87 Les thioltransférases : production et élimination de sulfure d’hydrogène ?, JeanChristophe Lec [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 Rôle fonctionnel d’une cavité interne hydrophobe dans l’urate oxydase, Nathalie Colloc’h [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Benzene-induced leukemogenesis: Irreversible inhibition of PTPN2, a tumor suppressor phosphatase involved in leukemia by the hematotoxic metabolite benzoquinone, Romain Duval [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 17 Cellular redox signaling by thiol peroxidase : Mechanisms responsible for the specificity of the redox relay H2O2/Orp1/Yap1 in S. cerevisiae, Antoine Bersweiler [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 Molecular basis of the alteration of brain glycogen metabolism by dithiocarbamate pesticides: impairment of brain glycogen phosphorylase, Cécile Mathieu [et al.] . 93 Réactivité de la carbon monoxide dehydrogenase à nickel avec l’oxygène, Meriem Merrouch [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 Regulation of thiol peroxidases in peroxide-dependent redox signaling: Thioredoxin vs. glutathione in reduction of hyperoxidized 2-Cys peroxiredoxin by Sulfiredoxin, Samia Boukhenouna [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . 95 Computer-aided engineering of a transglycosylase for the glucosylation of an unnatural disaccharide of relevance for bacterial antigen synthesis, Alizée Verges [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 Computational Enzyme Design through deterministic search and counting methods, Clément Viricel [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Towards the development of an in silico tools for kinetics prediction, Abdennour Braka [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 In silico experiments on biomolecules through the Static Modes: An efficient approach to predict and design function, Marie Brut . . . . . . . . . . . . . . . . . . 102 Proteus: dessin de protéine en backbone flexible, Karen Druart [et al.] . . . . . . 103 Molecular dynamics with excited normal modes reveals the role of the activation loop of Cyclin-Dependent Kinases in their open/closed conformational equilibrium, Nicolas Floquet [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 Design raisonné de procédés enzymatiques pour la dégradation améliorée de biopolymères, Marc Gueroult [et al.] . . . . [et . . al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 -mères, Marc Guéroult Ligand-Based QSAR studies on some Cis-Stilbenes as Cyclooxygenase Inhibitor, Safia Kellou-Taïri [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 FOCUSED LIGAND LIBRARIES FOR COVALENT DOCKING ON SERINE ACTIVE PROTEINS, Virginie Martiny [et al.] . . . . . . . . . . . . . . . . . . . 107 Inhibition sélective des ADN glycosylases : simulation par dynamique moléculaire et docking pour la recherche et la conception d’inhibiteurs, Charlotte Rieux [et al.] 109 Spectroscopic Fingerprints of the Structural Fluctuations of a Single Amino Acid, Fatima Barakat [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 18 Unravelling the structure/activity relationship between collagen derived peptides and the v3 integrin, Eléonore Lambert [et al.] . . . . . . . . . . . . . . . . . . . . 112 Mécanisme d’activation du récepteur T1R2-T1R3 impliqué dans la perception du goût sucré., Jean-Baptiste Cheron [et al.] . . . . . . . . . . . . . . . . . . . . . . . 113 Caractérisation du paysage énergétique de biomolécules flexibles avec un couplage d’algorithmes stochastiques, Juan Cortes . . . . . . . . . . . . . . . . . . . . . . . 114 Modeling methods for protein structure prediction, mechanistic and docking studies, Serge Crouzy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 Mitochondrial membrane fusion: computational modelling of mitofusins, Dario De Vecchis [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 UnityMol: Simulation et Visualisation Interactive à des fins d’Enseignement et de Recherche, Sébastien Doutreligne [et al.] . . . . . . . . . . . . . . . . . . . . . . . 118 Study of TIMP-1/LRP-1 interaction in neurons: a new approach based Sébastien on protein Mécanismes d’activation des RCPG impliqués dans les sens chimiques, dynamic,[etLaurie Fiorucci al.] . Verzeaux . . . . . .[et . .al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 SA-conf : un outil d’analyse et de comparaison de la variabilité de séquences et de structures d’un ensemble de conformères d’une protéine, Leslie Regad [et al.] . 121 Exploration of Large Amplitude Motions of GPCRs and their complexes at the molecular level, Nicolas Floquet [et al.] . . . . . . . . . . . . . . . . . . . . . . . . 123 HiRE-RNA: un modèle gros grain pour la simulation d’ARN et d’ADN, Cédric Gageat [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 PEPSI-SAXS - A very fast adaptive scheme for computation of small-angle X-ray scattering profiles via spherical harmonics expansions, Sergei Grudinin [et al.] . . 126 Conformational changes changes in in themophilic thermophilicand andmesophilic mesophilicenymes, enzymes, Marina Katava Conformational Marina Katava [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 Etude de la variabilité structurale et de l’interaction du peptide NFL-TBS.40-63 avec la tubuline., Yoann Laurin [et al.] . . . . . . . . . . . . . . . . . . . . . . . . 129 Molecular basis of Olfactory Receptors: in silico modeling and in vitro validation., Gwenaëlle Andre-Leroux . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 Molecular Modeling CoMFA and docking of a Novel Series of Potent 7-Azaindole Based Tri-Heterocyclic Compounds as CDK2/Cyclin E Inhibitors, Christine B. Baltus [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 19 Study of large-scale conformational transitions in c-Abl at the free energy level via a structure-based model, Ilaria Mereu . . . . . . . . . . . . . . . . . . . . . . 133 Cartographie des interactions atomiques dans le filament de dystrophine, Dominique Mias-Lucquin [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134 Développement d’une stratégie multi-échelle combinant des données expérimentales et in silico pour la reconstruction de complexes impliquant la dystrophine., AnneElisabeth Molza [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 Analysis of protein structure and dynamics to better understand their functional mechanisms, Damien Monet [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Conformational properties and transport of glucose by GLUT1 using in silico approaches, Matthieu Ng Fuk Chong [et al.] . . . . . . . . . . . . . . . . . . . . . 138 As-Rigid-As-Possible interpolation for structural biology, Minh Khoa Nguyen [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 What wins in determining protein regular secondary structures? The polar/non polar binary pattern or the intrinsic amino acid composition? A statistical analysis using the HCA approach., Joseph Rebehmed [et al.] . . . . . . . . . . . . . . . . 141 Molecular features switching off the melatonin-induced activity from MT1 to GPR50 receptors, Nicolas Renault [et al.] . . . . . . . . . . . . . . . . . . . . . . 143 Coarse-Graining Parameterization of Specific Cardiac Membrane Lipids, Edithe Selwa [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 Prediction of peptide conformational stability, Marie Amandine Laurent [et al.] . 145 Dynamique d’assemblage de la capside des norovirus, Thibault Tubiana [et al.] . 146 Identification and automated weighting of ensemble-averaged NOE restraints, Silke Wieninger [et al.] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 ListeListe des des participants auteurs 149 149 participants ListeListe des des auteurs 153 154 Session poster GT Enzymes 160 Session poster GGMM 161 20 Structures et mécanismes enzymatiques 21 Structures et mécanismes enzymatiques CONFERENCE PLENIERE Structure and function of bacterial FIC toxins Jacqueline Cherfils 1 ∗† 1 Ecole Normale Superieure (ENS de Cachan) – CNRS – Laboratoire de Biologie et Pharmacologie Appliquée- CNRS - ENS de Cachan, France Five years ago, the large family of bacterial FIC proteins was still uncharted territory. It has now become clear that many FIC domain-containing proteins are toxins that add diverse post-translational modifications to target proteins. I will describe our recent structural and biochemical studies of the FIC protein AnkX, a secreted effector from Legionella pneumophila (the bacteria that causes the legionnaire’s disease, a severe pneumonia). AnkX takes command of membrane traffic - the “cellular postal service” that shuttles biomolecules around the cell and organizes the structure of organelles - by adding a phosphocholine moiety to small GTPases of the Rab family, which are chief organizers of membrane traffic in the host cell. These studies highlight how FIC proteins exploit similar catalytic mechanisms to regulate a variety of processes using a broad range of substrates. Campanacci V., Mukherjee S., Roy C.R , Cherfils J. , EMBO Journal 2013 Roy C.R. and Cherfils J., Nature Reviews Microbiology (to be published) ∗ † Intervenant Auteur correspondant: [email protected] 22 Structures et mécanismes enzymatiques COMMUNICATION ORALE De quoi la NO-Synthase est elle le nom ? Jérôme Santolini 1 ∗ 1 CEA - DSV - SB2SM - LSOD (LSOD) – Centre national de la recherche scientifique - CNRS (France), CEA, Université Paris Sud - Paris XI – CEA-Saclay 91191 gif sur Yvette cedex, France Nitric Oxide Synthases (NOS), the exclusive source of NO in mammals, are at the core of a large number of signaling processes crucial in blood pressure regulation, neural communication, cell cycle... NOSs are also the source of an endogenous oxidative stress and are increasingly associated to numerous pathological conditions, including cardiovascular, inflammatory and neurodegenerative diseases. The improvement of the gene sequencing techniques has recently led to the discovery of numerous NOSs throughout the living kingdom. The first investigations have revealed a strong homology with mammalian NOSs but an extremely broad range of biological functions: from pathogenicity to detoxification, through metabolism and resilience. The current paradigm in the NOS field, namely NOS-NO-Signalling, has become insufficient to account for the multiple pathophysiological roles of mammalian NOSs and for the structural and biological biodiversity of NOSs throughout the living kingdom. There is currently no understanding of the discrepancy between the strong structural identity of NOSs and their implication in many different if not opposite biochemical processes. We have initiated an integrative approach that aims at establishing a relationship between the structural properties of NOSs and their biological functioning. This project combines Bioinformatics, Enzymology, Biophysics and Microbiology in order to address the structural, functional and biological diversity of this new family of enzymes. We will present our first results on - Mammalian NOSs : we showed the existence of two distinct catalytic cycles, alternatively leading to NO or to harmful nitrogen oxides. The partition between both cycles is specific to each mammalian NOS and depends on the physiological environment, which might explain the different contributions of NOSs to physiological and pathological processes. - Bacterial NOS-LPs. We showed that bacterial NOSs had the ability to catalyse oxygen activation but displayed specific electronic and structural properties. This might explain their unfitness to produce and release NO, which question their assignment as genuine NO synthases. - Plant NOSs. In the context of the non-existence of plant NOSs, we started characterizing NOSs from a green algae (otNOS) and cyanobacteria (spNOS). Our first results suggest that otNOS is a super NOS but raises questions about the actual biochemistry and function of spNOS. By developing an innovative and interdisciplinary project, our final goal is to generate a reliable Structure-Function-Environment Relationship that could predict the chemical and biological activity of any new NOS from its genomic sequence ∗ Intervenant 23 Structures et mécanismes enzymatiques COMMUNICATION ORALE Piston-driven activation mechanism of VKORC1, the human vitamin K epoxide reductase Nolan Chatron ∗ 1 , Florent Langenfeld 1 , Etienne Benoit 2 , Virginie Lattard 2 , Luba Tchertanov 1 1 Centre de Mathématiques et de Leurs Applications - ENS Cachan (CMLA) – École normale supérieure [ENS] - Cachan, École normale supérieure (ENS) - Cachan – ENS Cachan CNRS, PRES UniverSud, 61 Avenue du President Wilson 94230 Cachan, France 2 VetAgro Sup [Lyon] – Campus Vétérinaire – Université de Lyon, 1 avenue Bourgelat, 69280 Marcy l’Etoile, France Blood coagulation is a crucial physiological process, vital for many living organisms. Vitamin K epoxide reductase complex subunit 1 (VKORC1) plays a key role in this process, through the catalysis of vitamin K recycling - from its inactive epoxide form to the biologically active hydroquinone form [1]. VKORC1, an endoplasmic reticulum membrane protein, is the primary target for vitamin K antagonists (VKAs) [2]. Appearance of VKORC1 mutations promotes patient’s resistance to VKA drugs and/or alteration of VKORC1 activity. Our aim is to clarify the VKORC1 catalytic mechanisms and the resistance mechanisms to VKAs on the atomic scale. To the best of our knowledge, no structural data is available for the human VKORC1 (h-VKORC1 WT ), therefore in our study we used in silico modeling combined with molecular dynamics (MD) simulations. The first step consists to build a structural model of VKORC1 using the recent X-ray data for its bacterial homolog [3]. The generated model denotes a four-helix structure of VKORC1 (Fig. 1 A-B) that is consistent with the experimentally determined enzymatic mechanism regulating the electron transfer from cysteine residues 43-51 (in blue) to cysteine residues 132-135 (in green). Each pair of transmembrane helices (TM) is linked by either short loops (TM3-TM4 and TM2TM3) or a long and highly flexible luminal loop (Loop 1/2, linking TM1-TM2) with a small horizontal helix (HH) in the middle, overhanging the membrane surface. Molecular Dynamics (MD) simulations (2 x 100 ns) revealed significant conformational changes, evidenced as a twostate transition of the h-VKORC1 WT . The MD simulations data were explored by principal components analysis and cross-correlation analysis, which evidenced highly concerted motions of protein residues from Loop 1/2, HH and the four TMs. We observed that the two coiled subfragments of Loop 1/2, separated by HH, show anti-correlated movement, which highly correlates with the HH displacement. The longer the distance between the two coiled sub-fragments, the larger the extent between HH and TMs (Fig. 1 C-D). When the two coiled sub-fragments of Loop 1/2 adjoin, the HH moves towards the catalytic site, perturbing its topology by altering the inter-helices space. We denominate these highly concerted movements which involve nearly all structural subunits of h-VKORC1 WT and its all catalytic residues – C43 (LL), C51 (HH), C132 and C135 (TM4) – the ‘piston-driven mechanism’. This purely mechanistic description depicts plausibly a first step of the h-VKORC1 WT activation which precede the enzymatic reaction(s). ∗ Intervenant 24 Structures et mécanismes enzymatiques COMMUNICATION ORALE Validation of the proposed model and its mechanisms will be performed through the study of the VKORC1 mutants, resistant to VKAs, combining in silico, in vitro and in vivo approaches. 25 Structures et mécanismes enzymatiques COMMUNICATION ORALE Inhibition sélective des ADN glycosylases : approches structure-fonction Bertrand Castaing ∗† 1 , Stéphane Goffinont 1 , Franck Coste 1 , Françoise Culard 1 , Charlotte Rieux 1 , Norbert Garnier 1 , Stéphane Bourg 1 , Pascal Bonnet 2 1 2 Centre de Biophysique Moléculaire, UPR4301 CNRS (CBM) – CNRS – rue Charles Sadron, 45071 Orléans cedex 02, France Institut de Chimie Organique et Analytique, UMR7311 (ICOA) – CNRS, Université d’Orléans – Pôle de chimie de l’Université d’Orléans, Rue de Chartres, 45067 Orléans cedex 02, France Les ADN glycosylases sont des enzymes qui initient le système de réparation par excision de base (BER) en reconnaissant et éliminant les bases oxydées (de type radio-induites) dans l’ADN tels que les résidus formamidopyrimidiques (FapyG), la thymine glycol (Tg) (lésions potentiellement létales associées à un blocage de la réplication) et la 8-oxoguanine (8-oxoG, lésion mutagène associée à une haute fréquence de transversion G:C vers T:A) [1]. Bien que ces enzymes soient impliquées dans la stabilité génétique des organismes, des travaux récents indiquent que les systèmes de réparation de l’ADN et en particulier les enzymes du système BER constituent des cibles pharmacologiques pertinentes pour développer des stratégies anticancéreuses alternatives et combinatoires [2,3]. Ces systèmes de réparation peuvent être en effet à l’origine de mécanismes d’échappements aux traitements anticancéreux dont l’un des objectifs est d’endommager l’ADN de la cellule cancéreuse (exemple : la radiothérapie). Ces observations récentes justifient la recherche d’inhibiteurs de ces enzymes. Sur ce thème général, nous avons initié cette étude sur les ADN glycosylases de la surperfamille structurale “ H2TH ”. Une première approche structurefonction de l’inhibition de cette classe d’enzyme par des nucléobases sera présentée [4]. Dalhus, B., Laerdahl, J. K., Backe, P. H. and Bjoras, M. (2009) DNA base repair–recognition and initiation of catalysis. FEMS microbiology reviews 33, 1044-1078. Helleday, T. (2011) DNA repair as treatment target. Eur. J. Cancer 47 (Sup3), S333-S335. Taricani, L., Shanahan, F., Pierce, R.H., Guzi, T.J. and Parry, D. (2010) Phenotypic enhancement of thymidylate synthetase pathway inhibitors following ablation of Neil1 DNA glycosylase/lyase. Cell cycle 9, 4876-4883. Biela, A.; Coste, F.; Culard, F.; Guerin, M.; Goffinont, S.; Gasteiger, K.; Cieśla, J.; Winczura, A.; Kazimierczuk, Z.; Gasparutto, D.; Carell, T.; Tudek, B.; Castaing, B. (2014) Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Nucleic Acids Res. 42(16), 10748-10761. ∗ † Intervenant Auteur correspondant: [email protected] 26 Structures et mécanismes enzymatiques COMMUNICATION ORALE Structural characterization of Plasmodium falciparum CCT and fragment-based drug design approach for targeting phospholipid biosynthesis pathway Ewelina Guca ∗† 1 , François Hoh 2 , Jean-François Guichou 2 , Henri Vial 1 , Rachel Cerdan 1 1 Dynamique des interactions membranaires normales et pathologiques (DIMNP) – CNRS : UMR5235, Université de Montpellier – BT 24 CC 107 Place Eugène Bataillon 34095 MONTPELLIER CEDEX 5, France 2 Centre de Biochimie Structurale (CBS) – CNRS : UMR5048, Inserm : UMR1054, Université de Montpellier – 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Phospholipid synthesis metabolic pathways in Plasmodium falciparum are validated drug targets for new type of antimalarials. In the de novo Kennedy pathway of phosphatidylcholine biosynthesis, the second step catalyzed by CTP:phosphocholine cytidylytransferases [2.7.7.15] is rate limiting and appears essential for the parasite survival at its blood stage. We are focused on the structural characterization of this enzyme, the identification of effectors by fragment-based drug design approach (FBDD) and then their optimization to eventually design a lead. We solved the first reported crystal structure of the catalytic domain of the enzyme target (PfCCT) at resolution 2.2 Å, 3 enzyme-substrates complexes (CMP-, phosphocholine- and choline-bound forms) at resolutions 1.9-2 Å and an enzyme-product (CDP-choline) complex structure at resolution 2.4 Å that give detailed images of binding pocket, demonstrate conformational changes between apo- and holo-protein forms and provide the information about the mechanism of the catalytic reaction at atomic level. The FBDD method uses a library of small molecules (fragments) with molecular weight that does not exceed 300 Da to explore target binding sites. Primary screening of fragment library (300 molecules) has been investigated by fluorescence-based thermal shift assay and Nuclear Magnetic Resonance Saturation Transfer Difference (NMR STD) method is used as a secondary screen to eliminate false positive ligands. This combination of techniques identified so far 4 fragment hits that are currently evaluated for their binding modes and affinities. Co-crystallization of the protein-fragments complexes is carrying out to provide accurate information on the binding modes of the small molecules and topology of interactions will be used to rationally monitor every iterative round of the optimization process allowing subsequent rational design. ∗ † Intervenant Auteur correspondant: [email protected] 27 Structures et mécanismes enzymatiques COMMUNICATION ORALE Understanding the mechanism of UGT74B1 from Arabidopsis thaliana: S- or O-glycosyltransferase ? Pierre Lafite ∗ 1 , Sabine Montaut 2 , Stéphanie Marques 1 , Sami Marroun 3 , Gaël Coadou 3 , Hassan Oulyadi 3 , Marie Schuler 1 , Arnaud Tatibouet 1 , Patrick Rollin 1 , Richard Daniellou 1 1 Institut de Chimie Organique et Analytique (ICOA) – CNRS : UMR7311, Université d’Orléans – UFR Sciences Rue de Chartres - BP 6759 45067 ORLEANS CEDEX 2, France 2 Laurentian University – Dpt of Chemistry and BIOchemistry ON P3E 2C6, Canada 3 Chimie Organique et Bioorganique : Reactivité et Analyse (COBRA) – CNRS : UMR6014, Institut National des Sciences Appliquées [INSA] - Rouen – Rue Tesniere - 76821 - Mont Saint Aignan, France Carbohydrates play an important part in a vast array of biological processes and therefore glycomimetics are currently becoming a powerful class of novel therapeutics. Amongst them, thioglycosides, or S -glycosides in which a sulfur atom has replaced the glycosidic oxygen atom, are tolerated by most biological systems. Their major advantages rely on the fact that they adopt similar conformations than the corresponding O-glycosides and especially that they prove to be less sensitive to acid/base or enzyme-mediated hydrolysis. So far, few examples of natural S -glycosides were reported in the literature. Until recently, plant glucosinolates were the only group of S -glycosides that were characterized in Nature. These compounds are found in brassicae and are involved in the plant protective strategy, called “mustard oil bomb”, that occurs after their hydrolysis and subsequent degradation in toxic sulfur-containing compounds (thiocyanates, isothiocyanates, ...). Arabidopsis thaliana S -glycosyltransferase UGT74B1 catalyzes the formation of S-glucosidic bond in the aromatic glucosinolates bionsynthetic pathway, using UDP-glucose as sugar donor and thioxydromixate as thiol acceptor. In order to assess the potency of this enzyme as a biocatalyst tool to generate unnatural S glycosides, its versality towards sugar donor and acceptor was tested. This could be efficiently illustrated by the first chemo-enzymatic synthesis of glucosinolates analogues bearing other sugar moiety than glucose, using other UDP-sugar donors. Using a range of acceptors, UGT74B1 could perform S -glycosylation, as well as O-glycosylation, yet with a much lower efficiency. However, the specificity for thiol vs. alcohol was correlated not only to the nature of the atom, but also to the chemical properties of the acceptor (eg. pKa). This was experimentaly demontrasted by ‘tuning’ the pKa of a range of alcohol acceptors so that O-glycosylation rates increased to a level close to S -glycosylation. ∗ Intervenant 28 Structures et mécanismes enzymatiques COMMUNICATION ORALE Monitoring the transition of apo into holo forms of soluble glucose dehydrogenase by stopped-flow and crystallographic studies to decipher the mechanism of reconstitution/activation of this enzyme. Claire Stines-Chaumeil 3 ∗† 1 , François Mavre 2 , Brice Kauffmann , Benoit Limoges 2 , Nicolas Mano ∗ 1 1 Centre de recherches Paul Pascal (CRPP) – CNRS : UPR8641 – 115, Av Albert Schweitzer 33600 PESSAC, France 2 Laboratoire d’electrochimie moleculaire (LEM) – Université Paris VII - Paris Diderot – UMR CNRS P7 7591 Université Paris Diderot - Paris 7 Bât . Lavoisier, 15 rue Jean-Antoine de Baïf 7e Etage - case 7107 75205 Paris Cedex 13, France 3 Institut Européen de Chimie et Biologie (IECB) – CNRS : UMS3033, Université de Bordeaux (Bordeaux, France) – 2 rue Robert Escarpit, F-33607 Pessac, France Soluble glucose dehydrogenase (s-GDH) from Acinetobacter calcoaceticus belongs to the family of quinoproteins and catalyzes the oxidation of glucose into gluconolactone. This enzyme is widely use in biotechnology, e.g. for glucose biosensors or enzymatic biofuel cells(1). Here we focus on the mechanism of the reconstitution and activation process of the s-GDH which is produced under apo form in Escherichia coli. Understanding this process is of interest to improve its use in electrochemical devices such as immunosensors. If heterogeneous reconstitution studies have been recently published (2), there are no detailed studies of the homogeneous reconstitution of the s-GDH. To decipher this reconstitution/activation mechanism, we combined stopped-flow experiments, crystallographic studies and simulations. Our data indicates that this mechanism can be explained with a square schema mechanism with two different pathways. Flexer V. et al., Anal.Chem, 2011, 83 (14), 5721-7 Zhang L. et al., Anal. Chem, 2014, 86 (4), 2257-67. ∗ † Intervenant Auteur correspondant: [email protected] 29 Structures et mécanismes enzymatiques COMMUNICATION ORALE Mécanisme de la 3-mercaptopyruvate sulfurtransférase : une enzyme impliquée dans la production de sulfure d’hydrogène. Jean-Christophe Lec ∗ 1 , Sabrina Colin , Séverine Boutserin , Hortense Mazon , François Talfournier† , Sandrine Boschi-Muller‡ 1 UMR 7365 CNRS-Université de Lorraine (IMoPA) – CNRS : UMR7365, Université de Lorraine – 9 Avenue de la Foret de Haye, 54505 Vandoeuvre les Nancy, France La 3-mercaptopyruvate sulfurtransférase (3-MST) est une enzyme ubiquitaire qui participe à la formation de sulfure d’hydrogène (H2S), un messager cellulaire pour les cellules eucaryotes ayant également un effet cytoprotecteur. En effet, H2S est un gaz toxique, qui entraine une inhibition de la respiration mitochondriale via son action sur la cytochrome oxydase, mais également une molécule de signalisation qui interviendrait au niveau de la neuromodulation dans le cerveau et de la relaxation du muscle lisse dans le système vasculaire. La 3-MST eucaryote est à la fois mitochondriale et cytosolique, tandis que les autres systèmes enzymatiques qui produisent H2S sont exclusivement cytosoliques. La 3-MST est une enzyme à cystéine essentielle composée de deux domaines rhodanèses qui catalyse le transfert de l’atome de soufre du 3-mercaptopyruvate sur un accepteur de soufre (cyanure ou thiol in vitro), via la formation d’un intermédiaire persulfure sur sa cystéine catalytique. Dans le cas d’un accepteur à thiol, la décomposition du produit de la réaction conduit à la formation d’H2S. L’étude détaillée du mécanisme catalytique des 3MST humaine et d’Escherichia coli a été réalisée par des approches cinétiques (état stationnaire et cycle catalytique unique, systèmes enzymatiques couplés), de spectroscopie de fluorescence et de spectrométrie de masse, incluant l’élaboration de stratégies originales afin de pouvoir étudier les différentes étapes du mécanisme. Les résultats montrent que la première étape de transfert de soufre est très rapide, et que l’étape cinétiquement limitante est associée à la libération du pyruvate pour l’enzyme humaine et à la seconde étape de transfert de soufre pour l’enzyme bactérienne. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] † 30 Régulation et efficacité 31 Régulation et efficacité CONFERENCE PLENIERE Approches correlatives en analyse molecule-unique Terence Strick 1 ∗ 1 IJM (Institut Jacques Monod) – CNRS : UMR7592, Université de Paris Diderot – 15 rue Helene Brion 75013 Paris, France Les mesures sur molecules individuelles permettent d’obsever en temps reel des interactions moleculaires discretes et ainsi d’eviter le moyennage intrinseque a une mesure effectuee sur une population de molecules. Ces approches sont particulierement utiles pour l’analyse de systemes moleculaires multi-composantes et de leurs reactions typiquement multi-etapes. Cependant si d’un cote la manipulation de molecule unique permet de deceler par sa signature ”mecanique” une interaction moleculaire, et donc eventuellement un etat catalytique, elle permet difficilement de connaitre la composition exacte d’un complexe qui pourrait avoir une telle interaction. D’un autre cote la detection par fluorescence molecule-unique permet d’observer la (co)localisation de molecules individuelles, mais renseigne difficilement (en dehors de cas specfiques tels le TIRF) sur l’etat catalytique du systeme observe. La combinaison des deux approches permet ainsi de simultanement detecter en temps reel la composition et l’etat catalytique de systemes moleculaires complexes. Un tel systeme permet de reconstituer la voie de reparation dite transcriptionellement-couplee d’Escherichia coli comprenant six proteines distinctes, et ainsi commencer a etudier les liens entre composition et catalyse dans les processus de reparation d’ADN. ∗ Intervenant 32 Régulation et efficacité COMMUNICATION ORALE Régulation des IMPDHs bactériennes au travers des modules CBS Hélène Munier-Lehmann 1 ∗ 1 Institut Pasteur, Unité de Chimie et Biocatalyse, CNRS UMR3523 – Institut Pasteur de Paris, CNRS UMR3523 – France L’inosine 5’-monophosphate déshydrogénase (IMPDH) est une enzyme essentielle et ubiquitaire intervenant dans la voie de biosynthèse de novo du métabolisme des purines et responsable de la conversion de l’IMP en XMP (1,2). Les IMPDHs humaines ont été largement documentées et sont la cible de médicaments utilisées en clinique. Les IMPDHs sont décrites sous forme tétramérique : chaque monomère comprend un domaine central contenant le site actif, et un domaine Bateman constitué de deux modules cystathionineß-synthase (CBS). Par une approche multidisciplinaire, nous avons démontré que l’IMPDH de Pseudomonas aeruginosa est une enzyme allostérique et octamérique (3), deux propriétés qui n’avaient jamais été décrites jusqu’à présent. Ces travaux ont été étendus à sept autres IMPDHs bactériennes permettant de définir deux classes (4). Les IMPDHs de la classe 1 (incluant l’IMPDH de P. aeruginosa) présentent une coopérativité vis-à-vis de l’IMP avec une activation par le MgATP et sont sous forme octamérique quelles que soient les conditions testées. Les IMPDHs de la classe 2 ont une cinétique de type michaelienne, comme ce qui a été rapporté dans la littérature sur les IMPDHs eucaryotes. Par contre, et de façon surprenante, leur état d’oligomérisation est régulé par le MgATP en passant d’un état tétramérique à un état octamérique. Ce sont les modules CBS qui jouent un rôle clé soit dans la régulation de l’activité catalytique, soit dans la modulation de la structure quaternaire. Ainsi, les modules CBS sont fonctionnels au sein des IMPDHs, et pourraient être la cible d’inhibiteurs allostériques pour le développement de nouveaux antibiotiques. Références : 1. Hedstrom, L. (2009) IMP dehydrogenase: structure, mechanism, and inhibition. Chem. Rev. 109, 2903-2928 2. Pankiewicz, K. W., and Goldstein, B. M. (2003) Inosine Monophosphate Dehydrogenase: A Major Therapeutic Target. ACS Symposium Series 3. Labesse, G., Alexandre, T., Vaupre, L., Salard-Arnaud, I., Him, J. L., Raynal, B., Bron, P., and Munier-Lehmann, H. (2013) MgATP Regulates Allostery and Fiber Formation in IMPDHs. Structure 21, 975-985 4. Alexandre, T., Raynal, B., and Munier-Lehmann, H. (2015) Two classes of bacterial IMPDHs according to their quaternary structures and catalytic properties PloS one in press ∗ Intervenant 33 Régulation et efficacité COMMUNICATION ORALE Identification of Discriminant Conformation-Dependent Residues of Protein Kinases: a Proteometric Analysis Nicolas Bosc ∗† 1 , Berthold Wroblowski 2 , Samia Aci-Sèche 1 , Christophe Meyer 3 , Pascal Bonnet‡ 1 1 Institut de Chimie Organique et Analytique (ICOA) – CNRS : UMR7311, Université d’Orléans – UFR Sciences Rue de Chartres - BP 6759 45067 ORLEANS CEDEX 2, France 2 Janssen Research Development, a division of Janssen Pharmaceutica N.V. – Turnhoutseweg 30, 2340 Beerse, Belgique 3 Centre de Recherche Janssen-Cilag – Johnson Johnson – Campus de Maigremont - CS 10615, 27106 Val de Reuil CEDEX, France Imatinib, a Bcr-Abl tyrosine-kinase inhibitor, was the first protein kinase inhibitor that progressed to the market in 2002. Since then, pharmaceutical companies strongly pursued research efforts to discover novel kinase inhibitors. Today, seven kinase inhibitors binding to the inactive conformation of specific protein kinases have been approved by the FDA. Although imatinib is a Type-II inhibitor and four more Type-II inhibitors were approved in 2012, they still represent less than a third of approved protein kinase inhibitor class. Since part of their chemical structure binds outside of the ATP pocket, Type-II inhibitors could therefore increase kinase selectivity in comparison to the classical Type-I inhibitors binding the ATP site. Hence, the identification of key residues responsible for the binding of Type-II inhibitors could help understanding the protein conformational changes (active to inactive state) as well as designing better selective kinase inhibitors. The novel proteometric approach developed in the SB&C group, combines residue descriptors of protein kinase sequences and biological activities of several Type-II kinase inhibitors. Using Partial Least Squares (PLS) regression, we determined 29 key residues responsible for high biological activities of Type-II inhibitors. Among these residues, the gatekeeper residue was found to be the most relevant suggesting its essential role in protein kinase conformational changes. Using the newly developed proteometric model, we also predicted the propensity of each protein kinase to trap Type-II inhibitors. These results were further validated using two external datasets of protein-ligand activity pairs. Other residues present in the kinase domain, and more specifically in the binding site, have been highlighted by this approach, but their role in biological mechanisms is still under investigation. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] † 34 Régulation et efficacité COMMUNICATION ORALE La Carbon Monoxide Dehydrogenase (CODH) de Desulfovibrio vulgaris. Jessica Hadj-Said ∗† 1 , Maria-Eirini Pandélia 2 , Christophe Léger‡ 1 , Vincent Fourmont§ 1 , Sébastien Dementin¶ 1 1 2 Bioénergétique et ingénierie des protéines (BIP) – CNRS : UPR9036 – 31 Chemin Joseph Aiguier 13402 MARSEILLE CEDEX 20, France Department of Chemistry, The Pennsylvania State University – 224 Chemistry Building University Park, PA 16802 USA, États-Unis Les Carbon Monoxide Dehydrogenases (CODH) à nickel catalysent l’oxydation réversible du CO en CO2. Dans certains bactéries anaérobies, elles favorisent l’établissement d’une force proton motrice pour la synthèse d’ATP. Elles sont aussi impliquées dans la fixation du CO2 [1]. Ce sont des enzymes homodimériques qui contiennent deux sites actifs [Ni-4Fe-4S] et trois centres [4Fe-4S] [2]. Le mécanisme catalytique communément accepté implique la conversion du site actif de l’enzyme d’un état inactif, appelé Cox, en deux états actifs dans des conditions réductrices: Cred1 (Cox réduit par un électron) et Cred2 (Cred1 réduit par deux électrons) [3]. Le génome de Desulfovibrio vulgaris contient un opéron putatif codant pour une CODH (cooS) et une protéine de maturation (cooC) [4]. Par une combinaison d’approches biochimiques et spectroscopiques, nous avons caractérisé deux formes de la CODH produite en absence ou en présence de CooC, désignées CooS et CooSC, respectivement. CooS a un faible contenu en nickel et est presque inactive. Aucune signature du site actif n’est détectée par résonance électromagnétique électronique (RPE), ce qui renforce l’idée que CooC est requis pour promouvoir in vivo la construction d’un site actif fonctionnel. CooSC contient du nickel en quantité substoechiométrique, catalyse l’oxydation réversible du CO en CO2, mais n’est pas totalement active après purification. En effet, son activité n’est maximale qu’après incubation en présence de nickel exogène dans des conditions réductrices. Une caractérisation par RPE des échantillons de CooSC a cependant montré que le site actif est dans l’état Cred1 et/ou Cred2 aussi bien avant qu’après activation par le nickel. Nos résultats ont donc permis de mettre en évidence un processus d’activation inattendu de la CODH qui n’implique apparemment pas de changement structural du site actif. Ce mécanisme d’activation est indétectable par RPE et requiert le nickel exogène dont le rôle reste à déterminer. ∗ Intervenant Auteur correspondant: [email protected] ‡ ¶Auteur [email protected] Auteurcorrespondant: correspondant: § Auteur correspondant: ¶ Auteur correspondant: [email protected] † 35 Régulation et efficacité COMMUNICATION ORALE Can, Mehmet and Armstrong, Fraser A. and Ragsdale, Stephen W., Structure, Function, and Mechanism of the Nickel Metalloenzymes, CO Dehydrogenase, and Acetyl-CoA Synthase, Chem. Rev., 114, 4149–4174, 2014 Holger Dobbek, Vitali Svetlitchnyi, Lothar Gremer, Robert Huber, and Ortwin Meyer. Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science, 293(5533) :1281–1285, August 2001. Heo, J., Staples, C. R., Tesler, J., and Ludden, P. W. Rhodospirillum rubrum CO Dehydrogenase. Part 2. Spectroscopic Investigation and Assignment of Spin-Spin Coupling Signals. J Am Chem Soc 121, 11045-11057, 1999 Rajeev, Lara and Hillesland, Kristina L. and Zane, Grant M. and Zhou, Aifen and Joachimiak, Marcin P. and He, Zhili and Zhou, Jizhong and Arkin, Adam P. and Wall, Judy D. and Stahl, David A. Deletion of the Desulfovibrio vulgaris Carbon Monoxide Sensor Invokes Global Changes in Transcription. Journal of Bacteriology, 21(194):5783-5793, Nov 2012 36 Régulation et efficacité COMMUNICATION ORALE Study of the regulatory behavior of Plasmodium falciparum IMP-specific 5’-nucleotidase (PfISN1) Loic Carrique ∗ 1 , Lionel Ballut 1 , Sébastien Violot 1 , Nushin Aghajari† 1 1 Institut de biologie et chimie des protéines (IBCP) – Université Claude Bernard - Lyon I (UCBL), CNRS : UMR5086, Bases Moléculaires et Structurales des Systèmes Infectieux, Equipe Biocristallographie et Biologie Structurale des Cibles Thérapeutiques – 7 Passage du Vercors 69367 LYON CEDEX 07, France Approximately 300 million people worldwide are affected by malaria. Plasmodium falciparum induces a lethal form of malaria which causes more than 1-2 million deaths worldwide annually, with a large number of victims being children. It has a massive impact on human health in that it is the world’s second biggest killer after tuberculosis. Despite intense efforts an effective vaccine is still not available. Proteins involved in the purine salvage pathway are mandatory for regulating the pool of nucleotides during the inner red blood cells development of the parasite. Many of these proteins are active in transient- or stable oligomeric states which are dependent on time and on the osmolyte concentration present in the cells. One of these is an IMP-specific 5’-nucleotidase (Pf ISN1), for which enzymatic studies have shown that the protein is active in an oligomeric form with an allosteric regulation (Srinivasan & Balaram, 2007). Using different techniques, Dynamic Light Scattering (DLS), Size Exclusion Chromatography (SEC) and Multi-Angle Light Scattering (SEC-MALS), we were able to conclude that the protein adopts a tetrameric state when active, but also an octameric conformation. Screening of crystallization conditions have so far resulted in crystals diffracting X-rays to medium resolution. Due to the regulatory behavior of this enzyme, Small Angle X-ray Scattering studies combined with SEC-MALS are of high importance in order to contribute to the understanding of the influence of the environment on the quaternary structure formation and thereby on the nucleotidase activity. Results obtained so far from the combined use of biochemical- and biophysical approaches for the understanding of the reaction mechanism of this important parasite enzyme from the purine salvage pathway will be presented. References: Bharath Srinivasan and Hemalatha Balaram, ISN1 nucleotidases and HAD superfamily protein fold: in silico sequence and structure analysis, In Silico Biology 7, 0019 (2007) ∗ † Intervenant Auteur correspondant: [email protected] 37 Régulation et efficacité COMMUNICATION ORALE Cellular redox signaling by thiol peroxidase : Mechanisms responsible for the specificity of the redox relay H2O2/Orp1/Yap1 in S. cerevisiae Antoine Berweiler 1 , Alexandre Kriznik 1 , Guy Branlant 1 , Sophie Rahuel-Clermont ∗† 1 1 IMoPA UMR 7365 CNRS-Université de Lorraine (IMOPA) – CNRS : UMR7365, Université de Lorraine – Biopôle, campus Biologie-Santé, 9 Avenue de la Forêt de Haye, CS 50184 54505 Vandœuvre-lès-Nancy, France Thiol-peroxidases, described as antioxidant enzymes, have also been associated with peroxidedependent cell signaling as sensor and relay of the H2O2-mediated signal (1). One of the best documented examples of such a mechanism is the activation of the transcription factor Yap1, a key regulator of the transcriptional peroxide stress response in Saccharomyces cerevisiae, which depends on the formation of intramolecular disulfide bonds catalyzed by the thiol peroxidase Orp1 (2 ; 3). In this mechanism, it has been proposed that the relay occurs via the oxidation of Orp1 peroxidatic Cys as a sulfenic acid intermediate which reacts with Yap1 to form a mixed disulfide species (3). In addition, the Ybp1 protein has been identified as an essential partner for the activation of Yap1 by Orp1 (4). The intrinsic reactivity of Orp1 sulfenic acid species could potentially result in competition between Yap1 and other thiols, such as the regeneration Cys of Orp1 or other cellular thiols. This raises the question of the specificity of Yap1 activation by H2O2/Orp1. To address this question, and to elucidate the role of Ybp1 in this mechanism, we have used an approach based on the kinetic characterization of the two reactions in competition: the peroxydatic cycle of Orp1 and the reaction withYap1, using rapid kinetic stop flow and quench flow techniques. From the study of the impact of Ybp1 on these kinetics and the characterization of the protein-protein interactions between the three partners by fluorescence anisotropy and microcalorimetry, we propose that Ybp1 and Yap1 recruit Orp1 within a ternary complex, which restrains intramolecular disulfide formation within Orp1 and allows the reaction between Orp1 sulfenic intermediate and Yap1. ∗ † Intervenant Auteur correspondant: [email protected] 38 Régulation et efficacité COMMUNICATION ORALE Amyloid properties of a conserved domain in the N-Term domain of the Androgen Receptor - Implications for new therapeutic routes Julia Asencio Hernández 1,2 , Marc-André Delsuc ∗ 2 1 NMRTEC (NMRTEC) – NMRTEC – Boulevard Sébastien Brandt, Bioparc, Bat. B 67400 Illkirch–Graffenstaden, France 2 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) – CNRS : UMR7104, Inserm : U964, université de Strasbourg – Parc D’Innovation 1 Rue Laurent Fries - BP 10142 67404 ILLKIRCH CEDEX, France The prostate cancer is under a strict hormonal androgen control, and develops initially as an androgen-dependent disease that relies on the Androgen Receptor (AR) for growth and progression. The AR protein, in contrast with other nuclear receptors, has the peculiarity of presenting a very large N-Terminal Domain (NTD) of about 560 residues, which is flexible with a high degree of intrinsic disorder. The NTD has gain recent interest because of potential new anti-prostate cancer molecules targeting this domain[1]. We have recently shown [2], that a short domain of the NTD, highly conserved across all vertebrate species (fig. 1), is able to readily form amyloid fibrils upon dimerisation by disulfide bridge formation around Cys240. Unlike most amyloid systems, the fiber formation is reversible, and depend only onthe redox state of the peptide. Peptides as short as 11-residues as well as longer peptides, obtained from the AR primary sequence are able to trigger the fibrillation. This points to the fact that this highly conserved domain could be involved in the regulation of the activity of AR, through a control of the aggregation state. The possibility that amyloid formation is a general mechanism for the regulation of the activity of a protein has already been proposed[3]. The AR protein is already known to aggregates into amyloid fibers[4]. This aggregation property is usually associated to the presence of a poly-glutamine tract (polyQ), known to be involved in several pathologies[5]. Biophysical experiments, in-vivo experiments, and sequence analysis are presented, and confort the link between protein aggregation / redox state and prostate cancer pathology. If this hypothesis proves true, it could form a possible target for prostate cancer therapy, and in general for regulating the AR activity. Pre-screening of potential interactive molecules are currently in progress. J.K.Myung, C.A.Bañuelos, J.Garcia Fernandez, N.R.Mawji, J.Wang, A.H.Tien, Y.C.Yang, I.Tavakoli, S.Haile, K.Watt, I.J.McEwan, S.Plymate, R.J.Andersen, and M.D.Sadar. An androgen receptor N-terminal domain antagonist for treating prostate cancer. J. Clin. Invest. 123, 2948–2960 (2013). ∗ Intervenant 39 Régulation et efficacité COMMUNICATION ORALE J.Asencio-Hernández, C.Ruhlmann, A.McEwen, P.Eberling, Y.Nominé, J.Céraline, J-P.Starck and M-A.Delsuc (2014) ChemBioChem 15(16):2370-3. Reversible Amyloid Fiber Formation in the N Terminus of Androgen Receptor. F.Chiti, and C.M.Dobson (2006) Annu. Rev. Biochem. 75, 333–366. Protein misfolding, functional amyloid, and human disease. T.Jochum, M.E. Ritz, C.Schuster, S.F.Funderburk, K.Jehle, K.Schmitz, F.Brinkmann, M.Hirtz, D.Moss, and A.C.B.Cato Toxic and non-toxic aggregates from the SBMA and normal forms of androgen receptor have distinct oligomeric structures. Biochim Biophys Acta 1822, 1070–1078 (2012). R.Kumar, H.Atamna, M.N.Zakharov, S.Bhasin, S.H.Khan, and R.Jasuja, Role of the androgen receptor CAG repeat polymorphism in prostate cancer, and spinal and bulbar muscular atrophy. Life Sciences 88, 565–571 (2011). 40 Ingénierie enzymatique et évolution dirigée 41 Ingénierie enzymatique et évolution dirigée CONFERENCE PLENIERE Design and optimization of artificial enzymes: nearer to nature Donald Hilvert 1 ∗† 1 Laboratory of Organic Chemistry – ETH Zürich, Zurich, Suisse Protein design is a challenging problem. We do not fully understand the rules of protein folding, and our knowledge of structure-function relationships in these macromolecules is at best incomplete. Nature has solved the problem of protein design through the mechanism of Darwinian evolution. From primitive precursors, recursive cycles of mutation, selection and amplification of molecules with favorable traits have given rise to all of the many thousands of gene products in every one of our cells. An analogous process of natural selection can be profitably exploited in silico and in the laboratory on a human time scale to create, characterize and optimize artificial catalysts for tasks unimagined by Nature. Recent progress in combining computational and evolutionary approaches for enzyme design will be discussed, together with insights into enzyme function gained from studies of the engineered catalysts. ∗ † Intervenant Auteur correspondant: [email protected] 42 Ingénierie enzymatique et évolution dirigée COMMUNICATION ORALE Design computationnel de protéines avec une fonction d’énergie MMGBSA Thomas Gaillard ∗† 1 , Nicolas Panel 1 , David Mignon 1 , Thomas Simonson 1 1 Laboratoire de Biochimie (BIOC) – CNRS : UMR7654, Polytechnique - X – Laboratoire de Biochimie Ecole Polytechnique 91128 Palaiseau, France Le design de protéines a pour but la conception de nouvelles protéines ou la modification de protéines existantes pour atteindre une fonction donnée. Les approches computationnelles sont une aide précieuse pour le design de protéines, en aidant à rationaliser les prédictions et guider les tests expérimentaux. Le design computationnel de protéines (CPD) a stimulé d’importants efforts méthodologiques et a donné lieu à des succès spectaculaires comme la création d’une protéine présentant un nouveau repliement ou encore l’ingénierie de sites actifs d’enzymes. La principale difficulté du CPD réside dans le nombre astronomique de séquences et conformations possibles, de l’ordre de (20x10)^100 pour une protéine de 100 acides aminés. Des algorithmes d’exploration efficaces sont donc nécessaires. Un autre élément clé du succès du CPD est la fonction d’énergie utilisée pour évaluer et trier les séquences et conformations. Notre approche du CPD [1-10] se fonde sur un modèle atomique de la structure de la protéine et sur une fonction d’énergie de mécanique moléculaire. Un élément important est le traitement du solvant, représenté comme un continuum diélectrique à l’aide d’un terme de Generalized-Born, complété par un terme proportionnel à la surface accessible au solvant. Les éléments clés de notre implémentation sont : 1) le squelette de la protéine est maintenu fixe, 2) l’espace des conformations des chaînes latérales est réduit à une librairie discrète de rotamères, 3) la fonction d’énergie est décomposée en paires d’interactions précalculées. La première étape consiste à calculer une matrice des interactions entre chaque paire de rotamères. Dans l’étape suivante, l’espace des séquences et conformations est exploré à l’aide d’un algorithme d’optimisation. L’évaluation de l’énergie dans cette deuxième étape est rapide grâce au précalcul de la matrice d’énergie. L’implémentation de notre procédure de CPD sera d’abord présentée, puis les applications à la prédiction de conformations de chaînes latérales et au design de séquences entières seront abordées. A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis, T. Simonson, Proteins (2007), 67, 853-867. M. Schmidt am Busch, A. Lopes, N. Amara, C. Bathelt, T. Simonson, BMC Bioinformatics (2008), 9, 148. M. Schmidt am Busch, A. Lopes, D. Mignon, T. Simonson, J. Comput. Chem. (2008), 29, 1092-1102. ∗ † Intervenant Auteur correspondant: [email protected] 43 Ingénierie enzymatique et évolution dirigée COMMUNICATION ORALE M. Schmidt am Busch, D. Mignon, T. Simonson, Proteins (2009), 77, 139-158. A. Lopes, M. Schmidt am Busch, T. Simonson J. Comput. Chem. (2010), 31, 1273-1286. M. Schmidt am Busch, A. Sedano, T. Simonson, PLOS One (2010), 5, e10410. N. Amara, C. Aubard, P. Plateau, T. Simonson, G. Archontis, Proteins (2011), 79, 3448-3468. M. Schmidt am Busch, A. Lopes, D. Mignon, T. Gaillard, T. Simonson, in J. Zeng, R. Zhang, H. Treutlein (Ed.), Quantum Simulations of Materials and Biological Systems. Springer Verlag, New York, 2012. T. Simonson, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart, G. Archontis, J. Comput. Chem. (2013), 34, 2472-2484. T. Gaillard, T. Simonson, J. Comput. Chem. (2014), 35, 1371-1387. 44 Ingénierie enzymatique et évolution dirigée COMMUNICATION ORALE Cost Function Network Optimization: exact algorithms towards Computational Protein Design Seydou Traore ∗ 1 , Kyle Roberts 2 , David Allouche 3 , Bruce Donald 2 , Isabelle André 1 , Thomas Schiex 3 , Sophie Barbe† 1 1 Université de Toulouse; INSA,UPS,INP; LISBP (LISBP) – Institut National des Sciences Appliquées (INSA) - Toulouse, Institut national de la recherche agronomique (INRA) : UMR792, CNRS : UMR5504 – 135 Avenue de rangueil 31077 Toulouse cedex 04, France 2 Department of Biochemistry, Department of Computer Science, Department of Chemistry – Duke University, Durham, NC, États-Unis 3 Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA) – Institut national de la recherche agronomique (INRA) : UR875 – Chemin de Borde Rouge, 31320 Castanet Tolosan, France Computational protein design (CPD) aims at finding a set of sequences that can accommodate a given protein scaffold and accomplish some wanted biochemical properties. Other the last decade, it has demonstrated is potential to adequately capture fundamental aspects of molecular recognition and holds great interest for applications ranging from medicine, biotechnology and synthetic biology and nanotechnologies (see for example [1]). CPD is a challenging optimization problem. In the simplest form, the CPD problem assumes a fixed protein backbone and, for each type of amino acid considered at a given position, allows the side-chains to move only among a set of discrete and low-energy conformations, called rotamers. Hence, the optimization problem consists in identifying combinations of rotamers at designable specified positions such that an objective function is minimized (global minimum energy conformation or GMEC). This problem has been proven to be NP-hard [2]. The traditional exact approach is the combination of the Dead-End Elimination preprocessing and the A* search algorithm (DEE/A*). However, the DEE/A* framework becomes impractical for complex CPD instances, one of the main challenges being the exponential size of the conformational and sequence protein space that has to be handled. Because of these difficulties, meta-heuristic approaches including sampling methods (mainly based on the Monte Carlo algorithm) and population based approaches (such as the Genetic Algorithm) were privileged. However, only exact approaches can ensure that discrepancies between CPD predictions and experimental results come exclusively from the inadequacies of the biophysical model and not from the optimization algorithm. This is an important property in design cycles involving several runs of CPD modelling, computational optimization, and experimental testing. In addition, exact approaches may stop before meta-heuristic approaches because they can determine that the optimum is reached. Finally, empirical studies showed that the accuracy of meta-heuristics tends to degrade as the problem size increases [3]. ∗ † Intervenant Auteur correspondant: [email protected] 45 Ingénierie enzymatique et évolution dirigée COMMUNICATION ORALE Thence, in our previous works, we showed that a recent combinatorial optimization technique, defined in the field of “Cost Function Networks” (or Weighted Constraint satisfaction) can push CPD beyond the limit of usual tools [4-6]. The performance of the Cost Function Network (CFN) optimization was compared to several other well-known optimization strategies toward the GMEC identification problem. These methods included 0/1 Linear and Quadratic Programming, 0/1 Quadratic Optimization, Weighted Partial MaxSAT, Graphical Model optimization problems and the commonly used CPD dedicated framework Dead-End Elimination/A* (DEE/A*). The CFN framework outperformed all these methods both in terms of number of instances solved but also in terms of runtime performance. Following this methodology, we have developed and implemented new CFN-based search strategies and heuristics within the OSPREY CPD-dedicated software [7]. The performance of the algorithms was examined using a benchmark set of 30 CPD instances. These new methods bring important speedups compared to the well-known DEE /A* framework for solving numerous CPD problems. Among the new developments, we have introduced a new Best-First search strategy using the CFN lower bound as heuristics. This method led to an important speedup compared to the traditional A* algorithm. A new Side Chain Positioning (SCP)–based upper bounding heuristics have need developed for preprocessing pruning efficiency. This heuristic was extended to define a new branching scheme which incrementally performs SCP-based upper bounding during search. The new branching scheme allowed to more efficiently find the GMEC but more importantly, it enables to enumerate sub-optimal solutions over a larger energy range. These results open the door to the exact solving of CPD optimization problems with runtime performances that compete against those of heuristics while guaranteeing accuracy. Beyond providing a design framework and computational tools to facilitate the optimization of highly combinatorial design cases, our approach is also applicable to design strategies that integrate more flexibility with respect to backbone, and continuous sidechain modelling [8]. Acknowledgments This work has been funded by the “Agence Nationale de la Recherche”, references ANR 10-BLA0214 and ANR-12-MONU-0015-03. We thank the Computing Center of Region Midi-Pyrénées (CALMIP, Toulouse, France) and the GenoToul Bioinformatics Platform of INRA-Toulouse for providing computing resources and support. S. Traoré was supported by a grant from the INRA and the Region Midi-Pyrénées. K.E. Roberts and B.R. Donald supported by NIH Grant 2-R01GM-78031-5. References Khare,S.D. et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat. Chem. Biol., 8, 294–300. 2012. Pierce,N.A. and Winfree,E. (2002) Protein Design is NP-hard. Protein Engineering, 15, 779–782. Voigt,Christopher A. et al. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. Journal of Molecular Biology, 299, 789–803, 2000. D. Allouche, J. Davies, S. de Givry, G. Katsirelos, T. Schiex, S. Traoré, I. André, S. Barbe, S. Prestwich, B. O’Sullivan. Computational Protein Design as an Optimization Problem. Artificial Intelligence Journal, March 2014. 46 Ingénierie enzymatique et évolution dirigée COMMUNICATION ORALE Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Schiex T and Barbe S. A new framework for computational protein design through Cost function optimization. Bioinformatics, 2013. Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Barbe S and Schiex T. Computational Protein Design as a Cost Function Network Optimization Problem. CP2012 Proceedings. 18th International Conference on Principles and Practice of Constraint Programming, Québec, Canada, Oct, 8-12, 2012– Proceeding. P. Gainza et al. OSPREY: Protein design with ensembles, flexibility, and provable algorithms. Methods Enzymol. 2013;523:87-107. Hallen,M.A. et al. Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins, 81, 18–39. 2013. 47 Ingénierie enzymatique et évolution dirigée COMMUNICATION ORALE Computational approach to enzyme design David Rinaldo 1 ∗ 1 Schrödinger GmbH (SCH) – Dynamostraße 13 68165 Mannheim, Allemagne Enzyme design is an important area of ongoing research with a broad range of applications in protein therapeutics, biocatalysis, bioengineering, and other biomedical areas; however, significant challenges exist in the design of enzymes to catalyze specific reactions of interest. Here, we develop a computational protocol using an approach that combines molecular dynamics, docking, and MM-GBSA scoring to predict the catalytic activity of enzyme variants. Our primary focus is to understand the molecular basis of substrate recognition and catalysis. We apply the method to a variety of enzymes and substrates and in most cases correctly identify the mutations that yield the greatest improvements in enzyme activity. Also, we confirm that the computationally predicted structures reproduce experimental crystal structures, when available. Overall, the protocol developed here yields encouraging results and suggests that computational approaches can aid in the redesign of enzymes with improved catalytic efficiency. ∗ Intervenant 48 Les enzymes comme cibles thérapeutiques 49 Les enzymes comme cibles thérapeutiques CONFERENCE PLENIERE Enzymes as target class for approved drugs The case of secretory phospholipase A2 (sPLA2) family of proteins as novel therapeutic targets Dominique Douguet 1 ∗† 1 Institut de pharmacologie moléculaire et cellulaire – CNRS : UMR7275, Université Nice Sophia Antipolis (UNS) – CNRS-IPMC 660 Route des lucioles 06560 VALBONNE, France To facilitate drug discovery, there is a need to analyze the current landscape of approved drugs in terms of 3D chemical structures concomitantly with pharmacodynamics and pharmacokinetics data. We have addressed this question by constructing the public e-Drug3D database which contains FDA-approved drugs. e-Drug3D provides ready-to-screen electronic collections to assist in drug repurposing and fragment-based drug discovery. A short global review will be presented with a particular focus on enzyme inhibitors. Over the years, secretory phospholipase A2 (sPLA2) family of proteins has been shown to participate in several pathologies like neurodegenerative, inflammatory, cardiovascular, metabolic, infectious, and neoplastic diseases in humans. However, while the extracellular localization of sPLA2 isoforms makes them feasible targets for new therapeutics, such drug developments have failed. Here, we will make an overview of the structure-based design of inhibitors of human sPLA2s. ∗ † Intervenant Auteur correspondant: [email protected] 50 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE Développement d’antibactériens dirigés contre la ThyX de Mycobacterium tuberculosis Kamel Djaout 1 ∗† 1 , Marten Vos 1 , Hubert F. Becker 1 , Hannu Myllykallio 1 Laboratoire d’optique et biosciences (LOB) – Polytechnique - X, Inserm : U1182, CNRS : UMR7645 – Route de Saclay 91128 PALAISEAU CEDEX, France La tuberculose est un est problème de santé publique mondial, avec plus de 1.5 million de morts en 2013 (OMS). L’apparition et la propagation de souches multi et extensivement résistantes de Mycobacterium tuberculosis, bactérie causant la tuberculose, met en exergue le besoin urgent de développer nouvelle molécules thérapeutique. ThyX est une cible intéressante dans M. tuberculosis : elle est essentielle à la survie de la bactérie et ne présente pas d’homologie de structure ou de mecanisme avec son équivalent humain, ThyA. De plus, ThyX se retrouve surexprimée dans les souches de Mycobacterium tuberculosis résistantes aux molécules déjà sur le marché. ThyX est une thymidylate synthase flavine-dépendante. Elle catalyse la synthèse de novo de désoxythymidine monophosphate, un précurseur essentiel de l’ADN. Nous avons étudié le mécanisme réactionnel détaillé de la ThyX de Mycobacterium tuberculsosis et montrons des différences majeures de réactivité comparé aux autres ThyX décrites. Nous avons aussi criblé pour des inhibiteurs spécifiques de ThyX Mtb. Les molécules issues de ce crible présentent d’une part un nouveau mode d’inhibition des ThyX, ciblant les sous-sites de fixation d’au moins deux substrats; et d’autre part un pouvoir antibactérien sur Mycobacterium smegmatis et Mycobacterium tuberculosis, avec des CMI variant de 5 à 20 µg/ml. Nous mettons aujourd’hui en place des outils computationnels (modèles QSAR et pharmacophore) afin de cribler in silico pour de meilleurs candidats d’inhibition de la ThyX de Mycobacterium tuberculosis. ∗ † Intervenant Auteur correspondant: [email protected] 51 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE Molecular dynamics study of ligand recognition by DXR: implications for the design of new antibiotic compounds Fanny Krebs ∗ 1 , Roland Stote 1 , Annick Dejaegere 1 1 IGBMC – CNRS : UMR7104, Inserm : UMRU964, université de Strasbourg – Biocomputing group Structural Biology Genomics Dept. - IGBMC 1 rue Laurent Fries 67404 Illkirch-Graffenstaden Cedex, France Most eubacteria, including pathogenic ones, use the 2-C -methyl-D-erythritol 4-phosphate (MEP) pathway to synthesize the basic units that lead to the production of isoprenoids, which are important secondary metabolites that have diverse roles in different biological processes. Since the MEP pathway is not present in human, enzymes of this pathway are promising targets for the development of new antibiotic drugs. The second enzyme of the MEP pathway is 1-desoxyD-xylulose 5-phosphate reductoisomerase (DXR), which catalyzes the conversion of the 1-desoxyD-xylulose 5-phosphate (DXP) via an intra-molecular rearrangement in presence of a metallic cation (Mg2+, Mn2+), followed by a reduction involving the cofactor, nicotinamide adenine dinucleotide phosphate (NADPH). X-Ray structures studies identified large-scale conformational changes of active site loops that likely regulate ligand recognition. To investigate the mechanism of ligand binding to the enzyme active site, we used molecular dynamics simulations. Analysis of the simulations focused on the structural and functional impact of important active site residues. Understanding the interactions between ligands and the protein target as a function of conformation can contribute to the development of new therapeutic compounds. ∗ Intervenant 52 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE Discovery of Oligopyridyl scaffold molecules as potent Mcl-1 inhibitors Jana Sopkova-De Oliveira Santos ∗ 1 , Jade Fogha 1 , Anne Sophie Voisin-Chiret 1 , Ronan Bureau 1 , Laurent Poulain 2 , Céline Gloaguen 1 2 CERMN FR CNRS INC3M – Université de Caen Basse-Normandie : EA4258 – bd Becquerel 14032 Caen, France 2 BioTICLA Unit EA4656, Comprehensive Cancer Center François Baclesse – Université de Caen Basse-Normandie : EA4656 – 14032 Caen, France B-cell lymphoma 2 (Bcl-2) family proteins are crucial regulators of the intrinsic mitochondrial pathway of apoptosis and comprise both pro-apoptotic and anti-apoptotic proteins.(a) For instance, anti-apoptotic proteins Bcl-xL and Mcl-1 induce cell survival until they are inhibited by pro-apoptotic proteins (Puma, Noxa, Bim). In ovarian cancer, as in many others, these proteins expression is deregulated and play a causative role in chemoresistance. Bcl-xL and Mcl-1 anti-apoptotic proteins cooperate to protect tumor cells against apoptosis, and their concomitant inhibition leads to massive apoptosis.(b) Whereas a potent Bcl-xL inhibitor have been discovered (ABT-737 by Abbot Laboratories), Mcl-1 protein inhibition is still not completely resolved. As interaction among Bcl-2 family proteins occurs through -helices, our laboratory has developed a new family of compounds able to mimic -helix side chain distribution (abiotic foldamers) using as structural chemical units pyridine(c) and/or phenyl(d). The designed and synthesized oligopyridines potentially targeting the Mcl-1 hydrophobic pocket were evaluated by their capacity to inhibit Mcl-1 in live cells and to sensitize ovarian carcinoma cells to Bcl-xL-targeting strategies.(e) The structureactivity relationships were established and we focused our attention on MR29072, named pyridoclax as a very promising compound inhibiting specifically Mcl-1. ,(f) Its ability to bind directly to Mcl-1 was confirmed by surface plasmon resonance assay. (a) Cory, S.; Adams, J. M. The Bcl2 family: regulators of the cellular life-or-death switch. Nat. Rev. Cancer 2002, 2(9), 647-656. (b) Brotin, E.; Meryet-Figuière, M.; Simonin, K.; Duval1, R. E.; Villedieu, M.; Leroy-Dudal1, J.; Saison-Behmoaras, E.; Gauduchon, P.; Denoyelle, C.; Poulain, L. Bcl-xL and MCL-1 constitute pertinent targets in ovarian carcinoma and their concomitant inhibition is sufficient to induce apoptosis. Int. J. Cancer 2010, 126, 885-895. (c) Sopková-de Oliveira Santos, J.; Voisin-Chiret, A.-S.; Burzicki, G.; Sebaoun, L.; Sebban, M.; Lohier, J.-F.; Legay, R.; Oulyadi, H.; Bureau, R.; Rault, S. Structural Characterizations of Oligopyridyl Foldamers, -Helix Mimetics. J. Chem. Inf. Model. 2012, 52, 429-439 (d) Perato, S.; Fogha, J.; Sebban, M.; Voisin-Chiret, A.-S.; Sopkova-de Oliveira Santos, J.; Oulyadi, H.; Rault, S. Conformation Control of Abiotic -Helical Foldamers. J. Chem. Inf. Model.2013, 53(10), 2671-2680. ∗ Intervenant 53 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE (e) Gloaguen, C. ; Voisin-Chiret, A. S. ; Sopkova-de Oliveira Santos, J. ; Fogha, J. ; Gautier, F. ; De Giorgi, M. ; Burzicki, G. ; Perato, S. ; Pétigny-Lechartier, C. ; Simonin-Le Jeune, K. ; Brotin, E. ; Goux, D. ; N’Diaye, M. ; Lambert, B. ; Louis, M. H. ; Ligat,L. ; Lopez, F. ; Juin, P. ; Bureau, R. ; Rault, S. ; Poulain, P. J. Med. Chem., 2015, Just Accepted Manuscript. (f) Poulain L., Voisin-Chiret A. S., Sopkova- de Oliveira Santos J., Bureau R., Burzicki G., De Giorgi M., Perato S., Fogha J., Rault S., Juin Ph., Gautier F. Mcl-1 modulating compounds for cancer treatment. EP14305309.8. 2014. 54 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE Into the intimacy of an irreversible inhibition: SMD(QM/MM) simulations of the fibroblast growth factor receptor-1 (FGFR1) kinase domain. Yan Li , François Maurel , Patricia Busca , Guillaume Prestat , Laurence Legeai-Mallet , Rhuizheng Zhang , Rongjing Hu , Michel Delamar , Florent Barbault ∗ 1 1 ITODYS (ITODYS) – CNRS : UMR7086, Université Paris Diderot - Paris 7, Université Sorbonne Paris Cité (USPC) – 15 rue Jean de Baïf 75205, France The Fibroblast Growth Factor Receptor 1 (FGFR1) binds to Fibroblast Growth Factor (FGF) peptide ligands [1]. This association induces signaling pathways which appears to play critical roles in the cell development [1]. FGFR1, like the others FGFRs, has been studied in the context of tumor formation and progression [2]. FGFR1 has been found being amplified in squamous cell lung cancer specimens [3], especially of patients who smoke. Therefore, the inhibition of FGFR1 mainly aims to provide a therapeutic solution for smoker cancers. Inhibition of the tyrosine kinase domain of FGFR1 is an appealing approach to obstruct the biological role of this receptor. However, inhibitors which compete with ATP generally suffer from low selectivity. One way to overcome this drawback is to transform a reversible inhibitor to an irreversible one by adding a reactive moiety. This ”haute couture” strategy requires a meticulous design that cannot be performed by serendipity; Computational studies play thus here a pivotal role. The compound FIIN (fig. 1) is an irreversible inhibitor of FGFR1 [4] which makes a covalent bond to the Cys486 of its kinase domain through a Michael addition’s. We explored its reactivity with molecular simulations. Firstly, we performed structural analyses through molecular dynamics simulations of FGFR1 covalently linked with FIIN (FGFR1-FIIN) and FGFR1 associated with FIIN (FGFR1/FIIN). From this last trajectory we extracted 100 conformations where the sulfur of Cys486 is close to the reactive alkene. To study the reactivity of the FIIN compound, we realized QM/MM simulations where the Self-Consistent-Charge Density-Functional Tight-Binding method (SCC-DFTB) was chosen for the QM part [5]. We used the SMD technique [6] with a LCOD reaction pathway for 1ns (fig. 1) and obtained three different mechanisms. Only one mechanism is conceivable and works in two steps. The definitive free energy profile (fig. 1) explains the selectivity of FIIN and provides meaningful information for future drug-development of irreversible kinase inhibitors. Reference: [1] Koziczak M, et al. 2004 Oncogene 23, 3501–8 [2] Powers CJ, et al. 2000 Endocr. Relat. Cancer 7, 165–97 [3] Weiss J, et al. 2010 Sci. Transl. Med. 15:62ra93 [4] Zhou W, ∗ Intervenant 55 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE et al. 2010 Chem. Biol. 26, 285-95 [5] Frauenheim T, et al. 1998 Mat. Res. Soc. Symp. Proc. 491, 91 [6] Isralewitz B, et al. 1997 Biophys. J. 73, 2972-9 56 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE PatchSearch: a fast method for flexible recognition of protein binding sites Inès Rasolohery 1 ∗† 1 , Gautier Moroy 1 , Frédéric Guyon 1 Molécules Thérapeutiques in silico (MTi) – Université Paris Diderot - Paris 7 – France Inès Rasolohery, Gautier Moroy and Frédéric Guyon. Specific recognition of a therapeutic molecule by its target protein has raised a lot of issues in the pharmaceutical field. Indeed, non-specific interactions may lead to significant side effects. In order to determine whether or not a ligand is able to interact specifically with its target protein, we have developed a new method called PatchSearch. A patch is a set of atoms belonging to the protein surface and it can also be a binding site. The aim of our program is to identify similar patches in different protein surfaces. PatchSearch is based on a classic strategy of clique detection in a correspondence or product graph [1]. A clique of the product graph is a group of both geometrical and physicochemical consistent links between binding site atoms and protein surface atoms, and consequently providing a possible structural alignment. PatchSearch uses this kind of clique approach adapting it to protein structures. First, PatchSearch computes all maximum cliques of a reduced size graph constructed with a small distance tolerance criterion (in practice, less than 1Å). Then, the best clique is selected depending on its structural similarity score; this clique gives the rigid core of the query patch. Finally, this clique is enriched with all compatible links from the clique neighborhood. The resulting quasi-clique includes therefore both rigid and flexible parts of the query binding site. We first assessed PatchSearch ability to recognize protein binding sites specific to a same ligand. We used a dataset proposed by Kahraman and coworkers [2], consisting of 100 protein structures complexed with one of nine ligand types (AMP, ATP, FAD, FMN, Glucose, Heme, NAD, Phosphate or Steroid). We performed a ROC analysis and obtained an AUC value of 0.89 with patches extracted from this dataset, suggesting that PatchSearch is efficient to identify specific patches in proteins interacting with a same ligand. We also note that this AUC value is equivalent to or greater than the best results obtained by other programs [3] on the same dataset, namely 0.77 to 0.89. We have evaluated PatchSearch efficiency to find a patch from different conformations of a same protein. For that purpose, we used a benchmark, set up by Gunasekaran and coworkers [4], formed by 98 protein structures in both holo (in complex with ligand) and apo (unbound) forms. When binding sites have undergone some large conformational changes, quasi-cliques approach allows recognition of the whole patches, including flexible parts of the patches. ∗ † Intervenant Auteur correspondant: [email protected] 57 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE We have also applied PatchSearch on patches interacting with indometacin to mine for similar patches into the complete set of human protein structures. This non-steroidal anti-inflammatory drug commonly used to reduce fever and pain is well-known to lead to many side effects. 1. S.B. Seidman: Network structure and minimum degree. Social Networks 5,269-287 (1983). 2. A. Kahraman, R.J. Morris, R.A. Laskowski and J.M. Thornton: Shape Variation in Protein Binding Pockets and their Ligands. J. Mol. Biol. 368, 283-301 (2007). 3. B. Hoffmann, M. Zaslavskiy, J.P. Vert and V. Stoven: A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics. 11:99 (2010). 4. K. Gunasekaran and R. Nussinov: How Different are Structurally Flexible and Rigid Binding Sites Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. J. Mol. Biol. 365, 257-273 (2007). 58 Les enzymes comme cibles thérapeutiques COMMUNICATION ORALE PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins Hiba Abi Hussein ∗† 1 , Alexandre Borrel , Colette Geneix , Michel Petitjean , Leslie Regad , Anne-Claude Camproux‡ 1 Recherche de molécules à visée thérapeutique par approches In Silico (MTI) – Inserm : U973, Université Paris VII - Paris Diderot – Batiment Lamarck 35 rue Hélène Brion 75205 PARIS CEDEX 13, France Therapeutical molecules bind to preferred sites of action, which are in the majority of cases pockets located within proteins or at their surface. Therefore, estimation and characterization of pockets is a major issue in drug target discovery. Among the molecules, “drug-like molecules” are small molecules with particular properties as of small size, able to cross the digestive tract. Predicting protein pocket’s ability to bind drug-like molecules with high affinity, i.e., druggability, is a key step of compound clinical progression projects. Currently computational druggability prediction models are attached to one unique pocket estimation method despite pocket estimation uncertainties. Here, we present “PockDrug-Server” that predicts pocket druggability, efficient on both; estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure using several thresholds) and estimated pockets not guided by the ligand proximity (based on amino atoms that form the surface of potential binding cavities). PockDrug-Server is based on a statistical model corresponding to a combination of 7 linear discriminant analysis model using 9 pocket descriptors to provide a mean druggability. It provides consistent druggability results using different pocket estimation methods. It is robust with respect to pocket boundary and estimation uncertainties, thus efficient using apo pockets that are challenging to estimate. It clearly distinguishes druggable from less druggable pockets using different estimation methods and outperformed recent druggability models for apo pockets. It can be carried out from one or a set of apo/holo proteins. PockDrug-Server is publicly available at: http://pockdrug.rpbs.univ-paris-diderot.fr. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: † 59 Relations dynamique - fonction 60 Relations dynamique - fonction CONFERENCE PLENIERE Combining molecular dynamics and Markov state modelling to understand ligand transport in enzymes Jochen Blumberger ∗† 1 , David De Sancho 2 , Po-Hung Wang 3 , Adam Kubas 1 , Robert Best 4 1 University College London - London’s Global University – Gower Street - London, WC1E 6BT, Royaume-Uni 2 University of Cambridge (UK) – The Old Schools, Trinity Lane, Cambridge CB2 1TN, Royaume-Uni 3 RIKEN – 2-1 Hirosawa, Wako, Saitama 351-0198, Japon 4 National Institutes of Health (NIH) – 9000 Rockville Pike Bethesda, Maryland 20892 USA, États-Unis The diffusion of small ligands within enzymes and their binding to enzyme active sites are ubiquitous molecular processes in biology. The oxygen we breath diffuses to the catalytic site of cytochrome c oxidase where it combines with electrons to produce water and cellular energy. Atmospheric CO2 and N2 diffuse to the buried catalytic sites of proteins before being converted into precursors of biomass or renewable energy sources. In all these examples a small molecule must travel from the solvent to the small catalytic site, that is embedded in a large and densely packed heterogeneous protein matrix. Here we would like to understand how the ligand finds its way to the target. To this end we have recently developed a multiscale molecular simulation approach, where MD simulation and Markov state modelling are combined to shed light on the kinetics of ligand diffusion and binding [1]. First applications to wild-type and mutant hydrogenase enzymes[1,2] have given diffusion rates that are in good agreement with experimental measurements [3] validating the Markov state model used. For the proteins studied so far we have found that the ligands move within multiple hydrophobic cavities or ‘tunnels’ towards a central cavity from where the ligand makes the final transit to the catalytic site [1,2,4]. The functional role of the protein can be compared to the one of a funnel guiding the small molecules towards the target. Very recently we have extended our method to calculate sensitivity maps of the protein that identify residues (‘hot spots’) that are expected to show the greatest affect on ligand diffusion when mutated [5]. Such in-silico predictions could help protein engineers to optimize or control the kinetics of ligand, substrate or inhibitor diffusion in proteins. [1] P. Wang, R. B. Best, J. Blumberger, J. Am. Chem. Soc. 133, 3548 (2011). [2] P. Wang, J. Blumberger, Proc. Natl. Acad. Sci. USA , 109, 6399 (2012). [3] Leger, C. and coworkers Nat. Chem. Biol, 6, 63 (2010). [4] P. Wang, M Bruschi, L. De Gioia, J. Blumberger, J. Am. Chem. Soc. 135, 9493 (2013). [5] D. De Sancho, A. Kubas, P. Wang, J. Blumberger, R. B. Best, J. Chem. Theory Comput. Article ASAP, DOI: 10.1021/ct5011455 (2015). ∗ † Intervenant Auteur correspondant: [email protected] 61 Relations dynamique - fonction COMMUNICATION ORALE Structural dynamics of the retinoid X receptor ligand binding domain by accelerated molecular dynamics Jérôme Eberhardt ∗ 1 , Roland Stote 1 , Annick Dejaegere 1 1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) – CNRS : UMR7104, Inserm : U964, université de Strasbourg – Parc D’Innovation 1 Rue Laurent Fries - BP 10142 67404 ILLKIRCH CEDEX, France Nuclear Receptor proteins are ligand-dependent transcription activators that form one of the major signal transduction pathways in metazoans, by contributing to cellular communication networks involved in apoptosis, cell growth and differentiation, homeostasis (Altucci et al. 2001). Retinoic acid 9-cis, a metabolite of vitamin A, is a ligand of the retinoid X receptor (RXR) subclass of the nuclear receptor superfamily. This subclass is comprised of three RXR (, and ). RXRs are multi-domains proteins with a central DNA-binding domain (DBD) linked to C-terminal Ligand-binding domain (LBD). The protein is known to undergo large conformational changes in the course of activation. RXR is also a phosphoprotein and the phosphorylation of Ser260 in the LBD affects the transcriptional regulation of RXR dimer complexes. Aberrant phosphorylation of Ser260 is strongly associated with the development of various cancers, in particular hepatocellular carcinoma (HCC), a primitive liver cancer (Matsushima-Nishiwaki et al. 2001, Macoritto et al. 2008). Structurally, Ser260 is located near the ligand-binding pocket, in a loop between Helix 1 and 3 of the LBD. In earlier work, we showed that phosphorylation of the RAR LBD affects structural dynamics in a way that can subsequently modulate functionality (Samarut et al. 2011, Chebaro et al. 2013). The specific aim of this project is to understand how phosphorylation of the RXR LBD influences protein structure and dynamics by molecular dynamics simulations. However, conformational sampling by molecular dynamics simulations is, in itself, a challenging task and can often call for the application of new methods of enhanced sampling. In this work, we explored the ensemble of conformations of ligand bound and apo RXR by applying accelerated molecular dynamics (aMD) (Hamelberg et al. 2004). aMD is a new computational technology that permits more extensive conformational sampling. In this first application to nuclear receptor proteins, e.g. RXR, extensive validation was required. We developed and applied an aMD protocol to the unphosphorylated RXR receptor, taking advantage of the large amount of experimental information available for this receptor. Besides providing a means to validate our method, this study provided additional interpretation of published experimental data. Our application of this technique yielded very promising results for enhanced conformational sampling of nuclear receptor proteins. We will present results from this work as well as provide future perspectives, which involve the study of phosphorylated forms of RXR as well as implications for the development of new therapeutic compounds for the treatment of HCC. ∗ Intervenant 62 Relations dynamique - fonction COMMUNICATION ORALE Turning glycoside hydrolases into transglycosidases: an experimental and theoretical study of the internal water dynamics in the Thermus thermophilus -glycosidase Benoît David 1 ∗ 1 , Charles Tellier 1 , Yves-Henri Sanejouand 1 université de nantes (ufip) – CNRS : UMR6286 – 2 rue de la houssinière 44322 Nantes cedex 03, France Mostly known for their ability to hydrolyze glycosidic linkages, numerous glycoside hydrolases are also able to catalyze reverse hydrolysis (transglycosylation) which can be harnessed for the synthesis of complex oligosaccharides. Although hydrolysis usually prevails over the reverse reaction, transglycosylation propensity has already been increased through mutagenesis and directed evolution experiments [1, 2]. However, little is known about the regulation of the balance between both activities. A previous experimental study on the Thermus thermophilus (Ttgly) -glycosidase using deuterium exchange mass spectrometry has shown that amide hydrogens from buried parts of the protein were able to exchange with the solvent [3]. The discovery via molecular dynamic (MD) simulation of a potential water channel connecting the bulk to the active site along this peptide has supported a possible role of internal water dynamics on the hydrolytic acivity of Ttgly [3]. Using an improved simulation protocol, new MD simulations up to 500 ns have been conducted in order to extensively probe the internal water dynamics in Ttgly. Analysis of the internal water molecules trajectories allowed to characterized a total of six new potential water channels. Guided by sequence alignements, mutagenesis experiments conducted on vicinal residues along the largest channel allowed the identification of mutations influencing the balance between hydrolysis and transglycosylation. Within this context, it is tempting to speculate that this water channel could be involved in supplying water molecules to the active site and potentially regulating the hydrolytic activity of Ttgly. 1. Feng, H.-Y., Drone, J., Hoffmann, L., Tran, V., Tellier, C., Rabiller, C., and Dion, M. (2005). Converting a Glycosidase into a Transglycosidase by Directed Evolution. Journal of Biological Chemistry 280, 37088–37097. 2. Teze, D., Hendrickx, J., Czjzek, M., Ropartz, D., Sanejouand, Y.-H., Tran, V., Tellier, C., and Dion, M. (2014).Semi-rational approach for converting a GH1 glycosidase into a transglycosidase. Protein Engineering Design and Selection 27, 13–19. ∗ Intervenant 63 Relations dynamique - fonction COMMUNICATION ORALE 3. Teze, D., Hendrickx, J., Dion, M., Tellier, C., Woods, V.L., Tran, V., and Sanejouand, Y.-H. (201 3 ).Conserved Water Molecules in Family 1 Glycosidases: A DXMS and Molecular Dynamics Study. Biochemistry 52, 5900–5910. 64 Relations dynamique - fonction COMMUNICATION ORALE Description théorique d’un phénomène de ”substrate channeling” dans la biosynthèse des flavonoïdes. Julien Diharce ∗ 1 , Jérôme Golebiowski 1 , Sébastien Fiorucci 1 , Serge Antonczak† 1 1 Institut de Chimie de Nice (ICN) – CNRS : UMR7272, Université Nice Sophia Antipolis [UNS], Université Nice Sophia Antipolis (UNS) – Faculté des Sciences Parc Valrose 28 Avenue Valrose 06108 Nice cedex 2, France Dans tous les systèmes vivants, la concentration d’entités biologiques fonctionnelles (protéines, enzymes, peptides...) est très élevée. Dès lors, des structures multienzymatiques transitoires peuvent se créer et exister suffisamment longtemps pour permettre l’apparition de nouveaux systèmes fonctionnels appelés métabolons. Dans de telles structures impliquant un ensemble d’enzymes engagées séquentiellement dans un chemin de biosynthèse, le produit d’une réaction enzymatique est transféré directement dans le site actif de l’enzyme suivante où il devient substrat. Ce transfert direct diminue grandement les temps de diffusion lors du processus global ainsi que les transferts énergétiques impliqués lors des phénomènes de désolvatation/solvatation. L’effet catalytique général est ainsi optimisé. Ce phénomène est désigné sous le nom de “ Substrate Channeling ”. Il est désormais admis que la création de tels complexes est un élément essentiel des mécanismes de biosynthèse de molécules naturelles[1]. De récents travaux[2] mettent en avant la formation d’un tel complexe supramoléculaire lors de la production de flavonoïdes, molécules naturelles antioxydantes dont font partie les anthocyanes et les proanthocyanidines. Nous avons mis en place de nombreuses méthodes théoriques pour décrire les interactions à différents niveaux de complexité. Des méthodes de docking protéine-protéine en résolution gros grain ont permis de proposer des structures multi-enzymatiques alors que des procédures de dynamique moléculaire en résolution tout-atome ont mené à une description fine des interactions entre substrat, cofacteur et enzyme. Lors de ce travail, a été décrit le comportement dynamique de structures multienzymatiques impliquant trois enzymes en interaction avec une membrane cellulaire. Nous détaillerons plus spécifiquement le phénomène de diffusion du métabolite d’un site actif au suivant et mettrons en avant l’importance de la nature des interactions protéine/protéine sur la stabilité du complexe. L’analyse de la diffusion du métabolite montre clairement qu’il reste constamment en interaction avec les structures enzymatiques et que, dans cette configuration, le nombre de molécules d’eau dans son environnement est fortement réduit comparativement à une solvatation complète. 1. Møller, B.L., Dynamic Metabolons. Science, 2010. 330(6009): p. 1328-1329. 2. Crosby, K.C., et al., FEBS Letters, 2011. 585(14): p. 2193-2198. ∗ † Intervenant Auteur correspondant: [email protected] 65 Relations dynamique - fonction COMMUNICATION ORALE L’allostérie dynamique de la protéine CAP révélée par les forces inter-atomiques Maxime Louet 1 ∗ 1 Molécules Thérapeutiques In silico (MTi) – Université Paris Diderot - Inserm UMR-S 973 – Bât Lamarck A, 35 Rue Hélène Brion 75205 PARIS CEDEX 13, France La protéine Activatrice des Catabolites (Catabolite Activator Protein – CAP) est un cas d’école pour l’allostérie des protéines. L’activation et la liaison à l’ADN de cet homodimère requiert la liaison de deux Adénosine Mono-Phosphate cycliques (AMPc) qui se lient de manière anti-cooperative. Ce facteur de transcription qui joue un grand rôle dans la régulation de nombreux gènes au sein des procaryotes, tel que l’opéron lactose, a fait l’objet de plusieurs études expérimentales ayant montré une perte notable de son entropie conformationnelle après la liaison du second ligand. Il a donc été proposé que la cause de cette anti-cooperativité est essentiellement entropique et non due à un changement conformationnel. Cependant, les acides-aminés clés initiateurs de la modification de la dynamique globale de CAP sont encore inconnus. Nous présenterons nos résultats, à l’échelle atomique, concernant la régulation allostérique de la protéine CAP, par des méthodes de Dynamique Moléculaire et d’Analyse de Distribution de Force (Force Distribution Analysis – FDA) [1]. Il sera montré que nos simulations reproduisent la perte entropique observée expérimentalement. Cette entropie a été calculée de manière plus précise grâce à un outil développé au laboratoire se basant sur la covariance des forces et non des coordonnées [2]. A l’aide de la FDA nous avons également pu observer un chemin de communication allostérique au sein de la protéine CAP, d’une part entre les deux sites de fixation des AMPc et d’autre part avec des sites plus distants tels que les domaines de liaison à l’ADN. Nos résultats suggèrent que l’anti-coopérativité n’est pas uniquement entropique mais également enthalpique, notamment par la rotation de chaînes latérales bloquant le site de fixation du deuxième AMPc. 1. Costescu and Gräter. Time-resolved force distribution analysis. BMC Biophysics 2013, 6:5 2. Hensen, Gräter and Henchman. Macromolecular Entropy Can Be Accurately Computed from Force. J.Chem.Theory Comput. 2014, 10: 4777-4781 ∗ Intervenant 66 Relations dynamique - fonction COMMUNICATION ORALE Assessing the crowding of Membrane Proteins at the Mesoscale Matthieu Chavent 1 ∗ 1 , Anna Duncan 1 , Jean Hélie 1 , Tyler Reddy 1 , Mark Sansom 1 Department of Biochemistry (Oxford, UK) (SBCB) – South Parks Road, Oxford, OX1 3QU, Royaume-Uni With recent improvements in both experimental and computational techniques it is now possible to gain insight into increasingly complex biomembrane systems. Nevertheless, at the frontier between these two fields lies a twilight zone which we can refer to as the mesoscale. This zone ranges from a few dozen of nanometres to micrometres in size and from microseconds to millisecond in time. In this zone, proteins may adopt specific spatial organisations within a cell membrane impacting on a number of biological processes. For example, with our collaborators, we have combined molecular dynamics and microscopy to reveal the presence of “islands” of ~ 0.5 µm dimensions formed by the aggregation of porins in bacterial outer membranes. This phenomenon has an essential role in the turnover of proteins at the surface of gram negative bacteria [1]. Nevertheless, despite increasing efforts to cover this mesocale zone, it remains difficult to compare models and experimental observations. Furthermore, the complex dynamic interactions between lipids and proteins need to be better understood on a larger scale to take into account possible emergent phenomena which are not visible for smaller (nanoscale) system sizes. This is particularly true now with the rise of very large and complex models such as plasma membranes [2,3] or flu virion [4]. Here, we would like to present our different attempts to model and characterize large systems to assess the dynamical crowding of membrane proteins and how it has driven the development of new visualization programs to improved the understanding of these dynamical systems [5]. We will also discuss how a better characterization of these systems may be used to pave the way of simpler mathematical models to create systems of the micrometre scale. 1. Rassam, P. et al. Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria. Nature, accepted. 2. Ingólfsson, H. I. et al. Lipid organization of the plasma membrane. J. Am. Chem. Soc. 136, 14554–14559 (2014). 3. Koldsø, H., Shorthouse, D., Hélie, J. & Sansom, M. S. P. Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers. PLoS Comput Biol 10, e1003911 (2014). 4. Reddy, T. et al. Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza A Virion. Structure (London, England : 1993) (2015). doi:10.1016/j.str.2014.12.019 5. Chavent, M. et al. Methodologies for the analysis of instantaneous lipid diffusion in md ∗ Intervenant 67 Relations dynamique - fonction COMMUNICATION ORALE simulations of large membrane systems. Faraday discussions 169, 455–475 (2014). 68 Relations dynamique - fonction COMMUNICATION ORALE New way to fight against antibiotic resistance: reconstruction of a three-component efflux pump Kaouther Ben Ouirane ∗† 1 , Isabelle Broutin 2 , Catherine Etchebest 1 1 Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB) – Université Paris Diderot, Sorbonne Paris Cité, INTS, Inserm : U1134, Université Paris Diderot - Paris 7, Laboratoire d’excellence GrEx – 6 rue Alexandre Cabanel, 75739 Paris cedex 15, France 2 Laboratoire de cristallographie et RMN biologiques (LCRB) – CNRS : UMR8015, Université Paris V Paris Descartes – Faculté de Pharmacie 4 Avenue de l’Observatoire 75270 PARIS CEDEX 06, France Efflux pumps are present in Gram-negative bacteria and are a key mechanism to resist to antibiotics through expulsing them to the extracellular medium preventing them to reach their target. Thus, inhibition of this machinery can be an efficient strategy to fight against antibiotic resistance. Efflux pumps are active as macrocomplexes of three protein partners: MexB, a protein of the inner membrane, OprM, protein of the outer membrane and MexA, a periplasmic protein. Although each component has been well characterized, complex assembly remains misunderstood. The elucidation of their assembly mechanism, in particular in Pseudomonas aeruginosa, would identify key regions essential for complex function. We propose a new and original strategy to prevent the assembly of the efflux pump: This strategy consists in designing new drugs (”complex blockers”) avoiding the protein/protein recognition and/or rigidifying the different protein partners preventing their required structural adaptability for assembly. Using normal mode analysis and molecular dynamics simulations (coarse grain and all atoms) we characterized the conformational changes as well as the flexibility and dynamics of all partners: MexB and OprM in lipid bilayer environment. The reconstitution of functional complex is an intricate task, due to the particularity of its organization. In fact, efflux pump components adopt asymmetric conformations and function according to complex rotational mechanism. Another particularity is the uncertainty related to the periplasmic protein (MexA) stoechiometry. Due to the highly flexible nature of those proteins, especially mexA, we showed that rigid docking strategy is inadequate for this system. We developed then a new strategy to reconstitute the pump that consisted in using CG simulations to study protein-protein interactions instead of using rigid docking. We found that mexA auto-assembles with another molecule forming a stable dimmer for may hundreds of nanoseconds. Interestingly, our collaborators demonstrated that mexA associates into dimers and that it was the functional unit prerequisite for pump assembly. So now we are using the same original strategy based on successive molecular dynamic simulations for solving the problem of assembly between the other efflux pump partners. ∗ † Intervenant Auteur correspondant: [email protected] 69 Relations dynamique - fonction COMMUNICATION ORALE Étude de l’assemblage des protéines membranaires par simulation de dynamique moléculaire à gros grains et méthodes de Forces de Biais Adaptatif. Jean-Pierre Duneau 1 ∗ 1 , Marlon Sidore 1 , James Sturgis 1 Laboratoire d’ingénierie des systèmes macromoléculaires (LISM) – CNRS : UMR7255, Aix-Marseille Université - AMU – 31 Chemin Joseph Aiguier 13402 MARSEILLE CEDEX 20, France L’assemblage des protéines membranaires est le produit d’interactions complexes impliquant des contacts hiérarchisés au sein de multiples chaînes polypeptidiques et d’une grande diversité de lipides. Alors que les méthodes de biologie structurale donnent une vue plus précise des interactions mises en jeu au niveau purement protéique, encore très peu de données sont disponibles pour prendre la mesure du rôle de l’environnement lipidique. Dans le travail présenté, nous avons mis en œuvre des approches de modélisation de dynamique moléculaire à gros grains pour étudier la gamme et la portée des perturbations structurales et dynamiques induites par la présence de protéines sur différents lipides. Nos résultats montrent, la structuration d’un annulus lipidique dynamique au sein duquel les plus grands excès de densité correspondent à des zones d’ancrage privilégiées mais largement échangeables. Au delà de cette zone, une relaxation plus complexe qu’une simple relaxation élastique se met en œuvre jusqu’à de longues distances (> 40 Å). Aussi pour rendre compte de l’impact énergétique de ces altérations à longues portées sur l’association des protéines, nous avons développé une méthode de simulation utilisant des Forces de Biais Adaptatif (ABF) suivant des coordonnées qui permettent d’explorer l’espace conformationnel d’association de protéines suivant les orientations relatives de monomères. Nos simulations montrent que même à longues distances (80 Å) des biais d’orientation relative existent. La relation avec les perturbations de densité lipidique doit encore être établie. Ces travaux ont bénéficié d’un accès aux moyens de calcul du CINES au travers de l’allocation de ressources 2014-077044 attribuée par GENCI. ∗ Intervenant 70 Relations dynamique - fonction COMMUNICATION ORALE Tinker-HP : Dynamique moléculaire polarisable haute performance Christophe Narth 1 ∗ 1 , Jean-Philip Piquemal 1 Laboratoire de chimie théorique (LCT) – CNRS : UMR7616, Université Pierre et Marie Curie (UPMC) - Paris VI – 4 place Jussieu, CC-137, F-75252 Paris, France La dynamique moléculaire est aujourd’hui un outil puissant au service de la biochimie et pharmacologie, permettant de réaliser bon nombres d’études telle que des analyses conformationnelles, effet de solvatation, énergie libre ou encore simulation d’évènements rares. Cela a été rendu possible par l’accélération des codes de mécanique moléculaire classique, permettant ainsi d’atteindre des échelles de temps biologiques. D’autre part, afin de reproduire de manière plus réaliste les interactions intermoléculaires, des méthodes plus raffinées, dites polarisables ou encore de seconde génération, ont été développées, telles que AMOEBA[1] ou SIBFA[2]. Basées sur les multipoles, elles permettent de prendre en compte l’anisotropie des interactions électrostatiques, critique dans le cas de liaisons halogène (“sigma-hole“) ou d’empilement de benzènes (“stacking“). A cela s’ajoute la décomposition des termes d’énergies par la méthode SIBFA, reproduisant ainsi les énergies références (en chimie quantique) dû aux interactions non-liées. Jugés trop souvent comme plus coûteux, ces programmes ont pris du retard par rapport à la large utilisation des champs de forces classiques. Nous présentons ici une nouvelle implémentation du potentiel SIBFA au sein de Tinker-HP (open-source) mêlant rigueur méthodologique par la non-additivité de ses termes énergétiques couplées à une parallèlisation hybride offrant alors la possibilité de réaliser les premières dynamiques moléculaires SIBFA, ainsi que ses premières applications comme un nouveau modèle d’eau. Ponder, Jay W., et al. ”Current status of the AMOEBA polarizable force field.” The journal of physical chemistry B 114.8 (2010): 2549-2564 Cisneros, G. A., et al. ”Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics.” Multi-scale Quantum Models for Biocatalysis. Springer Netherlands, 2009. 137-172. ∗ Intervenant 71 Visualisation et prédiction structurale 72 Visualisation et prédiction structurale CONFERENCE PLENIERE Illustrative Molecular Visualizations Tobias Isenberg 1 ∗ 1 AVIZ (INRIA Saclay - Ile de France) – INRIA – DIGITEO, Bat. Claude Shannon - Université de Paris-Sud, Bâtiment 660, 91190 Gif-sur-Yvette, France Illustrative visualization is a relatively recent development within the larger research field of visualization. Illustrative visualization takes inspiration, in particular, from methods that have been used in traditional illustration for decades and centuries. Illustrative visualization techniques thus make use of concepts such as abstraction and emphasis as well as depiction style to facilitate the creation of better visualization. In particular in the context of the visualization of molecular data, several illustrative visualization techniques have been created. I will present a selection of these, both those created by my own research group and those of colleagues. For example, I will discuss an approach for the abstraction of visualizations of molecular structures in which a continuous abstraction space between structural abstraction, abstraction through spatial perception, and abstraction by means of ”illustrativeness” is created. Users can navigate this space to adjust visualization to their specific needs. Other techniques, for example, use different molecular surface representations at different scale levels based on current view of the data and support a seamless transition between them. With the talk I thus hope to introduce the audience to new visualization approaches and hope to begin a discussion on potential application fields of this work for specific scientific tasks and questions. ∗ Intervenant 73 Visualisation et prédiction structurale COMMUNICATION ORALE Modélisation de novo de structures protéiques par contacts évolutifs Fabrice Allain ∗† 1 , Benjamin Bardiaux 1 , Mickael Nilges 1 1 Institut Pasteur - CNRS UMR 3528 – Institut Pasteur de Paris, Centre National de la Recherche Scientifique - CNRS – Département de Biologie Structurale et Chimie 25,28 rue du Docteur Roux, 75015 PARIS, France Malgré les progrès constants des techniques de biologie structurale, la différence entre le nombre de structures et de séquences protéiques disponibles ne cesse de croître depuis l’arrivée des technologies de séquençage à haut débit. Les méthodes de prédiction structurale ont prouvées ces dernières années leur efficacité pour combler ce fossé(1,2). La croissance des informations génomiques a également rouvert la voie des techniques modélisant les protéines à partir des variations des séquences homologues. La conservation d’une fonction au cours de l’évolution contraint en effet les résidus en contact dans la structure à suivre la même trajectoire évolutive. Le but de ces méthodes est donc de détecter des paires de résidus covariants dans les alignements des séquences homologues d’une protéine cible et déterminer à terme l’architecture tridimensionnelle via des méthodes de modélisation. De récentes approches(3,4) ont ainsi démontrées qu’il était possible de prédire les contacts natifs mais aussi de déduire des conformations relativement proche de celle de référence à partir de ces informations. Malheureusement, ces méthodes présentent encore plusieurs limitations dont la détection des contacts faux positifs. Ces difficultés présentent des similitudes avec la résolution de structure en RMN (Résonnance Magnétique Nucléaire). La spectroscopie par RMN permet de détecter des couples de noyaux proches dans l’espace pour déterminer les conformations. Le logiciel ARIA (Ambiguous Restraints for Iterative Assignment)(5,6). intègre la détection des faux positifs utilisant en particulier le concept de contraintes de distances ambiguës et un processus itératif. Dans ce contexte, nous utilisons la méthodologie d’ARIA à partir des contacts évolutifs pour prédire des structures de protéine. Les premiers tests réalisés sur un jeu de données type avec le protocole d’ARIA montrent des résultats encourageant. Cependant, l’apparition de structures en miroirs topologiques nécessitera une augmentation du nombre de contacts évolutifs utilisés pour obtenir des structures plus juste. 1. Kryshtafovych, A., Fidelis, K. and Moult, J. (2014) Proteins, 82: 164–174. doi: 10.1002/prot.24448 2.Tai, C.-H., Bai, H., Taylor, T. J. and Lee, B. (2014) Proteins, 82: 57–83. doi: 10.1002/prot.24470 3. Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) PloS one, 6(12), e28766. ∗ † Intervenant Auteur correspondant: [email protected] 74 Visualisation et prédiction structurale COMMUNICATION ORALE 4. Michel, M., Hayat, S., Skwark, M. J., Sander, C., Marks, D. S., & Elofsson, A. (2014) Bioinformatics, 30 (17), i482-i488. 5. Rieping, W., Habeck, M., Bardiaux, B., Bernard, A., Malliavin, T. E., & Nilges, M. (2007) Bioinformatics, 23 (3), 381-382. 6. Bardiaux, B., Malliavin, T., & Nilges, M. (2012). In Protein NMR Techniques (pp. 453-483) Humana Press. 75 Visualisation et prédiction structurale COMMUNICATION ORALE Integrating the Solvent Accessible Surface Distance with cross-links-based modeling methods improves the conformational sampling of protein assemblies Mathias Ferber 1 ∗ , Guillaume Bouvier , Michael Nilges 1 Unite de Bioinformatique Structurale , CNRS UMR 3825 and Institut Pasteur (IP, CNRS UMR 3825) – Institut Pasteur de Paris – 28 rue du docteur Roux 75724 Paris, France Cross-linking mass spectrometry (XL-MS) is increasingly used for structural modeling of multi-subunit protein complexes. Here we use the log-harmonic potential as a formulation of spatial restraints that realistically reflects the experimentally observed cross-linking distances in solution. In combination with a Bayesian modeling framework that iteratively adjusts weights during optimization, conflicting restraints and conformational heterogeneity are appropriately dealt with. In addition, we developed a new geometric approach to quickly estimate the Solvent Accessible Surface Distance (SASD) between two residues in the context of protein assemblies. SASD allows to mimic the behavior of cross-linkers by bridging two atoms without penetrating the protein. We demonstrated on previously published systems that our computation method efficiently eliminates false positives while remaining compatible with experimental cross-linking data. At each step of the conformational sampling, SASD is computed to estimate data violation and enhance the Bayesian restraints re-weighting scheme. We obtain faster convergence towards meaningful conformations. ∗ Intervenant 76 Visualisation et prédiction structurale COMMUNICATION ORALE A Detailed Data-Driven Protein-Protein Interaction Potential Accelerated By Polar Fourier Correlation Emilie Neveu ∗† 1 , Sergei Grudinin 1 , Dave Ritchie 2 , Petr Popov 1 1 NANO-D (INRIA Grenoble Rhône-Alpes / LJK Laboratoire Jean Kuntzmann) – Institut polytechnique de Grenoble (Grenoble INP), Université Joseph Fourier - Grenoble I, CNRS : UMR5224, Laboratoire Jean Kuntzmann, INRIA – Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex, France 2 CAPSID (INRIA Nancy - Grand Est / LORIA) – INRIA, CNRS : UMR7503, Université de Lorraine – France In structural biology, medicine, and drug design, to find proteins that can act as inhibitors for viruses or bacteria, one has to know the structure of the complex to be formed. The Protein Data Bank [1] can help but only a small fraction of its proteins are complexes. Without good prior knowledge of the binding sites, computational prediction methods become necessary. Generally, existing methods first explore the six degrees of freedom search space of rigid body motions to locate position of one protein with respect to another one, typically using a very simple energy function. Then, they locally enhance the search space (adding flexibility) while using a more precise energy function. However, important solutions may be missed right at the first step. Our research focuses on improving the first stage predictions. We believe it will also improve the subsequent refinement searches. We present an algorithm that uses a more precise energy while exploring the whole search space of rigid-body motions. It combines a very fast FFT-accelerated exhaustive search with a detailed data-driven approximation to the binding free energy. More precisely, we are using protein geometry represented through 3-D Gauss-Laguerre expansion coefficients, the Spherical Polar Fourier transform to rapidly compute energy overlap integrals [2], and a convex optimization technique to learn the interaction potential. We describe the chemistry and the geometry of a protein with 20 3D grids for each protein in a complex and 210 pairwise distance-dependent interaction potentials that have been learned from the structures of known protein-protein interfaces using a convex optimization technique. The method runs in 5-10 minutes on a modern laptop for a mid-size protein complex. When tested on a set of 195 bound non-homologues protein hetero-dimer complexes, the method achieves correct rank-1 solutions in over 50% of cases, and it produces a correct solution within the top 10 solutions in 66% of cases. Here, a “correct solution” means one with a ligand rootmean-squared deviation (RMSD) of less than 5 Å from the native solution. We are currently adapting the method to predict the structures of protein complexes starting from their unbound structures. 1. H.M. Berman et al. The protein data bank. Acta Cryst. (2002), D58, 899-907. ∗ † Intervenant Auteur correspondant: [email protected] 77 Visualisation et prédiction structurale COMMUNICATION ORALE 2. D.W. Ritchie, D. Kozakov, and S. Vajda, Accelerating and Focusing Protein-Protein Docking Correlations Using Multi-Dimensional Rotational FFT Generating Functions, Bioinformatics (2008), 24 (17): 1865-1873. 78 Visualisation et prédiction structurale COMMUNICATION ORALE Fragment-based modeling of ssRNA-protein complexes Isaure Chauvot De Beauchene 1 ∗† 1 , Sjoerd De Vries 1 , Martin Zacharias‡ 1 Technische Universität München (TUM) – James-Franck-Strasse 1, 85748 Garching, Germany, Allemagne Rationale. Protein-RNA recognition supports a large variety of fundamental cellular functions. It is also a crucial therapeutic target : Abnormal or impaired protein-RNA interactions are responsible for neurodegenerative diseases [1] and cancers [2] ; many viral infections use the recognition of the viral RNA by proteins of the host [3]. Moreover, RNA’s non-toxicity and the high specificity of protein-RNA interactions confer an immense potential to the synthesis of RNA aptamers as modulators of proteins [4]. An atomistic prediction and description of protein-RNA complexes is essential to the rational conception of modulators of protein-RNA binding and their function [5]. However the experimental resolution of structures of these complexes is extremely difficult . Many interfaces are still uncharacterized at atomic scale, and require computational modeling. State of the art. However, protein-RNA docking is hampered by the high flexibility of RNA. Therefore, compared to protein-protein and protein-ligand docking, protein-RNA docking methods are lagging behind. Particularly challenging are single-stranded RNAs (ssRNAs) and singlestranded loops in RNAs, which encounter nonlinear conformational rearrangement over binding, such as base flipping. Yet these parts carry the specificity of recognition in most cases. The lack of methodology for modeling ssRNAs limits the accuracy of all current protein-RNA docking methods [6] [7]. Method. We present an original and effective fragment-based approach to tackle this problem, capable of accurate prediction of the structure of a ssRNA-protein complex, starting from the structure of the protein and the sequence of the RNA. The protocol is as follows: (i) The RNA sequence is cut in overlapping trinucleotides ; (ii) each trinucleotide is represented by a sequence-specific ensemble of conformers in an exhaustive fragment library built from all experimental protein-RNA complex structures; (iii) each conformer ensemble for the RNA sequence is docked on the protein; (iv) the compatible poses are selected and assembled in a realistic conformation, on a RMSD criteria of the overlapping nucleotides . Results. We tested our method on four sequences of ssRNA (6 to 11 nucleotides) bound to proteins containing two RNA-recognition motifs (RRMs). Without any information on specific contacts nor on the RNA structure, our method can accurately identify the RNA binding site on the protein within 10 Å precision. In addition, we tested two different regimes with limited information. First, by selecting the best conformers of our library for each fragment prior to ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] † 79 Visualisation et prédiction structurale COMMUNICATION ORALE docking, we could approximate the bound conformation of the RNA with ~ 1.5 Å RMSD on heavy atoms. Second, by assuming that at least one nucleotide interacts with each RRM in a canonical manner [8], without any knowledge on the RNA structure, the bound conformation was approximated with a precision of 2 to 3 Å RMSD. For both regimes, alternative incorrect structures were also generated, and future research will focus on identifying the correct structure (scoring). Still, this precision has never been reached so far by any protein-RNA docking method. If our method proves generalizable further, this will constitute a major methodological breakthrough in RNA-protein docking. 1. T. Vanderweyde, K. Youmans, L. Liu-Yesucevitz, and B. Wolozin, Gerontology, vol. 59, no. 6, pp. 524–533, 2013. 2. M. Derrigo, A. Cestelli, G. Savettieri, and I. Di Liegro, Int. J. Mol. Med., vol. 5, no. 2, pp. 111–134, Feb. 2000. 3. A. Ranji and K. Boris-Lawrie, RNA Biol., vol. 7, no. 6, pp. 775–787, Dec. 2010. 4. D. Peer and J. Lieberman, Gene Ther., vol. 18, no. 12, pp. 1127–1133, Dec. 2011. 5. S. Kandil, S. Biondaro, D. Vlachakis, A.-C. Cummins, A. Coluccia, C. Berry, P. Leyssen, J. Neyts, and A. Brancale, Bioorg. Med. Chem. Lett., vol. 19, no. 11, pp. 2935–2937, Jun. 2009. 6. S. Fulle and H. Gohlke, J. Mol. Recognit. JMR, vol. 23, no. 2, pp. 220–231, Apr. 2010. 7. N. Morozova, J. Allers, J. Myers, and Y. Shamoo, Bioinforma. Oxf. Engl., vol. 22, no. 22, pp. 2746–2752, Nov. 2006. 8. C. Maris, C. Dominguez, and F. H.-T. Allain, FEBS J., vol. 272, no. 9, pp. 2118–2131, May 2005. 80 Visualisation et prédiction structurale COMMUNICATION ORALE ORION : improving remote homology detection using a structural alphabet Yassine Ghouzam 1 , Guillaume Postic , Alexandre De Brevern 1 , Jean-Christophe Gelly ∗† 1 1 Biologie Intégrée du Globule Rouge - Equipe Dynamique des Systèmes et des Interactions des Macormolécules Biologiques (DSIMB) – Université Paris VII - Paris Diderot, Institut National de la Transfusion Sanguine (INTS), Inserm : U1134, Laboratoire d’excellence GrEx – 6 rue Alexandre Cabanel 75739 Paris cedex 15, France Protein structure prediction is crucial to apprehend protein functions. In this important field, the most successful strategies are comparative modeling methods. Given a protein target sequence with unknown structure, comparative modeling consists to build its structure from an evolutionary related protein with a known structure used as a template. Comparative modeling have mainly two steps (i) identify a suitable protein template candidate and (ii) building target structure from the template. The first stage is the main limiting step. Indeed many potential interesting templates are still unrecognizable using classical sequence alignment methods due to far evolutionary relationship between template and target proteins. Peculiar approaches are then specifically then developed for identify such far relationship. Such approaches are based on profile-profile sequence alignment, obtained from homologs sequences on both target and template. Nonetheless even with such strategies many potential interesting templates remain still undetected. Besides, structural features (e.g secondary structures) are three to ten times more conserved than sequence (Illergård et al. 2009). Therefore integration of structural data, mainly as secondary structure, can effectively boost the finding of distant relationship between proteins (Koretke et al. 1999). However, secondary structure states characterize local conformation only in three main states (helix, strand and coil) and are limited for describing the loops, which constitutes 45% of the local structure of the proteins. We have developed ORION, a new generation of profile-profile method combining both aminoacids profile and a new local conformation structural information. The key element of our method relies on Protein Blocks (PBs), a structural alphabet of 16 states of five residues long, able to finely describe local conformations and depict protein structure in term of a sequence constituted of 16 letters alphabet (de Brevern et al. 2000). Contrary to secondary structure, limited to only 3 states, it can finely approximate local conformation and can catch all transitions in protein structures. PBs are already been used successfully in many applications such as structural alignment and local structure prediction (for review: Joseph et al. 2010). The major steps of ORION are as follows: Starting from a query sequence, a sequence profile is computed using PSI-BLAST. This profile is also used for PB prediction with LOCUSTRA ∗ † Intervenant Auteur correspondant: [email protected] 81 Visualisation et prédiction structurale COMMUNICATION ORALE software (Zimmermann and Hansmann, 2008). Using dynamic programming, sequence profile and predicted structure of the query are then combined to search in a fold library of pre-computed sequence profiles and assigned PB built from structural alignments of families in HOMSTRAD databank (Mizuguchi et al, 1998). We showed that including PBs information increase both specificity and sensitivity in searching a remote homology template on a large benchmark based on HOMSTRAD databases (Figure 1). Moreover ORION systematically outperforms PSI-BLAST (Altschul SF et al, 1997) and HHsearch (Söding, 2005) one of the top leading method and winner of ninth Critical Assessment of Structure Prediction (CASP) in template-based modeling category, and detects around 10% more templates at fold and superfamily level. We also confronted our method to HHsearch and PSI-BLAST on previous CASP competitions (CASP 8, 9 and 10) experiments and demonstrated that at 12 % of False Positive Rate (FPR) ORION achieved a True Positive Rate (TPR) of 45 %, 2 times more than HHsearch and retrieved 8.6% more homologs than HHsearch in the top 10. Finally, we also successfully assessed a pre-version of ORION in CASP 11 experiment, the last edition of the international competition dedicated to assess the state of the art method in protein prediction in which we participated in 2014. References: Illergård K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence– a study of structural response in protein cores. Proteins. 2009 Nov 15;77(3):499-508 Koretke KK, Russell RB, Copley RR, Lupas AN. Fold recognition using sequence and secondary structure information. Proteins. 1999;Suppl 3:141-8.§ de Brevern AG, Etchebest C, Hazout S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins. 2000 Nov 15;41(3):271-87. Joseph AP, Agarwal G, Mahajan S, Gelly JC, Swapna LS, Offmann B, Cadet F, Bornot A, Tyagi M, Valadié H, Schneider B, Etchebest C, Srinivasan N, De Brevern AG. A short survey on protein blocks. Biophys Rev. 2010 Aug;2(3):137-147. Zimmermann O, Hansmann UH. LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach. J Chem Inf Model. 2008 Sep;48(9):1903-8. Mizuguchi K, Deane CM, Blundell TL, Overington JP. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 1998 Nov;7(11):2469-71. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005 Apr 1;21(7):951-60. 82 Visualisation et prédiction structurale COMMUNICATION ORALE SAMSON: Software for Adaptive Modeling and Simulation Of Nanosystems Nadhir Abdellatif , Svetlana Artemova , Marc Aubert , Jocelyn Gate , Sergei Grudinin , Leonard Jaillet , Khoa Nguyen , Mohamed Yengui , Stephane Redon ∗ 1 1 INRIA Rhône-Alpes (INRIA Grenoble Rhône-Alpes) – INRIA – ZIRST 655 Avenue de l’Europe Montbonnot 38334 Saint Ismier cedex, France SAMSON: Software for Adaptive Modeling and Simulation Of Nanosystems Nadhir Abdellatif, Svetlana Artemova, Marc Aubert, Jocelyn Gate, Sergei Grudinin, Leonard Jaillet, Khoa Nguyen, Mohamed Yengui, and Stephane Redon* NANO-D, INRIA Grenoble - Rhone-Alpes, 38334 Saint Ismier Cedex, Montbonnot, France; Laboratoire Jean Kuntzmann, B.P. 53 38041 Grenoble, Cedex 9, France. SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems), the software platform for computational nanoscience that we have been developing in the NANO-D group, is now available on SAMSON Connect at http://www.samson-connect.net. SAMSON integrates modeling and simulation to aid in the analysis and design of molecular systems. For instance, an interactive quantum chemistry module (ASED-MO level of theory) makes it possible for users to build and edit structures while interactively visualizing how the electronic density is updated (Figure – a); interactive flexing and twisting tools allow users to easily perform large-scale flexible deformations of e.g. proteins with a few mouse clicks (Figure – b); interactive virtual prototyping of hydrocarbon systems may be used to edit and constrain graphene sheets, nanotubes (Figure – c), etc. This integration is made possible via SAMSON’s data graph, which contains all information on models and simulators. Nanosystems are described through five types of models: structural models (geometry and topology), dynamical models (degrees of freedom), interaction models (potential energy, forces, electronic structure), visual models (graphical representations, e.g. Figure – d) and property models. SAMSON’s data graph relies on a signalling system that may be used to develop adaptive algorithms. For instance, an adaptively restrained state updater may control, at each time step of a simulation, which degrees of freedom should be updated in a dynamical model [1]. In turn, an interaction model may request from a dynamical model the list of positions that have been updated since the last simulation step, to incrementally update the potential energy, forces and electronic structure [2, 3, 4]. Most important, SAMSON has an open architecture: a Software Development Kit allows developers to extend SAMSON’s functionality by developing SAMSON Elements, i.e. new modules ∗ Intervenant 83 Visualisation et prédiction structurale COMMUNICATION ORALE for SAMSON such as new interaction models, editors (e.g. procedural generators), apps, wrappers or interfaces to existing software, connectors to web services, etc. The SAMSON Connect website (http://www.samson-connect.net) is open for developers and users to easily distribute and install SAMSON Elements. We will present the architecture of SAMSON and its general design principles, as well as the SAMSON SDK and SAMSON Connect. S. Artemova and S. Redon, Physical Review Letters, 109:19, 2012 M. Bosson et al, Journal of Computational Physics, 231:6, 2012 M. Bosson et al, Journal of Computational Chemistry, 34:6, 2013 R. Rossi et al, Bioinformatics, 23:13, 2007 84 Visualisation et prédiction structurale COMMUNICATION ORALE Integration of Chemical and Biological (’omics’) Data for the Prediction of Cancer Cell-Line Sensitivity Isidro Cortes ∗† 1 , Gerard J.p. Van Westen 2 , Guillaume Bouvier 3 , Mickael Nilges 1 , John P. Overington 2 , Andreas Bender 3 , Therese Malliavin 1 1 2 Unite de Bioinformatique Structurale – Institut Pasteur de Paris, CNRS : UMR3528 – 28 rue du docteur Roux 75724 Paris, France European Bioinformatics Institute [Cambridge] (EMBL-EBI) – EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK, Royaume-Uni 3 Centre for Molecular Science Informatics – Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, Royaume-Uni Cultured cell-lines have proved versatile disease models for cancer drug discovery [1]. In the last decades, large-scale multi-omics initiatives have catalogued the somatic alterations of cancer cell-line panels coupled with their pharmacological response to thousands of compounds [1,2,3]. Although these cell-line collections have proved valuable to identify genomic markers of drug sensitivity [2,3], the question now arises how these pharmacogenomic data can be meaningfully mined to discover cancer-specific drugs. Here, we propose the simultaneous modelling of chemical and cell-line information in single machine learning models to predict with error bars the growth inhibition 50% bioassay end-point (GI50) of 17,142 compounds screened against 59 cancer cell-lines from the NCI60 panel. The integration of these different, yet complementary, streams of information is often termed Proteochemometrics (PCM) or pharmacogenomic modelling (PGM) [4]. PCM is a computational method to simultaneously model the bioactivity of multiple ligands against multiple biomolecular targets, and therefore permits to explore the selectivity and promiscuity of ligands [4]. In typical PGM models, each compound-cell-line interaction is numerically encoded by the concatenation of compound and cell-line descriptors, which are related in single machine-learning models to a specific biological readout of interest. To describe the compounds we used Morgan fingerprints, whereas to describe the cell-lines, we downloaded and curated the following cell-line profiling data: gene expression, DNA copy-number variation, protein abundance, exome sequencing, miRNA abundance, and cell-line fingerprints. We benchmarked their predictive signal by training one model on each cell-line profiling data and on compound fingerprints, finding that protein, gene transcript, and miRNA abundance provide the highest predictive signal, significantly outperforming DNA copy-number variation or exome sequencing data (Tukey’s HSD, P < 0.05). The performance of the best model on the test set led to mean R20 and RMSE values of 0.83 and 0.40 pGI50 units, respectively. Comparable mean RMSE values were obtained when interpolating and extrapolating compound bioactivities to novel cell-lines (RMSE=0.43), and when interpolating compound bioactivities to structurally similar compounds (RMSE=48-0.65). Nevertheless, the mean RMSE value increased till 0.83 when extrapolating to ∗ † Intervenant Auteur correspondant: [email protected] 85 COMMUNICATION ORALE chemically dissimilar compounds, indicating that careful attention should be paid to not overstep the boundaries of the models applicability domain. Finally, we demonstrate that the predicted bioactivities can be used to predict growth inhibition patterns across the NCI60 panel for compounds excluded from the training set (e.g. methotrexate), and that significant drug-pathway associations are consistent with the experimental data published in the literature. Conceptually, this approach could also be extended to select personalized treatments on the basis of patients genomic makeup. JN Weinstein. Drug discovery: Cell lines battle cancer. Nature 2012, 483, 544–545. J Barretina, G Caponigro, N Stransky et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012, 483, 603–607. Garnett, MJ, EE Edelman, SJS Heidorn et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012, 483, 570–575. I Cortes-Ciriano, QU Ain, V Subramanian et al. Polypharmacology Modelling Using Proteochemometrics (PCM): Recent Methodological Developments, Applications to Target Families, and Future Prospects. Med. Chem. Commun., 2015, 6, 24-50. 86 Session poster GT Enzymes/GGMM 87 Communication par affiche Poster P1 Les thioltransférases : production et élimination de sulfure d’hydrogène ? Jean-Christophe Lec ∗ 1 , Séverine Boutserin 1 , Hortense Mazon 1 , François Talfournier ∗ † 1 , Sandrine Boschi-Muller ∗ ‡ 1 1 UMR 7365 CNRS-Université de Lorraine (IMoPA) – CNRS : UMR7365, Université de Lorraine – 9 Avenue de la Foret de Haye, 54505 Vandoeuvre les Nancy, France Les thioltransférases sont des enzymes ubiquitaires de la famille structurale des rhodanèses qui catalysent le transfert de soufre d’un substrat donneur vers un substrat accepteur, via la formation d’un intermédiaire persulfure sur la cystéine catalytique. Elles se répartissent en deux familles selon la nature du substrat donneur et leurs rôles physiologiques proposés : les 3-mercaptopyruvate sulfurtransférases (3-MST) utilisent le 3-mercaptopyruvate (3-MP) et sont impliquées dans la production de sulfure d’hydrogène, alors que les thiosulfate sulfurtransférases (TST) utilisent le thiosulfate (TS) et assurent des fonctions variées comme la détoxication du cyanure, la biosynthèse des centres Fe-S ou le catabolisme d’H2S au niveau mitochondrial. Afin de caractériser les mécanismes moléculaires associés aux rôles physiologiques proposés pour les thioltransférases, l’identification des bases moléculaires responsables de la spécificité structurale a été abordée en évaluant l’efficacité catalytique des deux étapes de transfert de soufre en présence de différents substrats donneurs et accepteurs. Les résultats obtenus sur des enzymes d’origine humaine et bactérienne montrent que, contrairement à ce qui est décrit dans la littérature, le 3-MP est un meilleur substrat donneur que le TS pour les deux familles d’enzymes. De plus, elles présentent des spécificités différentes pour le substrat accepteur : la thiorédoxine pour les 3-MST et le glutathion et le sulfite pour les TST. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] † 88 Communication par affiche Poster P2 Rôle fonctionnel d’une cavité interne hydrophobe dans l’urate oxydase Nathalie Colloc’h ∗ 1 , Thierry Prangé 2 1 Imagerie et stratégies thérapeutiques des pathologies cérébrales et tumorales (ISTCT) – Université de Caen Basse-Normandie, CNRS : UMR6301, CEA – GIP CYCERON UMR 6301- CNRS Boulevard Henri Becquerel BP 5229 14074 CAEN CEDEX, France 2 Laboratoire de cristallographie et RMN biologiques (LCRB) – CNRS : UMR8015, Université Paris V Paris Descartes – Faculté de Pharmacie 4 Avenue de l’Observatoire 75270 PARIS CEDEX 06, France L’urate oxydase est un homo-tetramère de 135 kDa qui possède une cavité hydrophobe enfouie dans chaque monomère et proche du site actif. Les structures cristallographiques sous pression modérée de gaz inerte (10-30 bar) ou sous haute pression hydrostatique (1500 bar) ont montré que la présence d’un gaz ou l’application de la pression entrainent tous deux une rigidification de la cavité et induisent une inhibition du mécanisme catalytique. La flexibilité de la cavité semble donc essentielle pour l’activité catalytique de cette enzyme. Elle peut donc être considérée comme un site allostérique qui donnerait de la flexibilité au site actif voisin, et aurait également un rôle de réservoir transitoire pour l’oxygène sur son chemin d’accès vers le site actif. ∗ Intervenant 89 Communication par affiche Poster P3 Benzene-induced leukemogenesis: Irreversible inhibition of PTPN2, a tumor suppressor phosphatase involved in leukemia by the hematotoxic metabolite benzoquinone Romain Duval ∗ , Linh Chi Bui 1 , Laeticia Durant , Cécile Mathieu 1 , Emile Petit , Jean-Marie Dupret , Jan Cools , Christine Chomienne , Fabien Guidez , Fernando Rodrigues-Lima† 1 1 Unité de Biologie Fonctionnelle et Adaptative (BFA- RMCX) – CNRS : UMR8251, Université Paris VII - Paris Diderot – UFR Sciences du Vivant - 4 rue Marie-Andrée Lagroua Weill-Hallé 75205 Paris Cedex 13, France Benzene (BZ) is a chemical compound of industrial and toxicological interest classified as a class I human carcinogen. Environmental and occupational exposure to BZ lead to bone marrow malignancies such as leukemia. The leukemogenic effects of BZ relies on its metabolization in bone marrow cells into reactive metabolites, in particular benzoquinone (BQ) that can react with macromolecules (arylation) and/or induce oxidative stress. Although BZ is well recognized as a leukemogenic chemical, most of the key molecular and cellular mechanisms underlying its hematotoxicity are not fully understood. PTPN2 is a protein tyrosine phosphatase (PTP) mainly expressed in hematopoietic cells and playing a key role in the homeostasis of the hematopoietic system. In particular, this PTP is an important modulator of growth factors and JAK/STAT signaling pathways. Loss of function analyses in patients with mutation/deletion of the PTPN2 gene and knock-out mouse models indicate that PTPN2 acts as a tumor suppressor in haematologic disorders such as leukemia. We found that BQ, the prime hematotoxic metabolite of BZ, is an irreversible inhibitor of human PTPN2. Kinetic and biochemical analyses using purified PTPN2 indicated that the irreversible inhibition of the enzyme by BQ is mainly due to arylation of its active site cysteine. Exposure of immortalized human hematopoietic cells (Jurkat T and THP-1 lines) to BQ leads to the irreversible inhibition of endogenous PTPN2 activity with a concomitant over activation of JAK/STAT signaling pathway. Irreversible BQ-dependent inhibition of PTPN2 in cells was found to be mainly due to overoxydation of its catalytic cysteine into sulfinic and/or sulfonic forms. In Vivo experiments conducted in mice confirmed that exposure to BZ leads to irreversible inhibition of PTPN2 in bone marrow and spleen cells. Our data provide the first mecanistic evidence that irreversible inhibition of PTPN2, a tumor suppressor tyrosine phosphatase, may contribute to benzene-dependent leukemogenesis. ∗ † Intervenant Auteur correspondant: 90 Communication par affiche Poster P4 Cellular redox signaling by thiol peroxidase : Mechanisms responsible for the specificity of the redox relay H2O2/Orp1/Yap1 in S. cerevisiae Antoine Bersweiler 1 , Hortense Mazon 1 , Alexandre Kriznik Branlant 1 , Sophie Rahuel-Clermont† 1 1 ∗ 1 , Guy IMoPA UMR 7365 CNRS-Université de Lorraine (IMOPA) – CNRS : UMR7365, Université de Lorraine – Biopôle, campus Biologie-Santé 9 Avenue de la Forêt de Haye, CS 50184 54505 Vandœuvre-lès-Nancy Cédex, France Thiol-peroxidases, described as antioxidant enzymes, have also been associated with peroxidedependent cell signaling as sensor and relay of the H2O2-mediated signal (1). One of the best documented examples of such a mechanism is the activation of the transcription factor Yap1, a key regulator of the transcriptional peroxide stress response in Saccharomyces cerevisiae, which depends on the formation of intramolecular disulfide bonds catalyzed by the thiol peroxidase Orp1 (2 ; 3). In this mechanism, it has been proposed that the relay occurs via the oxidation of Orp1 peroxidatic Cys as a sulfenic acid intermediate which reacts with Yap1 to form a mixed disulfide species (3). In addition, the Ybp1 protein has been identified as an essential partner for the activation of Yap1 by Orp1 (4). The intrinsic reactivity of Orp1 sulfenic acid species could potentially result in competition between Yap1 and other thiols, such as the regeneration Cys of Orp1 or other cellular thiols. This raises the question of the specificity of Yap1 activation by H2O2/Orp1. To address this question, and to elucidate the role of Ybp1 in this mechanism, we have used an approach based on the kinetic characterization of the two reactions in competition: the peroxydatic cycle of Orp1 and the reaction withYap1, using rapid kinetic stop flow and quench flow techniques. From the study of the impact of Ybp1 on these kinetics and the characterization of the protein-protein interactions between the three partners by fluorescence anisotropy and microcalorimetry, we propose that Ybp1 and Yap1 recruit Orp1 within a ternary complex, which restrains intramolecular disulfide formation within Orp1 and allows the reaction between Orp1 sulfenic intermediate and Yap1. (1) Fourquet S., Huang, M., D’Autreaux, B., Toledano, M.B. (2008), Antiox. Redox Sign. 10, 15565-76. (2) Delaunay, A., Isnard, A.D., Toledano, M.B. (2000) EMBO J. 19, 5157-66. (3) Delaunay, A., Pflieger, D., Barrault, M.B., Vinh, J., Toledano, M.B. (2002) Cell 111, 471-81. ∗ † Intervenant Auteur correspondant: [email protected] 91 Communication par affiche Poster P4 (4) Veal, E.A., Ross, S.J., Malakasi, P., Peacock, E., Morgan, B.A. (2003) J. Biol. Chem. 278, 30896-904. 92 Communication par affiche Poster P5 Molecular basis of the alteration of brain glycogen metabolism by dithiocarbamate pesticides: impairment of brain glycogen phosphorylase Cécile Mathieu ∗ 1 , Linh Chi Bui 1 , Solène Boitard 2 , Onnik Agbulut 2 , Jean-Marie Dupret 1 , Fernando Rodrigues-Lima 1 1 Unité de Biologie Fonctionnelle et Adaptative (BFA- RMCX) – CNRS : UMR8251, Université Paris VII - Paris Diderot – UFR Sciences du Vivant - 4 rue Marie-Andrée Lagroua Weill-Hallé 75205 Paris Cedex 13, France 2 Adaptation Biologique et Vieillissement – CNRS : UMR8256, Université Pierre et Marie Curie (UPMC) - Paris VI – Campus de Jussieu - 4 place Jussieu 75005 Paris, France Dithiocarbamates (DTC) are organosulfur compounds widely used as fungicide. Acute exposure is mainly a concern for agricultural and industrial workers but large population can be exposed through residues in food and water. The high reactivity of these chemical lead to numerous toxic effects and have been linked to Parkinson’s disease. Different biological processes have been suggested to be altered by DTC including glycogen (gln) metabolism. Gln is a glucose polymer found primarily in liver, muscles and brain where it represents the main storage-form of glucose. In brain, Gln is mainly found in astrocytes and appears to be critical for certain neurological processes such as learning and long term memory consolidation. Brain glycogen phosphorylase (bGP) is the key enzyme involved in mobilization of Gln. This enzyme is thighly regulated by both phosphorylation and binding of allosteric effectors. In order to better understand the molecular mechanisms of neurotoxicity linked to DTC, we studied the impact of Thiram (TH), a well known DTC, on bGP. Incubation of mouse brain extracts with TH impaired glycogen mobilization which is concomitant with the inhibition of bGP. Studies on recombinant human bGP showed that TH and its metabolites were potent inhibitors of bGP. Chemical-labelling, electrophoretic and mass spectrometry analyses suggested that inhibition of purified bGP by TH occured through modification of critical cysteines residue and formation of intramolecular/intermolecular disulfide bonds. Altogether our data indicate that certain DTC inhibit the glycogenolytic activity of bGP through the modification of key cysteine residues with subsequent impairment of Gln catabolism. This may lead to altered energy metabolism or toxic accumulation of Gln in astrocytes. More broadly, owing to the important role of Gln in neurological processes, impairment of bGP functions in brain could contribute to the neurotoxic effects of DTC. ∗ Intervenant 93 Communication par affiche Poster P6 Réactivité de la carbon monoxide dehydrogenase à nickel avec l’oxygène Meriem Merrouch ∗† 1 , Jessica Hadj-Said 1 , Lilith Domnik 2 , Holger Dobbek 2 , Sébastien Dementin 1 , Claude Léger 1 , Vincent Fourmond 1 1 Bioénergétique et Ingénierie des Protéines (BIP) – CNRS : UMR7281, Université de la Méditerranée Aix-Marseille II – 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France 2 Institut für Biologie, Strukturbiologie/Biochemie – Humboldt-Universität zu Berlin, 10099 Berlin, Allemagne Les Carbon Monoxide Dehydrogenases (CODH) catalysent l’oxydation réversible du CO en CO2 selon la réaction: CO + H2O CO2 + 2e- + 2H+ Le site actif des CODH isolées d’organismes anaérobies est constitué d’un centre [Ni-4Fe-4S] [1, 2]. Ces enzymes sont réputées être extrêmement sensibles à l’O2, cependant le mécanisme d’inactivation par l’oxygène n’est pas connu [3]. Nous avons étudié par électrochimie directe [4] l’effet de l’oxygène sur deux CODH : la CODH II de Carboxydothermus hydrogenoformans (Ch) et la CODH de Desulfovibrio vulgaris Hildenborough (Dv ). Nos résultats ont montré que l’oxygène interagit rapidement avec les sites actifs des deux CODH, cependant l’inactivation est réversible, principalement après une étape de réduction de l’enzyme. Nous montrons également que la réactivité des deux enzymes vis-à-vis de l’O2 est différente: la fraction de Dv CODH réactivée après exposition à l’O2 est beaucoup plus importante que celle de la Ch CODH. En particulier, dans les conditions de concentration d’O2 utilisées pendant notre étude, l’enzyme de Dv est réactivée presque complètement, ce qui n’est pas le cas pour l’enzyme de Ch. Nos travaux apportent pour la première fois des données mécanistiques concernant l’inhibition des CODH par l’O2 et montrent que la réactivité des CODH vis-à-vis de l’O2 n’est pas la même d’une espèce à l’autre, comme c’est le cas pour d’autres enzymes à Nickel, comme les hydrogénases. 1. Jeoung, J.-H., Dobbek, H. Science 2007, 318, 1461-1464. 2. Drennan, C., Doukov, T., Ragsdale, S. Journal of Biological Inorganic Chemistry 2004, 9, 511-515. 3. Can, M., Armstrong, F. A., Ragsdale, S. W. Chem. Rev. 2014, 114, 4149-4174. 4. Léger, C., Bertrand, P. Chem. Rev. 2008, 108, 2379-2438. ∗ † Intervenant Auteur correspondant: [email protected] 94 Communication par affiche Poster P7 Regulation of thiol peroxidases in peroxide-dependent redox signaling: Thioredoxin vs. glutathione in reduction of hyperoxidized 2-Cys peroxiredoxin by Sulfiredoxin Samia Boukhenouna 1 , Hortense Mazon 1 , Guy Branlant 1 , Christophe Jacob 1 , Michel Toledano 2 , Sophie Rahuel-Clermont ∗† 1 1 2 IMoPA UMR 7365 CNRS-Université de Lorraine (IMOPA) – CNRS : UMR7365, Université de Lorraine – Biopôle, campus Biologie-Santé 9 Avenue de la Forêt de Haye, CS 50184 54505 Vandœuvre-lès-Nancy Cédex, France Laboratoire Stress Oxydants et Cancer (LSOC) – CEA – CEA, iBiTecS, LSOC, Gif-sur-Yvette Cedex, France., France Due to its oxidant properties, hydrogen peroxide (H2O2) can act both as a toxic and as a cellular messenger. Typical 2-Cys-peroxiredoxins (Prx) are thiol peroxidases sensitive to H2O2mediated hyperoxidation of the catalytic Cys to the sulfinic acid state. This unique property is involved in regulation of Prx functions in peroxide-dependent redox signaling and is reversed by ATP-dependent reduction by Sulfiredoxin (Srx). Srx catalytic mechanism involves a unique enzymatic chemistry, which leads to the formation of a thiolsulfinate intermediate PrxSO-SSrx that must be reduced to complete the cycle. To evaluate the mechanism and efficiency of the cellular redox systems thioredoxin (Trx) and glutathione (GSH) in Srx recycling, we combined in vitro steady state and single turnover kinetic analyses of the reaction monitored by enzymatic coupled assay, Prx intrinsic fluorescence, SDS-PAGE or reverse phase chromatography coupled to mass spectrometry for the characterization of intermediate species, and in vivo approaches using S. cerevisiae strains depleted in Trx or GSH. In the case of S. cerevisiae, owing to the presence of an additional Cys residue, Srx recycling involves the formation of an oxidized Srx intermediate that is efficiently reduced by Trx. On the contrary, in the case of Srx lacking this resolving Cys48 as in mammals or plants (1-Cys Srxs), using S. cerevisiae Srx mutants lacking Cys48 as a model, we show that GSH reacts directly with the thiolsulfinate intermediate on the Srx moiety, releasing glutathionylated Srx as a catalytic intermediate. Unexpectedly, the results suggest that GSH binds to the thiolsulfinate complex, thus allowing efficient and non rate-limiting reduction. Total cellular depletion of GSH impacted the recycling of Srx, confirming in vivo that GSH is the physiologic reducer of 1-Cys Srx. ∗ † Intervenant Auteur correspondant: [email protected] 95 Communication par affiche Poster P8 Computer-aided engineering of a transglycosylase for the glucosylation of an unnatural disaccharide of relevance for bacterial antigen synthesis Alizée Verges 1 , Emmanuelle Cambon 1 , Sophie Barbe 1 , Stéphane Salamone 2 , Yann Le Guen 2 , Claire Moulis 1 , Laurence Mulard 2 , Magali Remaud-Siméon 1 , Isabelle André ∗ 1 1 Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés (LISBP) – Institut National des Sciences Appliquées [INSA], Centre national de la recherche scientifique - CNRS (France), Institut national de la recherche agronomique (INRA) – 135 Avenue de rangueil 31077 Toulouse cedex 04, France 2 Institut Pasteur, Unité de chimie des biomolécules – CNRS : UMR3523, Institut Pasteur de Paris – 28 rue du Docteur Roux 75724 Paris Cedex 15, France The exploration of chemo-enzymatic routes to complex carbohydrates has been hampered by the lack of appropriate enzymatic tools having the substrate specificity for new reactions. Here, we used a computer-aided design framework to guide the construction of a small, diversity controlled library of amino acid sequences of an a-transglucosylase, the sugar binding subsites of which were re-engineered to enable the challenging 1,2-cis -glucosylation of a partially protected -linked disaccharide – allyl (2-deoxy-2-trichloroacetamido--D-glucopyranosyl)-(12)--Lrhamnopyranoside, a potential intermediate in the synthesis of Shigella flexneri cell-surface oligosaccharides. The target disaccharide is not recognized by the parental wild-type enzyme and exhibits a molecular structure very distinct from that of the natural -(1,4)-linked acceptor. A profound reshaping of the binding pocket had thus to be performed. Following the selection of 23 amino acid positions from the first shell, mutations were sampled using RosettaDesign leading to a subset of 1,515 designed sequences, which were further analyzed by determining the amino acid variability among the designed sequences and their conservation in evolutionary related enzymes. A combinatorial library of 2.7 10^4 variants was finally designed, constructed and screened. One mutant showing the desired and totally new specificity was successfully identified from this first round of screening. Impressively, this mutant contained 7 substitutions in the first shell of the active site leading to a drastic reshaping of the catalytic pocket without significantly perturbing the original specificity for sucrose donor substrate. This work illustrates how computer-aided approaches can undoubtedly offer novel opportunities to design tailored carbohydrate-active enzymes of interest for glycochemistry or synthetic glycobiology. This work was supported by the ANR Project GLUCODESIGN (ANR-08-PCVI-002-02). A.V., E.C., S.B. contributed equally to the work. ∗ Intervenant 96 Communication par affiche Poster P8 References : Verges A., Cambon E., Barbe S., Salamone S., Le Guen Y., Moulis C., Mulard L.A., RemaudSiméon M., André I. 2015. Computer-aided engineering of a transglucosylase for the glucosylation of an unnatural disaccharide of relevance for bacterial antigen synthesis.ACS Catalysis. 5:11861198 97 Communication par affiche Poster P9 Computational Enzyme Design through deterministic search and counting methods Clément Viricel 1 , Seydou Traore 1 , David Simoncini 2 , David Allouche 2 , Simon De Givry 2 , Isabelle André 1 , Thomas Schiex 2 , Sophie Barbe ∗† 1 1 Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés (LISBP) – Institut National des Sciences Appliquées [INSA], Centre National de la Recherche Scientifique - CNRS, Institut national de la recherche agronomique (INRA) – 135 Avenue de rangueil 31077 Toulouse cedex 04, France 2 Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA) – Institut national de la recherche agronomique (INRA) : UR875 – Chemin de Borde Rouge, 31320 Castanet Tolosan, France Enzymes are powerful catalysts, which can be used for a wide range of innovative, efficient and eco-compatible processes that can open the way to many biotechnological applications. However, enzymes available in nature have evolved to operate under physiological conditions on a narrow range of substrates and they often do not display the physico-chemical properties required for their practical use in industrial-scale biocatalytic processes. Enzyme engineering has become a key technology to modulate both the structure and the function of polypeptides and generate enzymes displaying desired properties/activities. The integration of computational methods in enzyme engineering strategies has grown interest to increase the chances of success to tailor the wanted enzymes, while reducing the human and financial costs. Structure-based Computational Protein Design (CPD) aims at guiding evolution of proteins on relevant sequence space regions to achieve the desired function and thus reduce the size of mutant libraries to build and screen experimentally. Starting from an exponentially large space of possible sequences, CPD seeks to identify those that fold into stable three-dimensional structures and possess the desired functional properties. Despite notable achievements in the field, numerous limitations still need to be addressed in these computational methods to improve their efficiency, predictability and reliability. In this work, we have adapted and extended several cutting-edge deterministic combinatorial optimization techniques to solve various CPD problems. In particular, we have developed novel enzyme design approaches based on Cost Function Networks (CFN) (combining Depth First Branch and Bound search with Local Consistency properties) to search the sequence-conformation space to identify provably the optimal solution in regard to the design objective function (namely enzyme or enzyme-substrate complex stability in this work) [1-4]. These approaches are able to handle highly complex enzyme design problems that previously could not be solved exactly. Compared to deterministic methods commonly used in CPD, the CFN-based approaches speed up the search process by several orders of magnitude. Hence, the optimal solution is provably found for enzyme design problems with large sequence-conformation spaces. The CFN-based approach has also been extended to enable the generation of ensembles of near-optimal solutions that could be used for the rational design of sequence libraries. ∗ † Intervenant Auteur correspondant: [email protected] 98 Communication par affiche Poster P9 Moreover, the efficiency of the CFN optimization techniques has also been exploited to develop a scoring and search method aiming to optimize the enzyme-substrate binding affinity [5]. It combines a statistical mechanics-derived ensemble-based approach with the speed and the completeness of CFN algorithms to compute approximate enzyme-substrate binding constants with deterministic guarantees. Most recent developments and their application on various CPD problems will be presented. 1- Allouche D, Davies J, de Givry S, Katsirelos G, Schiex T, Traoré S, André I, Barbe S, Prestwitch S, O’Sullivan B. 2014. Computational Protein Design as an optimization Problem. Artificial Intelligence 212:59-79. 2- Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Schiex T, Barbe S. 2013. A New Framework for Computational Protein Design through Cost Function Network Optimization. Bioinformatics 29:2129-36 3- Allouche D, Traore S, André I, de Givry S, Katsirelos G, Barbe S, Schiex T. 2012. Computational Protein Design as a Cost Function Network Optimization Problem. In, Proceedings of the 18th international conference on Principles and Practice of Constraint Programming, Québec, Canada. 4- Traoré S, Roberts K-E, Allouche D, Donald B-R, André I, Schiex T, Barbe S. Fast search algorithms for Computational Protein Design. Submitted 5- Viricel C, Simoncini D, Allouche D, de Givry S, Barbe S, Schiex T. 2015. Approximate Counting with Deterministic guarantees for Affinity Computation. In, proceedings of the international conference on Modelling, Computation and Optimization in Information Systems and Management Sciences, MCO 2015, Metz, France: Advances in Intelligent Systems and Computing Springer. 99 Communication par affiche Poster P10 Towards the development of an in silico tools for kinetics prediction Abdennour Braka ∗ 1,2 , Stéphane Bourg 1,2,3 , Norbert Garnier 1 , Samia Aci-Sèche 2 , Pascal Bonnet 2 1 Centre de biophysique moléculaire (CBM) – CNRS : UPR4301 – Rue Charles Sadron 45071 ORLEANS CEDEX 2, France 2 Institut de Chimie Organique et Analytique (ICOA) – CNRS : UMR7311, Université d’Orléans – UFR Sciences Rue de Chartres - BP 6759 45067 ORLEANS CEDEX 2, France 3 Fédération de Recherche Physique et Chimie du Vivant – CNRS : FR2708 – Rue Charles Sadron, 45071 Orléans Cedex 2, France Molecular docking plays an increasing important role in drug discovery programs. While docking tools can accurately predict the binding mode of a ligand into the active site of a protein, the evaluation of binding affinity is still a major issue. One of the most important limitations is the treatment of protein flexibility during docking. The simplistic rigid model of ligand/protein complex is inadequate to represent the full motion of a protein structure during ligand binding. Moreover, most scoring functions are often correlated with activity-based data without taking into account the kinetics of ligand binding (koff and kon). This project aims to develop a new predictive method to improve the docking performance by considering protein flexibility. Protein kinases are promising therapeutic targets, which are highly flexible. In this study, we focus on the development of a novel in silico method using the p38 Map kinase as an example. To represent the motion of the protein, thousands of conformations were generated using molecular dynamics simulations (MD). We compared the performance of classical MD (cMD) with two biased methods: an in house restrained MD method (rMD) (1) and the Replica-Exchange MD (REMD) (2). As expected, the biased methods (rMD, REMD) widely outperform the cMD for the protein conformational sampling. We then used a clustering method based on k-means to select a representative subset of binding site conformations. A multiconformational docking is actually ongoing using this representative subset for the protein; and the ligands were extracted from the Directory of Useful Decoys (DUD-E) (3) database. Later, we envisage taking into account the association pathway of the ligand in order to predict kon association rate constant. The prediction of such biochemical data could be very useful for preclinical compound selection and optimization. References (1) Aci-Sèche, S.; Garnier, N.; Genest, D.; Bourg, S.; Marot, C.; Morin-Allory, L.; Genest, ∗ Intervenant 100 Communication par affiche Poster P10 M. A Restrained Molecular Dynamics Empirical Approach for Generating a Small Set of Structures Representative of the Internal Flexibility of a Receptor. QSAR Comb. Sci. 2009, 28, 959–968. (2) Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding. Chemical Physics Letters 1999, 314, 141–151. (3) Mysinger, M. M.; Carchia, M.; Irwin, J. J.; Shoichet, B. K. Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. J. Med. Chem. 2012, 55 (14), 6582–6594. 101 Communication par affiche Poster P11 In silico experiments on biomolecules through the Static Modes: An efficient approach to predict and design function Marie Brut ∗ 1 1 Laboratoire d’analyse et d’architecture des systèmes [Toulouse] (LAAS) – Institut National Polytechnique de Toulouse - INPT, Université Paul Sabatier (UPS) - Toulouse III, CNRS : UPR8001, Institut National des Sciences Appliquées [INSA] - Toulouse – 7 Av du colonel Roche 31077 TOULOUSE CEDEX 4, France A highly accurate understanding of the molecular mechanisms that govern biological processes is required to accelerate medical and pharmaceutical innovation. Molecular modeling and simulation have become indispensable tools to address this question and provide new insight where information is not available through experimentation alone. However, predicting the structure-activity relationship that determines biomolecular function remains an outstanding challenge for computational investigations. In this competitive background, the Static Mode method developed at LAAS-CNRS, is an innovative approach to account for biomolecular flexibility in the prediction of structure/activity relationship. Thanks to the pre-calculation of the intrinsic deformations of biomolecules submitted to custom designed stimuli, this method allows the user to design specific actions applied on single or multi-atom sites, and to anticipate the induced structural/mechanical changes. We will show how the Static Modes can be used to efficiently localize allosteric sites and to decipher allosteric mechanisms with atomic precision. We will also present selected results on various enzymes to propose a guideline for efficient, predictive and custom in silicoexperiments: ligand-induced accommodation, mutation effects, domain communication... In particular, we will focus on the case of Ras oncoproteins and will discuss how this low-cost computational approach offers unprecedented possibilities to explore Ras biomechanical properties and to mechanically simulate the activation/inactivation process. Our goal is to acquire a unique understanding of the biomolecular processes that govern Ras biological function and mutation effects, and consequently, how to reverse them by performing the screening of mutations impact in view of guiding mutation experiments. ∗ Intervenant 102 Communication par affiche Poster P12 Proteus: dessin de protéine en backbone flexible Karen Druart ∗† 1 , David Mignon 1 , Edouard Audit 2 , Georgios Archontis‡ 3 , Thomas Simonson§ 1 1 Laboratoire de Biochimie (BIOC) – CNRS : UMR7654, Polytechnique - X – Laboratoire de Biochimie Ecole Polytechnique 91128 Palaiseau, France 2 Maison de la Simulation (MDLS) – CEA – USR 3441 bât. 565 CEA Saclay 91191 Gif-sur-Yvette cedex, France 3 Theoretical and Computational Biophysics Group – Department of Physics University of Cyprus P.O BOX 20537 1678 Nicosia Cyprus, Chypre Le dessin computationnel de protéine (CPD) est une méthode qui permet de prédire les mutations pertinentes à réaliser pour conférer aux enzymes de nouvelles propriétés. Un logiciel de CPD assez complet, Proteus, a été developpé dans l’équipe de Thomas Simonson à l’Ecole Polytechnique (Simonson et al, 2013); il s’appuie sur un modèle de mécanique moléculaire fourni par le programme XPLOR. Brièvement, XPLOR précalcule les énergies d’interaction entre toutes les paires de résidus de la protéine. Ces calculs sont réalisés en maintenant le backbone fixe, sur lequel les rotamères d’une librairie discrète sont positionnés. Les énergies sont ensuite relues par un autre programme (“proteus”), qui permet une exploration Monte Carlo de l’espace des séquences et conformations. Cependant, la rigidité du backbone limite l’espace conformationnel de la protéine et diminue en principe la qualité du modèle. Très récemment, nous avons ajouté la possibilité de prendre en compte un ensemble de conformations du backbone, au lieu d’une seule, avec la possibilité pendant le Monte Carlo de passer d’une conformation à l’autre. Pour obtenir un taux d’acceptation raisonnable, le saut de backbone est suivi par une courte relaxation dans l’espace des rotamères. Le changement global, saut de backbone puis relaxation rotamérique, est accepté ou rejeté selon un test de Metropolis généralisé, qui garantit en principe une exploration selon une distribution de Boltzmann des séquences et des structures. Les premiers résultats obtenus sur 3 systèmes tests (tyrosyl-ARNt synthétase, domaines SH3 et SH2) seront présentés. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] § Auteur correspondant: [email protected] † 103 Communication par affiche Poster P1 Molecular dynamics with excited normal modes reveals the role of the activation loop of Cyclin-Dependent Kinases in their open/closed conformational equilibrium Nicolas Floquet ∗ 1 , Mauricio G.s. Costa 2 , Paulo R. Batista , Pedro Renault 3 , Paulo M. Bisch , Florent Raussin , Jean Martinez , May C. Morris , David Perahia 4 1 Institut des Biomolécules Max Mousseron (IBMM) – CNRS : UMR5247, Université de Montpellier – Faculté de Pharmacie, 15 Av. Charles Flahault, BP 14491, 34093 Montpellier, Cedex 05, France 2 Programa de Computação Científica, Fundação Oswaldo Cruz – 21949900, Rio de Janeiro, Brésil 3 Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro – 21949-901, Rio de Janeiro, Brésil 4 Laboratoire de Biotechnologie et Pharmacologie génétique Appliquée (LBPA) – CNRS : UMR8113, École normale supérieure (ENS) - Cachan – 61 AVENUE DU PRESIDENT WILSON 94235 CACHAN CEDEX, France Cyclin-dependent kinases are central for timely regulation of cell cycle progression and constitute attractive pharmacological targets. Characterization of the structural and dynamic features of these kinases is essential to gain in-depth insight into their structure-activity relationships. Structural studies of CDK2/Cyclin A have yielded a wealth of information concerning the conformations of the monomeric and heterodimeric forms of this kinase. There is however much less structural information available for other CDK/Cyclin complexes, including CDK4/Cyclin D complexes. In this study, we performed Normal Modes Analyses on CDK2/Cyclin A and CDK4/Cyclin D1 X-ray structures, which display a different position of the Cyclin partner relative to the CDK, CDK2/Cyclin A being in a “closed” conformation in contrast to the “open” conformation of CDK4/Cyclin D1. Interestingly, we observed that the lowest frequency NM computed for each of these complexes described the transition between the “ open ” and the “ closed ” conformations. Exploration of this motion with an explicit representation of the solvent using the Molecular Dynamics with Excited Normal Modes (MDeNM) method confirmed that the closed conformation was the most stable for the CDK2/Cyclin A complex, in agreement with all available structures in the PDB. On the contrary, we clearly show that an open closed equilibrium may exist in CDK4/Cyclin D1, with closed conformations resembling that captured for CDK2/Cyclin A. Using the same approach, the putative roles of both the phosphoryl group on Thr160 and of the conformation of the T-loop on this conformational equilibrium were investigated. These results provide, for the first time, a dynamic view of Cyclin-dependent kinases and reveal the existence of intermediate conformations which have not yet been characterized for CDK members other than CDK2, and which will be useful for the design of inhibitors, targeting critical conformational transitions. ∗ Intervenant 104 Communication par affiche Poster P14 Design raisonné de procédés enzymatiques pour la dégradation améliorée de biopolymères Marc Gueroult 1 ∗ 1 , Pablo Alvarez 1,2 , Emilie Amillastré Duquesne 1 , Sophie Barbe ∗ , Alain Marty 1,3 , Isabelle André 1,2 , Sophie ∗ † 1 1 Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés (LISBP) – Institut National des Sciences Appliquées [INSA], Institut national de la recherche agronomique (INRA) : UMR792, CNRS : UMR5504 – 135 Avenue de rangueil 31077 Toulouse cedex 04, France 2 Toulouse White Biotechnology (TWB) – Institut national de la recherche agronomique (INRA) : UMR1337, CNRS : UMS3582 – 3 rue des satellites F-31400 Toulouse, France 3 Carbios – Carbios – biopole Clermont Limagne rue Emile Duclaux, F-63360 St Beauzire, France Le recyclage des plastiques d’origine biosourcée est un enjeu économique d’importance de nos jours. Au sein du laboratoire, des approches génomiques ont permis d’isoler une serine protéase qui montre une activité hydrolytique importante vis-à-vis de certains biopolymères couramment utilisés dans l’industrie, tel que l’acide polylactique (PLA). Cependant, l’activité de dégradation de cette enzyme n’est pas suffisante pour envisager son utilisation dans des procédés industriels. Ainsi, pour améliorer son activité catalytique, une approche d’ingénierie enzymatique a été développée au sein de notre équipe. Elle s’appuie sur des techniques de modélisation moléculaire pour d’une part mieux comprendre les déterminants moléculaires impliqués dans la reconnaissance du polymère par l’enzyme et d’autre part, pour proposer des modifications à apporter notamment par des mutations d’acides aminés, qui permettraient d’améliorer les performances catalytiques de l’enzyme et contrôler la nature des produits obtenus. Dans le cadre de ces travaux, nous avons mis en place une stratégie de modélisation moléculaire multi-échelles pour étudier différentes facettes du procédé enzymatique de dégradation des polymères et guider de façon raisonnée l’ingénierie de ces enzymes. Ces approches combinent l’utilisation de modèles atomiques et de modèles “ gros grain ” à des outils dédiés à l’étude des interactions moléculaires pour modéliser l’ensemble du processus enzymatique de dégradation des polymères. L’étude réalisée pour l’amélioration du procédé enzymatique de dégradation du PLA sera rapportée. Financement : Cette étude a été financée dans le cadre du Projet FUI ThanaplastTM en collaboration avec la société CARBIOS ∗ † Intervenant Auteur correspondant: [email protected] 105 Communication par affiche Poster P1 Ligand-Based QSAR studies on some Cis-Stilbenes as Cyclooxygenase Inhibitor Safia Kellou-Taïri 1 ∗ 1 , Zohra Bouakouk-Chitti Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB) – BP 32 EL ALIA 16111 BAB EZZOUAR ALGER, Algérie Cyclooxygenase (COX), which is the key enzyme in the synthesis of prostaglandins (PGs) from arachidonic acid, exists in two isoforms: COX-1 and COX-2. COX-1 is constitutively expressed in a variety of cell types and is mainly involved in the synthesis of cytoprotective PGs in gastrointestinal (GI) tract, whereas COX-2 is expressed during inflammatory conditions. Nonsteroidal anti-inflammatory drugs (NSAIDs) act through the inhibition of COX. All classical NSAIDs are capable of inhibiting both isoforms; however, they are found to be bound more tightly to COX-1. As a result, those drugs are associated with a high risk of adverse effects on the GI tract as well as on the renal function. Owing to these problems, a novel NSAIDs generation has been developed by increasing the selectivity of COX-2. However, the use of specific COX-2 selective drugs was a failure owing to their cardiovascular side effects. Alternative to those drugs are natural products, which offer a great hope for the identification of bioactive lead compounds and their development into drugs. Stilbenes are a group of phytochemicals that can be commonly found in higher plants with a wide global distribution. Experimental studies have indicated their multiple chemopreventive properties and anti-inflammatory activity [1, 2]. Moreover, various laboratories are interested in the design, synthesis, and biological evaluation of cis-Stilbene derivatives. All the world’s major pharmaceutical and biotechnology companies use computational design tools. The ligand-based computer-aided drug discovery (LB-CADD) approach involves the analysis of ligands known to interact with a target of interest. The studies presented in this work describe a series of cis-stilbene analogs selected in literature for their anti-inflammatory effect. We used the Canvas module of Schrödinger software [3], which allows for novel QSAR methodologies to provide predictive and interpretable models. The results obtained will be used in understanding the possible structural modification of these molecules to improve their inhibitory potency. References: A. Cassidy, B. Hanley, R. M. Lamuela Raventos. J. Sci. Food Agric. 2000; 80:1044-1062. P. Fresco, F. Borges, C. Diniz, M. P. Marques. Med. Res. Rev. 2006; 26:747–766. Canvas, Version 2.2, Schrödinger, LLC, NY2014. ∗ Intervenant 106 Communication par affiche Poster P FOCUSED LIGAND LIBRARIES FOR COVALENT DOCKING ON SERINE ACTIVE PROTEINS Virginie Martiny 1 ∗ 1,2 , Edithe Selwa 1 , Hanna Debiec 2 , Pierre Ronco 2 , Bogdan Iorga 1 Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT – CNRS : UPR2301 – Avenue de la Terrasse, Bat. 27, 91198 Gif-sur-Yvette, France 2 Laboratoire « Des maladies rénales rares aux maladies fréquentes, remodelage et réparation », INSERM UMRS 1155 − −Inserm : U M RS1155 − −HpitalT enon, 4ruedelaChine, 75970P arisCedex20, F rance The use of covalent inhibitors has known a very important development in recent years [1-4]. Currently, 30 % of the molecules approved for clinical use present a covalent mechanism [3]. The covalent docking technique also became more and more popular, being now implemented in most major software packages (GOLD, Glide, AutoDock, ICM, MOE, etc.) and on several dedicated web servers (DOCKovalent, Covalent Dock Cloud, etc.). A major limitation that hampers the use of covalent docking on large scale is the availability of chemical libraries with ligands prepared in a particular format, compatible with this technique. Indeed, the existing chemical libraries cannot be used directly in covalent docking and require a special preparation for this specific purpose. In this work, we have generated focused ligand libraries, compatible with the GOLD docking program, suitable for covalent docking on serine active proteins. For this purpose, we collected from the literature and available databases (PDB, DrugBank, etc.) all known structural patterns allowing a covalent binding with a serine active residue. In order to avoid the side effects due to non-specific interactions, an additional filter was applied and we kept only the functional groups with a low to moderate electrophilic reactivity. A number of 18 structural patterns were thus selected, then translated into SMARTS strings that were further used for substructure search in the ZINC databank ( 22 millions compounds). In this way, we identified commercially available molecules possessing the pattern of interest and constituted one focused library per pattern. All identified compounds were converted into a form suitable for covalent docking using SMIRKS reactions and in-house developed scripts based on the CACTVS Chemoinformatics Toolkit [5]. These focused libraries of covalent ligands are currently being used for virtual screening campaigns on serine active proteins of therapeutic interest. Singh J., Petter R.C., Baillie T.A., Whitty A. The resurgence of covalent drugs. Nat. Rev. Drug Discov. 2011;10(4):307-17 Bachovchin D.A., Cravatt B.F. The pharmacological landscape and therapeutic potential of serine hydrolases. Nat. Rev. Drug. Discov. 2012;11(1):52-68 ∗ Intervenant 107 Communication par affiche Poster P1 Johnson D.S., Weerapana E., Cravatt B.F. Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. Future Med. Chem. 2012;2(6):949-964 Maryanoff B.E., Costanzo M.J. Inhibitors of proteases and amide hydrolases that employ an alpha-ketoheterocycle as a key enabling functionality. Bioorg. Med. Chem. 2008;16(4):1562-95 Ihlenfeldt W.D., Takahashi Y., Abe H., Sasaki S. I. Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility. J. Chem. Inf. Comp. Sci. 1994;34:109-116 (www.xemistry.com). 108 Communication par affiche Poster P1 Inhibition sélective des ADN glycosylases : simulation par dynamique moléculaire et docking pour la recherche et la conception d’inhibiteurs Charlotte Rieux ∗ 1 , Franck Coste 1 , Françoise Culard 1 , Stéphane Goffinont 1 , Stéphane Bourg 1,2 , Bertrand Castaing 1 , Norbert Garnier 1 1 2 Centre de biophysique moléculaire (CBM) – CNRS : UPR4301 – Rue Charles Sadron 45071 ORLEANS CEDEX 2, France Institut de Chimie Organique et Analytique (ICOA) – CNRS : UMR7311, Université d’Orléans – UFR Sciences Rue de Chartres - BP 6759 45067 ORLEANS CEDEX 2, France Les organismes vivants sont constamment soumis aux effets de facteurs endogènes ou exogènes tels que des agents chimiques (oxydants et alkylants) ou physiques (radiations UV et gamma) qui peuvent endommager leur ADN. Pour survivre sans contrepartie aux effets néfastes de ces lésions de l’ADN, des mécanismes moléculaires de réparation ont été mis en place, notamment le système de réparation par excision de base (BER). Les ADN-glycosylases sont les enzymes qui participent au BER en détectant les bases altérées de l’ADN (oxydées, alkylées et/ou dégradées) telle que la 8-oxoguanine (une des lésions extrêmement mutagène) [1]. Bien qu’impliqué dans la stabilité génétique des organismes, le système BER peut cependant induire une résistance aux traitements par radiothérapie. En effet, ce type de traitement entraine des lésions oxydatives sur l’ADN qui peuvent être prises en charge par le BER. La recherche d’inhibiteurs des enzymes du BER présente donc un enjeu thérapeutique dans la lutte contre le cancer. Dans ce cadre, nous avons choisi de cibler les ADN glycosylases. Ces enzymes initient le système BER. Notre étude se focalise en particulier sur les ADN glycosylases de la superfamille H2TH (Hélice 2 Tours Hélice) telles que les protéines bactériennes Fpg, Nei et les protéines humaines hNeil1, hNeil2 et hNeil3 qui réparent les pyrimidines et purines oxydées [1]. Dans un premier temps, nous nous sommes intéressés aux mécanismes d’interaction de ces enzymes libres ou complexées à l’ADN endommagé, avec des ligands de types nucléobases récemment identifiés comme des inhibiteurs. Pour cela nous utilisons principalement des simulations de dynamique moléculaire et des méthodes d’amarrage moléculaire. Les résultats préliminaires seront alors confrontés aux nombreuses données structurales et fonctionnelles de l’inhibition de ces enzymes disponibles dans la littérature [2, 3]. L’objectif à plus long terme de cette étude est de mettre en place une méthode de tri moléculaire virtuel pour cribler des banques de molécules synthétiques ou naturelles afin de faciliter la recherche d’inhibiteurs. Prakash, A.; Doublié, S.; Wallace, S.S. (2012) ∗ Intervenant 109 Communication par affiche Poster P1 The Fpg/Nei Family of DNA Glycosylases : Substrates, Structures and Search of Damage. Prog Mol Biol Transl Sci. 110, 71-91. Biela, A.; Coste, F.; Culard, F.; Guerin, M.; Goffinont, S.; Gasteiger, K.; Cieśla, J.; Winczura, A.; Kazimierczuk, Z.; Gasparutto, D.; Carell, T.; Tudek, B.; Castaing, B. (2014) Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Nucleic Acids Res. 42(16), 10748-10761. Jacobs, A.C.; Calkins, M.J.; Jadhav, A.; Dorjsuren, D.; Maloney D.; Simeonov, A.; Jaruga, P.; Dizdaroglu, M.; McCullough, A.K.; Lloyd, R.S. (2013) Inhibition of DNA glycosylases via small molecule purine analogs. PLoS One. 8(12), e81667 110 Communication par affiche Poster P1 Spectroscopic Fingerprints of the Structural Fluctuations of a Single Amino Acid Fatima Barakat 1 ∗ 1 , Patrice Delarue† 1 , Patrick Senet‡ 1 Laboratoire Interdisciplinaire Carnot de Bourgogne (ICB) – CNRS : UMR6303, Université de Bourgogne – 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France Thanks to the nanoscience revolution, nowadays it is possible to study a single amino-acid experimentally by using the Surface Enhanced Raman Spectroscopy. In contrast to bulk Raman measurements that average over an ensemble of molecules, single-molecule spectroscopy on a single amino acid produces a set of high-resolution heterogeneous spectra. Several reasons might be the cause of the heterogeneity of the spectra as the experimental noise, the amino-acid interactions with the SERS nanodevice and the (intrinsic) conformational fluctuations of the amino acid. To examine the latter hypothesis from a theoretical point of view, classical infrared spectra as well as Raman spectra were computed for blocked hydrated amino-acids. One thousand conformations of hydrated amino-acids were selected every 100 ps from classical molecular dynamics trajectories of 100 ns of duration at 300 K in explicit solvent (water). Normal mode analysis was performed for every conformation and the infrared and Raman spectra were computed. The calculations produce heterogeneous ensembles of infrared and Raman spectra, similar to those measured in SERS. The fluctuations of the spectra relative to the average spectrum were studied by using principal component analysis. The role of the hydration on the fluctuations was clearly identified. A correlation between the amino-acid conformational fluctuations and the fluctuations of the spectra was rationalized by calculating an effective local force constant on each of the atom. The present work strongly supports that the origin of the time-dependent fluctuations of the Raman spectra observed in SERS are mainly due to the multiple minima of the free-energy surface of a single amino acid in solution. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] † 111 Communication par affiche Poster P1 Unravelling the structure/activity relationship between collagen derived peptides and the v3 integrin Eléonore Lambert 1 , Manuel Dauchez 1,2 , Sylvie Pasco-Brassart 1 , Stéphanie Baud ∗† 1,2 1 UMR CNRS/URCA 7369 (MEDyC), Reims (1) – Université de Reims - Champagne Ardenne, CNRS : UMR7369 – Moulin de la Housse, 51687 Reims Cedex 2, France 2 Plateau de Modélisation Moléculaire Multiéchelle (P3M), Reims (2) – Université de Reims Champagne Ardenne, CNRS : UMR7369 – Moulin de la Housse, 51687 Reims Cedex 2, France The Extra Cellular Matrix (ECM) is a connective tissue formed by a complex network of macromolecules. Upon degradation by Matrix MetalloProteinases (MMP), elastases or collagenases, the ECM releases bio-active fragments named matrikines. In particular, the NC1 domain of the a4 chain of collagen IV, named tetrastatin was demonstrated to inhibit in vitro melanoma cell proliferation and invasion and in vivo tumor growth through V3 integrinbinding. The interaction with the integrin V3 was demonstrated by Surface Plasmon Resonance [1]. The aim of the present in silico study is to gain insight into the molecular and atomistic aspects of the interaction between tetrastatin-derived peptides and the V3 integrin. Since it was possible to identify the tetrastatin minimal active sequence QKISRCQVCVKYS (corresponding to the peptide named QS-13), we are characterizing V3/QS-13 interactions using multiple molecular docking experiments and statistical analyses. We are then able to identify five “preferred areas of interactions” as well as the key residues implicated in the interactions. In addition, our results demonstrate the important role played by the presence of a disulfide bridge in QS-13 peptide. 1. Brassart-Pasco, S., Sénéchal, K., Thevenard, J., Ramont, L., Devy, J., Di Stefano, L., DupontDeshorgue, A., Brézillon, S., Feru, J., Jazeron, J. F., Diebold, M. D., Ricard-Blum, S., Maquart, F. X., and Monboisse, J. C. (2012). Tetrastatin, the nc1 domain of the 4(iv) collagen chain: a novel potent anti-tumor matrikine. PLoS One, 7(4) ∗ † Intervenant Auteur correspondant: [email protected] 112 Communication par affiche Poster P Mécanisme d’activation du récepteur T1R2-T1R3 impliqué dans la perception du goût sucré. Jean-Baptiste Cheron ∗ 1 , Jérôme Golebiowski 1 , Serge Antonczak 1 , Sébastien Fiorucci† 1 1 Institut de Chimie de Nice (ICN) – CNRS : UMR7272, Université Nice Sophia Antipolis [UNS], Université Nice Sophia Antipolis (UNS) – Faculté des Sciences Parc Valrose 28 Avenue Valrose 06108 Nice cedex 2, France La stimulation chimique du récepteur T1R2-T1R3 est à l’origine de la perception du goût sucré. Ce Récepteur Couplé aux Protéines G (RCPG) de classe C est un hétérodimère caractérisé par un grand domaine N-terminal appelé Venus Flytrap Domain (VFD) lié au domaine à 7 segments transmembranaire (7TM) par un domaine riche en cystéines (CRD). Il a été montré que les molécules influençant l’activité du récepteur interagissent avec les différents domaines [1] : les agonistes naturels lient le site orthosterique localisé dans le VFD de T1R2, les modulateurs allostériques interagissent avec le domaine à 7TM de T1R3 et les protéines à pouvoir sucrant lient le CRD de T1R3. Malgré la connaissance de ces sites de liaison, les mécanismes moléculaires impliqués dans la transmission du signal d’activation du VFD de T1R2 à la partie cytosolique du domaine à 7TM reste à élucider. Dans cette perspective d’étude in silico, l’obtention de la structure 3D du récepteur est nécessaire pour caractériser la relation structure-activité impliquée dans la perception du goût sucré et in fine définir de nouveaux édulcorants. L’absence de données structurales sur le récepteur T1R2-T1R3 requière une étape de modélisation par homologie à l’aide de contraintes expérimentales : i) les données cristallographiques disponibles du récepteur métabotropique au glutamate (RCPG de classe C) [2,3] ii) les régions d’interactions des domaines à 7TM [4] iii) les résidus clés définis par mutagenèses dirigées [5,6]. Les simulations de dynamiques moléculaires et les calculs de modes normaux sont utilisés pour décrire les processus moléculaires impliqués dans la liaison des ligands et le mécanisme d’activation du récepteur. Références: Behrens M. et al., Angew. Chem. Int. Ed, 2011, 50, 2220-2242. Wu H. et al., Science, 2014, 344 (6179), 58-64. Doré A.S. et al., Nature, 2014, 511, 557–562. Xue L. et al., Nat. Chem. Biol., 2015, 11, 134-140. Zhang F. et al., PNAS, 2010, 107(10), 4752-4757. ∗ † Intervenant Auteur correspondant: [email protected] 113 Communication par affiche Poster P Caractérisation du paysage énergétique de biomolécules flexibles avec un couplage d’algorithmes stochastiques Juan Cortes 1 ∗ 1 LAAS-CNRS (LAAS-CNRS) – CNRS : UPR8001 – France La caractérisation du paysage énergétique de biomolécules flexibles est essentielle pour l’analyse de ses propriétés physico-chimiques et ses fonctions biologiques. Les peptides sont un cas d’étude particulièrement intéressant, car ces molécules exploitent leur flexibilité structurale pour moduler leur fonction. Malgré leur petite taille (par rapport aux protéines), la modélisation des peptides reste un sujet difficile à cause de l’existence d’une multitude d’états métastables et de transitions possibles entre eux. Nous proposons une approche basée sur le couplage d’algorithmes stochastiques. Premièrement, une version simple de l’algorithme Basin Hopping est utilisée pour échantillonner des régions de basse énergie de manière à identifier un ensemble d’états métastables. Ensuite, plusieurs variantes d’un algorithme issu de la robotique, appelé Transition-based Rapidly-exploring Random Tree (T-RRT), sont proposées pour calculer de manière efficace les chemins de transition entre ces états. L’approche est illustrée sur la met-enképhaline. ∗ Intervenant 114 Poster 3 Communication par affiche Modeling methods for protein structure prediction, mechanistic and docking studies Serge Crouzy 1 ∗† 1 Laboratoire de Chimie et Biologie des Métaux (LCBM) – CEA, Université Joseph Fourier - Grenoble I, CNRS : UMR5249 – 17, rue des Martyrs 38054 GRENOBLE CEDEX 9, France Nous nous efforçons, dans notre petit groupe, de répondre à des problèmes expérimentaux par des modèles théoriques et des simulations. Il s’agit soit de modèles structuraux basés sur la mécanique ou la dynamique moléculaire, soit de mécanismes réactionnels basés sur les calculs d’énergie libre ou la chimie thèorique. Depuis les modèles “ gros-grain ” jusqu’à une description électronique, nos modèles couvrent une large gamme de temps (ps à ms) et d’espace (nm à µm). Nous présentons brièvement cinq résultats récents couvrant ces domaines à l’exception du niveau électronique. 1- La structure X de NccX, un senseur transmembranaire de métal, a été déterminée à une résolution de 3,12 Å en détergent. Cette structure ne correspond pas au modèle basé sur le domaine périplasmique largement caractérisé de son homologue le plus proche CnrX. Des simulations de dynamique moléculaire “ gros-grain ” de NccX immergée dans une bicouche de phospholipides modèles ont permis d’isoler le segment transmembranaire de la protéine malencontreusement attaché à une région hydrophobe dans la structure en détergent.2- Les Récepteurs Couplés aux Canaux Ioniques (ICCR) sont des protéines artificielles construites à partir d’un récepteur couplé à la protéine G et d’un canal ionique, utilisés comme biocapteurs moléculaires. Le canal potassique rectifiant entrant Kir6.2 a ainsi été couplé avec succès au récepteur muscarinique M2 ou dopaminergique D2. Le mécanisme moléculaire expliquant la différence de comportement (courant ionique à travers le canal) entre les 2 ICCR après liaison de leur activateur respectif reste à élucider. En particulier, il était important de déterminer comment l’activation de l’acétylcholine M2 par son agoniste déclenche la modulation du canal Kir6.2 via la liaison M2Kir6.2. Nous avons développé et validé une approche computationnelle permettant de construire des modèles de M2-Kir6.2 qui a produit deux modèles possibles correspondant à deux orientations différentes de M2. 3- La protéine FUR (régulateur de l’absorption ferrique) est un régulateur transcriptionnel global spécifique des bactéries. C’est une cible de choix pour le développement de molécules visant à réduire la virulence des bactéries sans développer des résistances. Des peptides anti-FUR de 13 acides aminés ont été identifiés, capables d’interagir avec FUR d’Escherichia coliet ainsi inhiber sa liaison à l’ADN conduisant à sa pathogénicité. Une combinaison originale d’approches théoriques (“ docking ” et DM) et expérimentales a été utilisée pour étudier le mécanisme d’inhibition de FUR par ces peptides.4- L’ATPase à cuivre humaine ATP7A (Menkès) est essentielle pour l’homéostasie intracellulaire du cuivre. Le domaine N-terminal de la protéine se compose de six séquences répétitives de 60-70 acides aminés (Mnk1-Mnk6) qui se replient en domaines de liaison métallique individuels (MBD) liant un ion Cu(I) grâce à deux résidus cystéine. La structure de chaque MBD est connue par RMN et nous nous sommes intéressés ∗ † Intervenant Auteur correspondant: 115 Communication par affiche Poster P à la stabilité et la dynamique de chaque MBD isolé dans sa forme apo et holo ainsi qu’à leurs interactions avec la métallochaperone soluble Hah1 qui délivre le cuivre à ATP7A. Nous avons paramétrisé le métal dans ces protéines et réalisé des simulations de DM dans ce but.5- Les interactions entre la -cyclodextrine, (BCD) et le chlorure de p-toluènesulfonyl (TsCl) ont été étudiées en utilisant des simulations de DM, dans le vide, se rapprochant de l’environnement de la cavité hydrophobe de la CD, et en présence d’eau. Dans les deux cas, les chemins d’énergie adiabatique minimale, et les potentiels de force moyenne (profils d’énergie libre) pour l’insertion des TsCl le long d’une coordonnée de réaction perpendiculaire au plan de la CD, ont été calculés pour les deux orientations possibles de TsCl. Les résultats montrent une entrée préférentielle de TsCl dans la cavité de CD par la face à hydroxyles primaires en excellent accord avec les données de RMN. 1- Ziani W, Maillard AP, Petit-Härtlein I, Garnier N, Crouzy S, Girard E. and Covès J. J Biol Chem. 289 31160-31172 (2014). 2- Sapay N., Estrada A., Moreau C., Vivaudou M. and Crouzy S. Proteins 82 1694-1707 (2014) 3- Cissé C., Mathieu S.V., Abeih M.B., Flanagan L., Vitale S., Catty P., Boturyn D., MichaudSoret I.. and Crouzy S. ACS Chem Biol . 9 2779-2786 (2014) 4- Arumugam K. and Crouzy S. Biochemistry. 51 8885-8906 (2012) 5- Law H., Benito J.M., Garcia Fernandez J.M., Jicsinszky J., Crouzy S. and Defaye J. J Phys Chem B. 115, 7524-7532. (2011) 116 Communication par affiche Poster P Mitochondrial membrane fusion: computational modelling of mitofusins Dario De Vecchis 1 ∗† 1 , Antoine Taly 1 , Marc Baaden 1 , Jérôme Hénin 1 Institut de biologie physico-chimique (IBPC) – CNRS : FRC550 – 13 Rue Pierre et Marie Curie 75005 PARIS, France Mitochondria are highly dynamic organelles that continuously alter their shape, ranging from a filamentous network to a collection of isolated fragments. This process is controlled by fusion-fission equilibrium which is a largely unexplored topic despite its importance in cell function, evolution and ageing. Fusion of mitochondrial outer membranes (MOM) involves mitofusins, large GTPases of the Dynamin-Related Proteins (DRPs) superfamily, one of which is Fzo1. Although several hypotheses have been proposed, many aspects of Fzo1 function are yet debated, and many important questions remain unanswered. Recent data indicate that the GTPase domain of Fzo1 would induce a conformational switch from a closed to an open state concomitant with mitochondrial tethering. Such a conformational switch resembles that of the bacterial dynamin-like protein (BDLP), a close relative of Fzo1, whose structure is known in two conformational states: binding of GTP analogues by BDLP results in a switch from a compact structure, seen with bound GDP, to an open conformation that stimulates BDLP oligomerization and favours its ability to shape the morphology of liposomes. BDLP structural properties and Fzo1 behaviour during MOM fusion suggest that mitofusins may promote membrane fusion by switching from closed to open conformation, although the molecular fusion mechanism remains unknown. In this project we use homology modelling approach and atomistic simulations in close link to experiment to study Fzo1 based on the open and closed BDLP crystal structures. The refined models may generate hypotheses for the conformational transition between open and closed forms and predict the phenotype of interesting mutations to be tested and performed by Mickael Cohen lab, as a part of the collaboration. Since sequence and function of mitofusins are conserved throughout evolution, our approach may unravel novel functional domains and provide fundamental insights about molecular mechanisms by which mitofusins and more generally DRPs, catalyse membrane fusion. ∗ † Intervenant Auteur correspondant: [email protected] 117 Communication par affiche Poster P UnityMol: Simulation et Visualisation Interactive à des fins d’Enseignement et de Recherche Sébastien Doutreligne ∗ 1 , Cédric Gageat 1 , Tristan Cragnolini 1 , Antoine Taly 1 , Samuela Pasquali 1 , Marc Baaden 1 , Philippe Derreumaux 1 1 Laboratoire de biochimie théorique (LBT) – CNRS : UPR9080, Université Paris VII - Paris Diderot – 13 Rue Pierre et Marie Curie 75005 PARIS, France Nous présentons UnityMol, une base logicielle pour développer des solutions de visualisation, analyse et exploration de données biologiques. Une des originalités de UnityMol est son implémentation à travers un moteur de jeu vidéo. Nous venons de connecter ce logiciel de visualisation à des simulations de dynamique moléculaire pour interagir directement avec la molécule d’intérêt. Cette manipulation apporte une nouvelle dimension très concrète et intuitive à l’exploration de la structure des biomolécules. Ici nous présentons nos essais sur les molécules d’ARN. Nous utilisons un moteur de simulation qui implémente le modèle gros-grain HiRE-RNA développé au laboratoire. Une des applications possibles est l’enseignement. A présent, UnityMol a été utilisé avec des groupes d’étudiants de Licence en Biologie et en Bioinformatique, soit un total de près de 100 personnes. Ces expériences créent un contact concret avec les simulations et leur fonctionnement et nous permettent de tester et valider nos choix techniques pour ensuite proposer un espace d’expérimentation virtuel pour la recherche. ∗ Intervenant 118 Communication par affiche Poster P Study of TIMP-1/LRP-1 interaction in neurons: a new approach based on protein dynamic Laurie Verzeaux *1, Nicolas Belloy 2, 3 , Hervé Emonard 1, Manuel Dauchez 2, 3 , Laurent Martiny 1, Nicolas Etique 1 and Emmanuelle Charpentier 1 1 – Unité MeDyC UMR CNRS URCA 7369, Equipe “Protéolyse et cancer”, Reims 2 – Unité MeDyC UMR CNRS URCA 7369, Equipe “Vieillissement matriciel et Remodelage vasculaire”, Reims 3 – Plateau de Modélisation Moléculaire Multi-échelle (P3M), Maison de la Simulation de Champagne-Ardenne (MaSCA), Reims TIMP-1, a member of the Tissue Inhibitor of Metalloproteinases (TIMPs) family, has been first characterized for its ability to inhibit Matrix Metalloproteinases (MMPs) and can also act as a cytokine by binding to cell surface complex receptors. In mouse cortical neurons, we have recently identified the LDL receptor-related protein-1 (LRP-1) as a new receptor for TIMP-1. The binding of TIMP-1 to LRP-1 reduces neurite outgrowth and modulates growth cone morphology. The characterization of TIMP-1/LRP1 interaction could help to develop new therapeutic strategies in neurodegenerative diseases. Whether the TIMP1 structure is well characterized, the lack of structural data about LRP1 doesn’t allow the use of molecular docking algorithms. Based on the observation that ligand/receptor interaction requires conformational changes of both partners, we have hypothesized that understanding the intrinsic dynamic of TIMP-1 could help us to highlight regions that govern its interaction with LRP-1. Normal Modes Analysis (NMA) and/or Molecular Dynamics (MD) simulations are usefulness in silico methods to study protein dynamics. In this study, we used these theoretical methods in conjunction with experimental data to identify residues or regions that might be involved in TIMP-1/LRP-1 interaction and signaling. Normal Mode Analysis led us to identify a movement of the N-terminal domain relative to the C-terminal domain which could be assimilated to a clamp movement. In these modes, study of residues deformation energy has highlighted a cavity which could govern this movement and potentially its interaction with LRP-1. Molecular dynamic studies of TIMP-1 and particularly carbon α atomic fluctuation representation have also designed this cavity as essential for the TIMP-1 intrinsic dynamic. In this area, three residues have been pointed out and mutated into alanine in order to disturb the movement. The three single mutants have been produced and purified by affinity chromatography. Determination of both Ki (inhibitory constant) and Kon (association constant) revealed that the three mutants conserved their inhibitory effects towards MMP-1, -2, -3 and -9. As expected, the three single mutants are not able to reduce neurite length in mouse cortical neurons. Surprisingly, surface plasmon resonance analyses show that the three mutants are able to bind LRP-1. However, the LRP-1-mediated endocytosis, evaluated by confocal microscopy, is altered for the three mutants. In this study, we have identified a TIMP-1 region essential for LRP-1-mediated endocytosis and associated biological effects in neurons. Our findings could help to design molecules that specifically block the cytokine-like effects of TIMP-1 through LRP-1 and open new perspectives in 119 Communication par affiche Poster P neurodegenerative disease therapy. This work also suggests the utility of our in silico approach in other topics where there is a lack of structural data for studying ligand-receptor interactions. ____________________________ * Intervenant 120 Communication par affiche Poster P SA-conf : un outil d’analyse et de comparaison de la variabilité de séquences et de structures d’un ensemble de conformères d’une protéine Leslie Regad 1 , Jean-Baptiste Cheron 2 , Caroline Senac 3 , Delphine Flatters ∗ 1 , Anne-Claude Camproux 1 1 Recherche de molécules à visée thérapeutique par approches In Silico (MTI) – Inserm : U973, Université Paris VII - Paris Diderot – Batiment Lamarck A (case 7113), 35 rue Hélène Brion 75205 PARIS CEDEX 13, France 2 Institut de Chimie de Nice (UMR 7272 CNRS) – CNRS : UMR7272, Université Nice Sophia Antipolis – Parc Valrose, 06108 Nice Cedex 2, France 3 Laboratoire d’imagerie biomédicale – CNRS : UMR7371, Inserm : UMRS1146, Université Paris VI Pierre et Marie Curie – Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d’imagerie biomédicale, F-75006 Paris, France Actuellement, plus de 100.000 structures protéiques sont disponibles dans la Protein Data Bank (PDB). La PDB inclut souvent plusieurs conformères correspondant à une même protéine obtenue dans différentes conditions expérimentales, par exemple par cristallographie ou RMN, complexée ou non avec un partenaire (protéine, un ligand, un ADN/ARN), sous une forme mutante ou sauvage. Ces différents conformères présentent des variations structurales subtiles pouvant illustrer la “ plasticité ” de la protéine. A l’heure actuelle, il n’existe pas d’outil disponible d’analyse fine, systématique et rapide d’un ensemble de conformères. Or cette analyse permettrait (i) d’identifier les régions structurellement variables pouvant être associées à la plasticité d’une protéine, (ii) d’aider à la détermination des régions importantes pour la fonction biologique de la protéine. Dans ce contexte, nous avons développé un outil, nommé SA-conf, permettant d’étudier et de comparer un ensemble de conformères d’une protéine et analyser leur diversité de séquences et de structure. Tout d’abord, SA-conf offre une description de chaque conformère en termes de méthode expérimentale, de résolution, de nombre et taille de(s) chaîne(s) le composant. Puis, SA-conf construit un alignement multiple des séquences (AMS) extraites des différents conformères. Afin de proposer une comparaison entre la variabilité des séquences et de structures locales des structures, SA-conf construit un alignement des structures locales extraites des différents conformères. L’extraction des structures locales est basée sur un l’alphabet structural HMM-SA (Camproux et al., 2004) qui permet de simplifier chaque conformère en une séquence de lettres structurales (LS) où chaque LS correspond à la géométrie d’un fragment de 4 résidus, i.e. structure locale du résidu en prenant en compte son environnement. Chaque acide aminé du AMS est ensuite remplacé par la LS correspondante produisant ainsi l’alignement des conformations locales (ACL). L’analyse du AMS permet de caractériser les séquences du jeu de conformères en identifiant les séquences mutantes, celles qui contiennent des insertions/délétions ou des régions non résolues et de différencier les séquences provenant de différents organismes. L’analyse des ACL permet ∗ Intervenant 121 Communication par affiche Poster P d’identifier les conformères ayant des particularités structurales, les régions et positions structurellement variables, i.e positions pour lesquelles plusieurs conformations locales sont observées sur ACL. Cette variabilité structurale des conformères peut alors être analyser/interpréter en fonction des différentes conditions expérimentales, comme par exemple la présence d’un partenaire (ligands, protéines, ...), la présence de mutations, .... De plus, SA-conf produit des représentations graphiques qui permettent de localiser ces positions variables et conservées sur la structure tri-dimensionnelle de la protéine. En conclusion SA-conf est un outil rapide d’analyse et de comparaison d’un ensemble des conformères d’une protéine, en termes de séquence et structure. SA-conf permet à l’utilisateur d’identifier les séquences mutées, et de différencier les séquences provenant de différents organismes. SA-conf est aussi un outil efficace pour étudier la diversité structurale locale des différents conformères d’une protéine ce qui permet une première analyse rapide de la plasticité de cette protéine. L’analyse conjointe des conformères obtenus dans différentes conditions expérimentales et des régions variables de la protéine permet d’apporter des premiers éléments de réponse sur les raisons expliquant cette plasticité : flexibilité intrinsèque, mutations, fixation d’un partenaire, et ainsi d’identifier des régions importantes pour la fonction biologique de la protéine. 122 Communication par affiche Poster P Exploration of Large Amplitude Motions of GPCRs and their complexes at the molecular level Nicolas Floquet ∗ 1 , Mauricio Costa 2 , Marjorie Damian 1 , Sophie Mary 1 , Jean-Alain Fehrentz 1 , Jacky Marie 1 , Jean Martinez 1 , Jean-Louis Banarès 1 , David Perahia 3 1 Institut des Biomolécules Max Mousseron (IBMM) – CNRS : UMR5247, Université de Montpellier – Faculté de Pharmacie, 15 Av. Charles Flahault, BP 14491, 34093 Montpellier, Cedex 05, France 2 Programa de Computação Científica, Fundação Oswaldo Cruz, 21949900, Rio de Janeiro, Brazil. – Brésil 3 Laboratoire de Biotechnologie et Pharmacologie génétique Appliquée (LBPA) – CNRS : UMR8113, École normale supérieure (ENS) - Cachan – 61 AVENUE DU PRESIDENT WILSON 94235 CACHAN CEDEX, France Class-A G-Proteins Coupled Receptors (GPCRs) and G-Proteins together form protein:protein complexes that mediate a large panel of physiological responses, and therefore constitute attractive targets for the design of new drugs. The number of available X-ray structures describing either isolated, or complexed GPCRs has considerably increased since 2007. However, and despite of this, the crucial question of the activation mechanism of these large protein:protein complexes at the molecular level is still controversial. In the literature, the conformational change observed between the isolated and the G-protein complexed receptor is still described as the holy-grail. However, many experimental data have now evidenced the existence of G-Proteins pre-coupled GPCRs, suggesting that the activation mechanism is a key feature of the complex and not of the isolated, uncoupled, partners. In agreement, beyond frozen X-ray data, a better understanding of the dynamical behavior of these large molecular assemblies is of crucial importance for the design of more specific drugs, with more controlled effects. In a recent paper, we used Normal Modes Analyses in vacuo, to show that the conformational diversity of GPCRs is considerably reduced upon complexation to G-proteins [1]. These results even pointed to a unique motion possibly being the activation motion of GPCRs in the complex. Here we used the “Molecular Dynamics with Excited Normal Modes” (MDeNM) method to explore such a large amplitude motion of the complex with an explicit representation of the surrounding medium (membrane+water). Among the lowest frequencies Normal Modes of the complex, one motion was in particularly good agreement with experimental results obtained in our laboratory on the Ghrelin Receptor/Gq model and showing the increase/decrease of up to 10 Angströms of both intra- and inter-molecular distances in the protein:protein complex [2]. These data provide direct evidence of a mechanism in which transition of the receptor from an inactive to an active conformation is accompanied by a large conformational rearrangement of a preassembled receptor: G protein complex, ultimately leading to G protein activation and signaling. 1. Louet M, Karakas E, Perret A, Perahia D, Martinez J, and Floquet N. (2013) Conformational ∗ Intervenant 123 Communication par affiche Poster P restriction of G-proteins Coupled Receptors (GPCRs) upon complexation to G-proteins: a putative activation mode of GPCRs? FEBS Lett. 587(16):2656-61. 2. Damian M, Mary S, Maingot M, M’Kadmi C, Gagne D, Leyris JP, Denoyelle S, Gaibelet G, Gavara L, Garcia de Souza Costa M, Perahia D, Trinquet E, Mouillac B, Galandrin S, Galès C, Fehrentz JA, Floquet N, Martinez J, Marie J, Banères JL. (2015) Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor:Gq complex. Proc Natl Acad Sci U S A. 112(5):1601-6. 124 Communication par affiche Poster P HiRE-RNA: un modèle gros grain pour la simulation d’ARN et d’ADN Cédric Gageat 1 ∗ 1 , Samuela Pasquali 1 , Philippe Derreumaux 1 Laboratoire de biochimie théorique (LBT) – CNRS : UPR9080, Université Paris VII - Paris Diderot – 13 Rue Pierre et Marie Curie 75005 PARIS, France Malgré que l’ARN joue de nombreux rôles au sein des cellules, nous disposons de très peu de structures 3D hautes définitions. Du fait de la grande flexibilité des ARN, l’obtention de structures par RMN ou rayon X reste un défi actuel. Des modèles issus de prédictions théoriques sont donc proposés afin de combler le manque de données expérimentales. Malheureusement, les modèles tout-atome, sont eux aussi limités par les puissances de calcul actuelles, ce qui permet uniquement l’étude de petits systèmes. Pour permettre l’étude de plus gros systèmes d’intérêts biologiques, un modèle gros grain haute résolution, HiRE-RNA [1, 2], a été développé dans notre laboratoire. Ce modèle a été testé et validé en couplage avec différentes techniques d’échantillonnage de conformations (Dynamique moléculaire simple, avec échange de répliques, interactive, ...). Nous présentons ici notre modèle et ses termes énergétiques au travers de ses deux spécialisations : la première pour l’ARN, la seconde pour l’ADN. Nous présentons également l’étude d’une large molécule d’ADN (178 nucléotides) [3] ainsi que l’étude de petites molécules à la géométrie complexe : des quadruplexes. Cragnolini T, Laurin Y, Derreumaux P, Pasquali S, The coarse-grained HiRE-RNA model for de novo calculations of RNA free energy surfaces, fodling pathways and complex structure prediction. Submitted Cragnolini T, Derreumaux P, Pasquali S, Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B. 2013 ;117(27):8047-60 Kanevsky I, Chaminade F, Chen Y, Godet J, René B, Darlix J-L, Mély Y, Mauffret O, Fossé P, Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein. Nucl. Acids Res. 2011;39 (18):8148-8162. ∗ Intervenant 125 Communication par affiche Poster P PEPSI-SAXS - A very fast adaptive scheme for computation of small-angle X-ray scattering profiles via spherical harmonics expansions Sergei Grudinin ∗† 1 , Maria Garkavenko 2 , Andrei Kazennov 2 , Team Nano-D 1 1 NANO-D (INRIA Grenoble Rhône-Alpes / LJK Laboratoire Jean Kuntzmann) – Institut polytechnique de Grenoble (Grenoble INP), Université Joseph Fourier - Grenoble I, CNRS : UMR5224, Laboratoire Jean Kuntzmann, INRIA – Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex, France 2 Moscow Institute of Physics and Technology (MIPT) – 141700, 9, Institutskii per., Dolgoprudny, Moscow Region, Russia, Russie Small angle scattering is an important tool in structural biology. It allow to investigate the three-dimensional structures and structural changes of biological objects. Thanks to recent advances in experimental methods, the amount of experimental small-angle X-ray scattering data is increasing dramatically [1,2]. Therefore, there is an urgent need for very efficient computational tools to analyze this data. We present PEPSI-SAXS, a new method that uses spherical harmonics expansions, adaptive resolution, and smooth interpolation of scattering amplitudes in the reciprocal space to rapidly compute solution scattering of macromolecules starting from their known atomic structure. The method can either predict the intensity curve, or to fit the experimental scattering curve using two fitting parameters, the averaged displaced volume and the contrast of the hydration layer. Additionally, our method can automatically subtract the constant background noise from experimental curves, which improves the fitting result. Compared to other state-of-the-art methods such as Crysol [3], FoXS [4], and SAStbx [5], PEPSISAXS uses the adaptive resolution of its expansion coefficients and a very accurate model of the solvation shell to improve the quality of the predicted scattering curve. Additionally, fast summations based on the evaluation of the partial intensities and shared-memory parallelization allows PEPSI-SAXS to significantly out-perform the other methods in computational efficiency. More precisely, on a modern laptop our method runs in 5-50 times faster compared to the other tested methods. The PEPSI-SAXS method was exhaustively tested on all available structural models from the BIOISIS [4] and SASDB [5] databases. Table 1 provides comparison of the four tested methods listing the average timings and quality of fit to experimental curves for 28 models from BIOISIS [1] and 23 models from SASDB [2]. As can be seen from the table, PEPSI-SAXS significantly outperforms all other methods both in speed and model quality. We have also developed a graphical user interface for the PEPSI-SAXS method as a module for the SAMSON modular ∗ † Intervenant Auteur correspondant: [email protected] 126 Communication par affiche Poster P software package developed in our team (see Figure 1), which is available at http://www.samsonconnect.net. http://www.bioisis.net. Erica Valentini, Alexey G Kikhney, Gianpietro Previtali, Cy M Jeffries, and Dmitri I Svergun. Sasbdb, a repository for biological small-angle scattering data. Nucleic acids research, pages D357–63, 2015. D Svergun, C Barberato, and MHJ Koch. Crysol-a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. Journal of applied crys- tallography, 28(6):768–773, 1995. Dina Schneidman-Duhovny, Michal Hammel, John A Tainer, and Andrej Sali. Accurate saxs profile computation and its assessment by contrast variation experiments. Biophysical journal, 105(4):962–974, 2013. Haiguang Liu, Richard J Morris, Alexander Hexemer, Scott Grandison, and Peter H Zwart. Computation of small-angle scattering profiles with three-dimensional zernike polynomials. Acta Crystallographica Section A: Foundations of Crystallography, 68(2):278–285, 2012. 127 Communication par affiche Poster P Conformational changesinin themophilic Conformational changes thermophilic andand mesophilic enymes mesophilic enzymes Marina Katava ∗ 1 , Fabio Sterpone ∗ 1 1 Laboratoire de Biochimie Théorique (LBT) – CNRS : UPR9080, Université Paris Diderot - Paris 7 – 13, Rue Pierre et Marie Curie - 75005 PARIS, France We study the conformational changes that occur during the enzymatic activity of two homologous proteins from the mesophile E. coli (optimum growth at 37◦ ) and the thermophile S. solfataricus (optimum growth at 87◦ ). The enzymatic activity is energized by GTP to GDP conversion and is a necessary part of the polypeptide elongation process. In the mesophile protein, activity is granted by a dramatic secondary structure to conversion occurring in a conserved region (switch I), and following the GTP/GDP catalysis [1]. This region is the most thermally unstable region of the protein [2]. As no to conversion has been observed in the thermophilic EF-1, we are interested in the conformational changes occurring in the analogous portion as they will help us identify the differences between the protein molecular mechanisms in the meso- and the thermophile. We mimicked the conformational changes induced by the enzymatic reactions by performing Molecular Dynamics simulations of the g-domains in different secondary structures bound to the reactant (GTP) and product state (GDP). Results show that the protein matrix is rigid in the /GTP form, and that it becomes more flexible in the /GDP form, which could be the trigger the transition to the state. The thermophile shows similar behavior. The conformational changes in the switch I fragment will be better explored by means of enhanced sampling techniques. Jurnak et al., Structure, 1996. Sterpone et al., J. Phys. Chem. B, 2013. ∗ Intervenant 128 Communication par affiche Poster P Etude de la variabilité structurale et de l’interaction du peptide NFL-TBS.40-63 avec la tubuline. Yoann Laurin ∗ 1 , Philippe Savarin 2 , Charles Robert 1 , Chantal Prevost 1 , Sophie Sacquin-Mora 1 1 Laboratoire Biochimie Théorique CNRS UPR9080 (LBT) – CNRS : UPR9080 – IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France 2 Université Paris 13, Sorbonne Paris Cité, CSPBAT, CNRS UMR7244 – CNRS : UMR7244 – 74 rue Marcel Cachin, 93017 Bobigny, France NFL-TBS.40-63 is a 24 amino acid peptide corresponding to the tubulin-binding site located on the light neurofilament subunit, which selectively enters glioblastoma cells, where it disrupts their microtubule network and inhibits their proliferation. We investigated its structural variability and binding modes on a tubulin hetero-dimer using a combination of NMR experiments, docking and molecular dynamics (MD) simulations. Our results show that, while lacking a stable structure, the peptide preferentially binds on a specific single site located near the -tubulin C-terminal end, thus giving us precious hints regarding the mechanism of action of the NFLTBS.40-63 peptide’s antimitotic activity on the molecular level. Le peptide de 24 acides aminés NFL-TBS.40-63 est un Tubulin-Binding Site (TBS, site de liaison à la tubuline) localisé sur le neurofilament léger. Il pénètre spécifiquement dans les cellules des glioblastomes, où il va inhiber la formation du réseau de microtubules. Nous avons étudié sa variabilité structurale et son interaction avec un hétérodimère de tubuline grâce à des expériences de RMN, de docking et des simulations de dynamique moléculaire. Nos résultats montrent que, malgré l’absence d’une structure stable, le peptide interagit préférentiellement sur un site spécifique situé aux abords de l’extrémité C-terminale de la sous unité de la tubuline. Ces observations sont de précieux indices afin de comprendre le mécanisme de l’action antimitotique du peptide NFL-TBS.40-63 au niveau moléculaire. ∗ Intervenant 129 Communication par affiche Poster P Molecular basis of Olfactory Receptors: in silico modeling and in vitro validation. Gwenaëlle Andre-Leroux ∗† 1 1 André-Leroux (Inra MaIAGE) – Institut National de la Recherche Agronomique - INRA (FRANCE) – Unité Mathématiques et Informatique Appliquées, du Génome à l’Environnement (MaIAGE) INRA Bat233 Domaine de Vilvert - 78352 Jouy-en-Josas, France Adrien Aquistapace1, Véronique Martin2, Jean-François Gibrat2, Guenhaël Sanz1 and Gwenaëlle André-Leroux2 1Inra, NBO UR1197, Bât 440 & 2Inra, MaIAGE UR1404, Bât 233, Domaine de Vilvert, 78352 Jouy-en-Josas [email protected] G protein-coupled receptors (GPCRs) are a highly versatile family of membrane proteins with a broad spectrum of functional behaviours in response to diffusible ligands. Upon activation by external stimuli, which can be photons, odors, pheromones, hormones and neurotransmitters, GPCRs trigger specific cellular responses and recruit downstream activators such as G proteins. The human genome accounts for as much as 3% of GPCR genes which associate with numerous biological sensing functions including olfaction, vision, taste, pain, etc. Noteworthy, most of the human GPCRs are olfactory receptors (ORs), responsible for olfaction, expressed in the olfactory epithelium where they signal diverse odorants [1-2]. Additionally, ORs is employed to detect steroid hormones in non-olfactory tissues, regulate serotonin secretion in the gut, cell migration or adhesion in muscle [3-6]. Deciphering how OR functional behaviour reconciles with structural properties is a challenge, because there is no experimental structure available for ORs and because most of them are orphans, i.e their physiological agonists are unknown. Nevertheless during the last decade, more than 25 high-resolution X-ray structures of GPCRs have been solved, tremendously augmenting insights into their structure/function relationships [7]. GPCRs share a conserved topology of 7 transmembranes (TM) helix bundle that shows 36 topologically equivalent positions with conserved residues or motifs, referred as Ballesteros–Weinstein (BW) numbering scheme [8]. Any mutation in 14 out of 36 of these BW positions modifies the receptor activity, be it a loss or an increase of activity. Although similarity of OR sequences can be very low compared to GPCRs, these conserved motifs could be topological markers that anchor the alignments of the TMs and participate in ligand binding. This hypothesis prompted us to investigate in silico the molecular basis of folding and ligand binding in ORs. Experimental validations were performed on PSGR -Prostate Specific G-Coupled Receptor- a RO for which we have an activity test and we know some agonists. ∗ † Intervenant Auteur correspondant: [email protected] 130 Communication par affiche Poster P From the multiple sequences alignment of non-redundant clustered ORs of the human genome, we found out consensus motifs, with respect to GPCRs in general and within ORs in particular. We were able to propose to mutation six residues referred as BW 3.32, 3.33, 3.36, 6.48, 6.51 and 7.39 that could form the ligand site, by analogy with the solved GPCRs [7]. Homology models of PSGR were built using modeler [9], then agonist molecules, centered at those BW positions, were docked with CHARMm [10]. Four of the six residues subjected to alanine mutagenesis in PSGR result in functional impairment in vitro, thus validating our computational analysis. Ligand specificity in ORs is now addressed that discriminates agonists from antagonists. Eventually, this work will allow a more accurate version of our GPCR automodel webservice [11]. Buck L et al. (1991) Cell 65: 175-187 Niimura Y et al. (2007) PLoS One 2: e708 Neuhaus EM et al. (2009) J Biol Chem 284: 16218-16225. Braun T et al. (2007) Gastroenterology 132: 1890-1901 Kidd M et al. (2008) Am J Physiol Gastrointest Liver Physiol 295: G260-272 Griffin CA et al. (2009) Dev Cell 17: 649-661 Venkatakrishnan A. J et al. (2013) Nature 494: 185-194 Ballesteros J A and Weinstein H. Methods. Neurosci. 1995, 25, 366-428. Sali & Blundell (1999) J Mol Biol 234: 779-815 Brooks B.R et al. (2009) J Comput Chem 30: 1545-1614 Launay G et al. (2012) PEDS 25: 377-386 131 Communication par affiche Poster P Molecular Modeling CoMFA and docking of a Novel Series of Potent 7-Azaindole Based Tri-Heterocyclic Compounds as CDK2/Cyclin E Inhibitors Christine B. Baltus 1 , Radek Jorda 2 , Christophe Marot ∗† 1 , Karel Berka 3,4 , Václav Bazgier 4,5 , Vladimír Kryštof 5 , Gildas Prié 1 , Marie-Claude Viaud-Massuard 1 1 Génétique, Immunothérapie, Chimie et Cancer (GICC) – CNRS : UMR7292, Université François Rabelais - Tours – Faculty of Pharmacy, 31 avenue Monge, 37200 Tours, France 2 Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany – AS CR, Šlechtitelů 11, CZ-78371 Olomouc, République tchèque 3 Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry – Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 77146 Olomouc, République tchèque 4 Department of Physical Chemistry, Faculty of Science, Palacký University – 17. Listopadu 1192/12, 771 46 Olomouc, République tchèque 5 Laboratory of Growth Regulators Department of Chemical Biology and Genetics – Šlechtitelů 11, CZ-78371 Olomouc, République tchèque From four molecules inspired by the structural features of fascaplysin, with an interesting potential to inhibit the complex CDK2/cyclin E, we designed a new series of tri-heterocyclic derivatives based on 1H -pyrrolo[2,3-b]pyridine (7-azaindole) and triazole heterocycles. Comparative molecular field analysis (CoMFA), based on three-dimensional quantitative structureactivity relationship (3D-QSAR) studies, was conducted on a series of 30 compounds from the literature with high to low known inhibitory activity towards the complex CDK2/cyclin E and was validated by a test set of 5 compounds giving satisfactory predictive r2 value of 0.92. Remarkably, it also gave us a good prediction of pIC50 for our tri-heterocyclic series which reinforce the validation of this model for the pIC50 prediction of external set compounds. ∗ † Intervenant Auteur correspondant: [email protected] 132 Communication par affiche Poster P Study of large-scale conformational transitions in c-Abl at the free energy level via a structure-based model Ilaria Mereu 1 ∗† 1 Karlsruhe Institute of Technology [Eggenstein-Leopoldshafen] (KIT) – Campus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen, Allemagne The c-Abl protein is a non-receptor tyrosine kinase of primary relevance in cancer research. It is regulated by a complex interplay of conformational transitions that are currently difficult to simulate in full atomistic detail for free energy calculation purposes. The computational approach of structure-based models, though, makes an efficient study of conformational transitions of large amplitude feasible, even with limited computational resources. We integrated a highly accurate, non-standard structure-based model (that we previously contributed to develop) with the metadynamics method for enhanced sampling. This protocol was applied to a rich set of conformational transitions that take place in the regulation process of c-Abl 1b (the activation loop opening, the DFG motif flip, the displacement of the SH2 and SH3 domains, the hinge motion and others) and gave us access to the free energy profile associated to each transition. This work compares three constructs of increasing length: the isolated kinase domain (kd), SH2+kd and SH3+SH2+kd. The performance of the model on three constructs at the free energy level was compared with the aim of elucidating the role of each domain and conformational transition in c-Abl activation mechanism. ∗ † Intervenant Auteur correspondant: [email protected] 133 Communication par affiche Poster P Cartographie des interactions atomiques dans le filament de dystrophine Dominique Mias-Lucquin ∗ 1 , Olivier Delalande 1 , Elisabeth Le Rumeur 1 , Anne-Elisabeth Molza 1 , Jean-Francois Hubert 1 1 IGDR – Universite de Rennes 1, CNRS : UMR6290 – France La dystrophine est une protéine de très grande taille (427kDa) qui a pour rôle de maintenir la cohésion du sarcolemme au cours des cycles de contractionélongation du muscle. Le domaine central de la protéine est constitué de 24 répétitions repliées en faisceaux d’hélices alpha de type spectrine. Dans les hélices, la succession d’acides aminés hydrophobes tous les 3 et 4 résidus en alternance définit les heptades qui permettent le repliement en faisceaux des trois hélices A, B et C d’une même répétition. La récente résolution de modèles structuraux par flexible fitting sous contraintes expérimentales de diffusion des rayons X aux petits angles (SAXS) nous permet d’atteindre un niveau de compréhension atomique pour les propriétés structurales et dynamiques du faisceau d’hélices qui confèrent à la dystrophine sa fonction de préservation du muscle. Nous avons développé un outil d’analyse des interactions atomiques (Dys-CCC) qui nous permet d’établir une cartographie précise des interactions hydrophobes, des liaisons hydrogènes et des ponts salins, au sein du domaine central de la dystrophine. Sur la base d’une carte de proximité spatiale et de mesures de potentiels hydrophobes, Dys-CC génère différentes représentations graphiques complémentaires pour l’étude des contacts inter-hélices. Les premiers résultats obtenus mettent en évidence la prédominance des interactions hydrophobes entre hélices d’une même répétition, parfois renforcées par des liaisons hydrogènes ou ponts salins. Même si les interactions hydrophobes s’organisent principalement autour d’une heptade de résidus, des variations existent autour de ce motif et pourraient expliquer la diversité structurale obesrvée tout au long du filament que compose le domaine central de la dystrophine. Dys-CCC est basé sur la bibliothèque Pynteract développée dans le laboratoire. Cette API peut également être utilisée pour traiter des interactions au sein de complexes moléculaires (contacts intermoléculaires), comme pour l’analyse de résultats de docking. ∗ Intervenant 134 Communication par affiche Poster P Développement d’une stratégie multi-échelle combinant des données expérimentales et in silico pour la reconstruction de complexes impliquant la dystrophine. Anne-Elisabeth Molza ∗† 1 , Khushdeep Manga 2 , Olivier Delalande 1 , Nicolas Ferey 3 , Marc Baaden 4 , Chantal Prevost 4 , Sébastien Fiorucci 5 , Mirjam Czjzek 6 , Nick Menhart 2 , Denis Chrétien 1 , Elisabeth Le Rumeur 1 , Jean-François Hubert 1 1 IGDR, Université Rennes 1 – CNRS : UMR6290, Universite de Rennes 1 – Rennes, France 2 Illinois Institute of Technology – Chicago IL, États-Unis 3 LIMSI (3) – CNRS : UPR3251 – CNRS UPR 3251- IUT d’Orsay, Université PARIS XI, Paris, France 4 Laboratoire de Biochimie Théorique - Institut de Biologie Physico-Chimique – CNRS : UPR9080, Université Paris VII - Paris Diderot – Institut de Biologie Physico-Chimique 13, rue Pierre et Marie Curie, F-75005 Paris, France 5 Institut de Chimie de Nice (5) – CNRS : UMR7272, Université Nice Sophia Antipolis [UNS], Université Nice Sophia Antipolis (UNS) – Faculté des Sciences Parc Valrose 28 Avenue Valrose 06108 Nice cedex 2, France 6 Station Biologique de Roscoff – CNRS : UMR8227 – Roscoff, France La dystrophine est une très grande protéine sous-sarcolemmique de 427kDa codée le gène DMD. Cette protéine joue un rôle essentiel dans le maintien de l’intégrité de la cellule musculaire lors des cycles de contraction/relaxation. La dystrophine est composée de quatre principaux domaines structuraux dont le domaine central composé de 24 répétitions et quatre charnières. Chaque répétition est organisée en faisceau de trois -hélices homologues à la spectrine et appelé “ coiled-coil ”. Des mutations du gène DMD sont à l’origine des myopathies de Duchenne et de Becker, lesquelles s’accompagnent de ruptures fréquentes de la membrane des cellules musculaires. Malgré le rôle important que joue la dystrophine, il existe peu de données sur sa structure et ses interactions avec ses principaux partenaires cellulaires. Afin de pallier à ce manque, nous avons développés une approche multi-échelle combinant des données expérimentales et des données in silico [1]. Cette méthodologie nous a permis d’une part d’obtenir des modèles tout-atome de fragments de la dystrophine native et mutée, en se basant sur des données de diffusion des rayons X aux petits angles (SAXS) et des méthodes de simulations interactives. ∗ † Intervenant Auteur correspondant: 135 Communication par affiche Poster P D’autre part, nous avons utilisés des méthodes d’amarrage moléculaires afin d’obtenir des modèles de complexes impliquant l’actine filamenteuse (actine-F) ou le domaine PDZ de la nNOS (nNOS-PDZ) avec les répétitions R11-15 ou R16-17 de la dystrophine native ou de mutants BMD de la protéine. Cette stratégie a permis de reconstruire un modèle tout-atome du complexe macromoléculaire impliquant les répétitions R11-17 de la dystrophine, l’actine-F, nNOS-PDZ et les phospholipides membranaires. 1. Molza, A.-E. et al. (2014) Faraday Discuss. 169, 45–62 136 Communication par affiche Poster P Analysis of protein structure and dynamics to better understand their functional mechanisms Damien Monet ∗ 1 , Nathan Desdouits 1 , Michael Nilges 1 , Arnaud Blondel 1 1 Unité de Bioinformatique structurale – CNRS : UMR3528, Institut Pasteur de Paris – 28, rue du Docteur Roux - 75724 Paris Cedex 15, France In many cases, proteins exert their function through internal motions. Accurate understanding of protein functional mechanisms can be useful, for example, to elaborate innovative inhibition strategies attempting to use small molecules to block protein motions. This approach is illustrated on two targets involved in different pathologies, the Rift Valley Fever Virus envelope protein (Gc), and the nicotinic Acetylcholine Receptors (nAChRs), which both act through large functional transitions. Analysis of cavities on molecular dynamics of Gc helped us to find molecular levers on its action mechanism. nAChRs have been studied for decades, but solving their structures remains a challenge. To tackle this class of targets we first needed to build high quality comparative models for both the open and closed forms of the same protein sequence. For that we devised a specific approach gathering and sorting the information from known structures of many different homologuous proteins in different states to selectively build models representing the active/inactive forms. These models will be used as starting points for transition path calculations by the POE approach developed in the laboratory. ∗ Intervenant 137 Communication par affiche Poster P Conformational properties and transport of glucose by GLUT1 using in silico approaches Matthieu Ng Fuk Chong ∗† 1 , Catherine Etchebest‡ 1 1 Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB) – Université Paris Diderot, Sorbonne Paris Cité, INTS, Inserm : UMRS1134 – 6 rue Alexandre Cabanel, 75739 Paris cedex 15, France Glucose is an essential source of energy for the mammalian cells. Its transport is achieved by facilitative diffusion by the glucose transporter GLUT1 into erythrocytes and endothelial cells of the blood brain barrier. Thus, inactivating mutation or low expression of GLUT1 is medically important, as it will lead to a lack of glucose supply to the brain. On the other hand, the expression levels of GLUT1 are often elevated in malignant cells due to the accelerated metabolism and high glucose requirements of the cells. GLUT1 belongs to the family of sugar transporter, a subfamily of the major facilitator superfamily (MFS). The MFS transporters are known to alternate between different conformational states in which access to the central binding site is switched from the extracellular medium (outward open conformation) to the intracellular compartment (inward open conformation) in order to transport a substrate across the plasma membrane. Recently, a mutant form of GLUT1 was purified and structurally characterized by X-ray crystallography [1]. The structure was trapped in an inward-open state with a molecule of -nonyl glucoside (BNG), a glucose-derivative, located within a cavity. Even if this atomic 3D structure is valuable, it does not allow to fully elucidate the transport mechanism of glucose by GLUT1. To address this question, we first modeled the 3D structure of the wild-type (WT) form using the crystal structure of the GLUT1 mutant. Then, we performed molecular dynamics simulations of the WT protein embedded in a POPC bilayer where the crystallized ligand was either replaced by a -D-glucose or suppressed. In the holo state (i.e. with a bound glucose in the central cavity), the glucose translocates out of the protein. In the cytoplasmic half of the channel, glucose interacts predominantly with polar or charged residues and underwent several rotations before leaving the binding site and exiting the protein. In the apo state (i.e. without glucose in the central cavity), the results of 1 µs equilibrium MD simulations of GLUT1 showed the partial closure of the cytoplasmic end of the protein. This state was similar to the intermediate state, namely the occluded state seen in the bacterial homologue XylE, in which the solvated central cavity is inaccessible from either side of the membrane. For the first time, these results enlighten the role of the different amino acids in the conformational changes and in the translocation mechanism. 1. Deng D, Xu C, Sun P, Wu J, Yan C, et al. (2014) Crystal structure of the human glucose transporter GLUT1. Nature 510: 121-125. ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] † 138 Communication par affiche Poster P As-Rigid-As-Possible interpolation for structural biology Minh Khoa Nguyen 1 ∗† 1 , Léonard Jaillet 1 , Stephane Redon 1 INRIA Rhône-Alpes (INRIA Grenoble Rhône-Alpes) – INRIA – ZIRST 655 Avenue de l’Europe Montbonnot 38334 Saint Ismier cedex, France Finding the transition pathway or minimum energy path (MEP) between two conformations is a complicated problem in structural biology, because the search space typically has high dimension. Methods such as Nudged Elastic Band (NEB) [1] and zero temperature string [2] search for a MEP from an initial guess of the pathway. A common way to choose the initial guess is to use the linear interpolation between the start and goal conformations. However, such a guess does not necessarily give a realistic path, and it has been shown that it can lead to low convergence or failure of the chosen method [3]. In the field of computer graphics, methods for interpolating between a complicated shape and a deformed version of it have been applied to find a smooth and realistic motion between two poses of a figure [4] [5] [6]. Inspired by this research, we apply the As-Rigid-As-Possible (ARAP) interpolation between two given conformations. This method attempts to preserve the rigidity of the structure, i.e. changes in bond lengths and angles are minimized as much as possible during the interpolation process. Consequently, the interpolation creates a series of low-change-of-energy transitions from one conformation to another. This method can find a good initial guess for other algorithms such as NEB. In our method, a large molecule is divided into smaller connected regions. The amount of rotation of each region is calculated from two given conformations and then interpolated. The interpolated image of the entire molecule is a result of combining all individual interpolations. As a result, this method produces little local deformations. For evaluation purposes, this method is compared with linear interpolation. NEB is applied to minimize the energy of the initial guesses obtained by ARAP interpolation and linear interpolation. The tests were performed on the folding of a graphene sheet into a nanotube, as well as a few other benchmarks. Results show that the initial guess produced by the ARAP interpolation method gives an appropriate transition path in a shorter time than that from linear interpolation. Our method has several advantages: force field independence, low energy changes along the pathway due to local rigidity preservation, and high parallelization capability. It will be applied to more complicated molecules such as proteins and RNA in the future. References: H. Jónsson, G. Mills, K. W. Jacobsen, “Nudged Elastic Band Method for Finding Minimum En∗ † Intervenant Auteur correspondant: [email protected] 139 Communication par affiche Poster P ergy Paths of Transitions,” Classical and Quantum Dynamics in Condensed Phase Simulations, ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998), 385. E. Weinan, W. Ren, E. Vanden-Eijnden, “Simplified and improved string method for computing the minimum energy paths in barrier-crossing events,” The Journal of Chemical Physics (2007), 126 (16), 164103. B. Peters, A. Heyden, AT. Bell, A. Chakraborty, “A growing string method for determining transition states: comparison to the nudged elastic band and string methods,” The Journal of Chemical Physics (2004), 120(17), 7877-7886. O. Sorkine, M. Alexa, “As-rigid-as-possible surface modeling,” In Proceedings of the fifth Eurographics symposium on Geometry processing (SGP ’07). Eurographics Association, Aire-la-Ville, Switzerland, Switzerland, 109-116. Z. Zhang, G. Li, H. Lu, Y. Ouyang, M. Yin, C. Xian, “Fast as-isometric-as-possible shape interpolation,” Computers & Graphics (2015), 46, 244-256. W. Baxter, P. Barla, K. Anjyo. “Rigid shape interpolation using normal equations,” In Proceedings of the 6th international symposium on Non-photorealistic animation and rendering (NPAR ’08). ACM, New York, NY, USA, 59-64. 140 Communication par affiche Poster P What wins in determining protein regular secondary structures? The polar/non polar binary pattern or the intrinsic amino acid composition? A statistical analysis using the HCA approach. Joseph Rebehmed ∗ 1 , Jean-Paul Mornon 1 , Isabelle Callebaut† 1 1 Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC) – Institut de recherche pour le développement [IRD] : UR206, Université Pierre et Marie Curie (UPMC) - Paris VI, CNRS : UMR7590, Muséum National d’Histoire Naturelle (MNHN) – Tour 23 - Barre 22-23 - 4e étage BC 115 4 place Jussieu 75252 PARIS, France The intrinsic preferences of a polypeptidic chain to form -helices or -strands can be overwhelmed by the polar/nonpolar periodicity and the drive to form amphiphilic structures capable of burying hydrophobic surface area. As a consequence, the precise identity of a amino acid at a particular location in a sequence may be less important than the simple choice of whether it is polar or nonpolar. In this study, we considered two sets of 3D structures extracted from the SCOP database (classes a, b, c, d, e) at two levels of redundancy (ASTRAL 95 and ASTRAL 40) in order to clarify the roles played respectively by binary patterns and amino acid compositions in the formation of regular secondary structures (RSS). We considered HCA-derived hydrophobic clusters (HC), which are constrained binary patterns particularly well fitting RSS limits, to investigate the preferences of binary patterns towards RSS and estimate the influence of amino acid composition. We first used a “Quark” code, to decompose each HC into its basic units and thereby evaluate how its main periodicity correlates with its main state in terms of RSS. Results showed that -helices are more permissive to -strand patterns than -strands are to -helix patterns. Then, we calculated the propensities of amino acids for the different states of secondary structures, considering all the RSS associated with each HC or distinguishing between -helices and strands. Concordant and discordant behaviors are then assigned following the agreement/disagreement of the observed RSS with that expected from the HC dictionary. In agreement with previous reports, three classes of amino acids are highlighted, with preferences for -helices (A,L,M,E,Q,K,R), -strands (V,I,F,W,Y,C,T) and coils (P,G,D,N,S). Histidine (H) has quasi-equal preferences for the three states. On this basis, distinct behaviors can be highlighted between the concordant and discordant HC. In “-strand” HC, the weight of aliphatic hydrophobic amino acids appears to be prominent for shifting from a concordant to a discordant behavior, whereas in “-helix” HC, all the amino acids with preferences for -helices globally decrease at the benefit of non-hydrophobic ∗ † Intervenant Auteur correspondant: [email protected] 141 Communication par affiche Poster P amino acids with preference for -strands and coils. Altogether, our results enlighten the respective role played by binary pattern and amino acid composition for RSS formation. The original approach described here could complement the currently available methods to predict secondary structures in proteins and could assist protein engineering and design, from the only information of a single amino acid sequence. 142 Communication par affiche Poster P Molecular features switching off the melatonin-induced activity from MT1 to GPR50 receptors Nicolas Renault ∗† 1 , Xavier Laurent 1 , Nathalie Clement 2 , Jean-Luc Guillaume 2 , Amaury Farce 1 , Ralf Jockers 2 , Philippe Chavatte 1,3 1 Faculté des Sciences Pharmaceutiques de Lille – Université Lille 2 - LIRIC U995 Inserm – 3, rue du Professeur Laguesse - 59000 Lille, France 2 Institut Cochin – CNRS : UMR8104, Inserm : U1016, Université Paris V - Paris Descartes – 22 rue Méchain, 75014 Paris, France 3 Institut de Chimie Pharmaceutique Albert Lespagnol – Université Lille II - Droit et santé – 3, rue du Professeur Laguesse. 59000 LILLE, France Recent crystal structures of G protein-coupled receptors (GPCRs) highlight the previously unappreciated role of the second extracellular loop (E2) in ligand binding, ligand gating or receptor activation. In agreement with functional in vitro assays, molecular dynamics simulations reveal the critical role of E2 in activation of the melatonin MT1 receptor and in inactivation of the closely related orphan GPR50 receptor. ∗ † Intervenant Auteur correspondant: [email protected] 143 Communication par affiche Poster P Coarse-Graining Parameterization of Specific Cardiac Membrane Lipids Edithe Selwa 1 ∗ 1 , Bogdan Iorga 1 Institut de Chimie des Substances Naturelles (ICSN) – CNRS : UPR2301 – Avenue de la terrasse 91198 Gif sur yvette cedex, France Recently, a Cardiac Targeting Peptide (CTP) [1] was shown to be able to transduce specifically the myocardium and can be used as a new strategy to deliver therapeutic drugs in the framework of treating heart failure [2,3]. Our general aim is to understand how CTP interacts and penetrates the cardiomyocyte membrane by molecular dynamics simulations. However, simulation of such large biological systems is challenging, because of the multitude of spatial and temporal scales involved. Biological processes, such as self-assembly of lipid bilayers, remain inaccessible by all-atom simulations, since these time-consuming approaches are computationally expensive. Coarse grained (CG) models, which have gained a lot of popularity lately, overcome these limits, by replacing full-atomistic details by lower resolution particles, while retaining chemical specificity. In this work, given the complexity and the size of the system, we have used a CG representation of the system components, based on MARTINI force field [4,5]. We have parameterized a number of missing molecules using this force field, and then generated a realistic model of the cardiomyocyte membrane that will be used in the future for the study of the interaction with CTP. ∗ Intervenant 144 Communication par affiche Poster P Prediction of peptide conformational stability Marie Amandine Laurent 1 , Raphael Licha 1 , Jananan Pathmanathan 1 , Jacques Chomilier 1 , Dirk Stratmann ∗ 1 1 Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC) – Institut de recherche pour le développement [IRD] : UR206, Université Pierre et Marie Curie (UPMC) - Paris VI, CNRS : UMR7590, Muséum National d’Histoire Naturelle (MNHN) – Tour 23 - Barre 22-23 - 4e étage BC 115 4 place Jussieu 75252 PARIS, France Protein-protein interactions play a key role in biological functions. Their inhibition become an important issue for drug design. Peptides are suitable candidates to target specific interactions especially if they are extracted from the interaction interface. Among these protein fragments, Tightened End Fragments (TEF) (**) have the advantage to be potentially more stable in terms of their conformation. This should confer them a better affinity. A TEF is not unique at the interaction interface and the choice can be optimized in term of stability and affinity. Our study is about the aspect of conformational stability. Using molecular dynamics simulations, we developed a protocol for peptide conformational stability prediction. To validate our method, we assembled a benchmark of peptide structures associated with protein fragments. Our method succeeds in distinguishing stable from unstable peptides. In addition, it allowed us to identify some fragments that are stable outside the protein. (**) http://www.impmc.upmc.fr/software/tef ∗ Intervenant 145 Communication par affiche Poster P Dynamique d’assemblage de la capside des norovirus Thibault Tubiana ∗† 1,2 , Stéphane Bressanelli‡ 1,2 , Yves Boulard§ 1,2 1 Institut de Biologie Intégrative de la Cellule (I2BC) – CNRS : UMR9198 – Bâtiment 21 Avenue de la Terrasse 91190 Gif-sur-Yvette Cedex, France 2 Institut de Biologie et de Technologies de Saclay (IBITECS / SB2SM) – CEA – CEA Saclay bat 532 91191 Gif sur Yvette cedex, France Les norovirus sont des petits virus non enveloppés à ARN simple brin de polarité positive. Ils sont la cause principale des gastroentérites virales aigues chez les humains et les animaux et présentent un intérêt mondial pour la santé. Leur capside est composée de 180 copies d’une seule protéine structurale VP1 composée de deux domaines principaux : le domaine shell (S) et le domaine protruding (P) qui contient 2 sous domaines (P1 et P2)[1]. Le domaine P est la partie exposée au milieu biologique, il permet notamment de stabiliser et d’ajuster la taille de la capside[2]. Le domaine S quant à lui est le module d’assemblage de la capside virale[2]. Des études ont montré que les capsides de certains norovirus (NB2-VLP, NV-VLP) peuvent être désassemblées et réassemblées in vitro selon le pH du milieu[3] et que l’assemblage de NB2VLP (NewBury2 – Virus-Like particles) à partir de dimères de VP1 est un processus en deux étapes : une apparition rapide d’intermédiaires moléculaires puis une formation lente de la capside, ce qui est en désaccord avec les modèles actuels d’assemblage de capside[4]. Ces études nous conduisent à l’hypothèse que le bras N-terminal serait un bon candidat dans la stabilisation allostérique des intermédiaires et que la (dé)protonation de certains résidus serait impliquée dans l’assemblage ou le désassemblage (dépendant au pH) de la capside in vitro. A l’aide d’approches computationnelles, nous cherchons donc à étendre ces études cinétiques aux norovirus humains et ainsi à déterminer les bases moléculaires du mécanisme physique original d’assemblage des norovirus. Des techniques de bioinformatique telles que des alignements de séquences et modélisations par homologie ont été appliquées afin d’obtenir une structure tridimensionnelle du dimère de NB2-VP1 (Génogroupe III), basée sur la structure cristallographique de son homologue du génogroupe I : le Norwalk Virus (1IHM[1]). Ce modèle a ensuite été utilisé dans des simulations de dynamique moléculaire et de recuits simulés afin d’analyser le comportement du bras N-terminal dans un environnement aqueux. Nos résultats préliminaires étendent les études réalisées auparavant dans l’équipe [3,4]. Ces résultats montrent que sous sa forme déprotonée le bras N-terminal établit de nombreuses interactions polaires de type pont-salins permettent sa stabilisation sous le domaine S de la protéine. Ces pont-salins ont ensuite été neutralisés par protonation des acides aminés acides impliqués dans ∗ Intervenant Auteur correspondant: [email protected] ‡ Auteur correspondant: [email protected] § Auteur correspondant: [email protected] † 146 Communication par affiche Poster P4 l’interaction afin d’étudier l’importance de ces liaisons pour la stabilité du bras N-terminal. 1. Prasad BV V. X-ray Crystallographic Structure of the Norwalk Virus Capsid. Science (80- ). 1999;286: 287–290. doi:10.1126/science.286.5438.287 2. Bertolotti-Ciarlet A, White LJ, Chen R, Prasad BV V., Estes MK. Structural Requirements for the Assembly of Norwalk Virus-Like Particles. J Virol. 2002;76: 4044–4055. doi:10.1128/JVI.76.8.40444055.2002 3. Tresset G, Decouche V, Bryche J-F, Charpilienne A, Le Cœur C, Barbier C, et al. Unusual self-assembly properties of Norovirus Newbury2 virus-like particles. Arch Biochem Biophys. Elsevier Inc.; 2013;537: 144–52. doi:10.1016/j.abb.2013.07.003 4. Tresset G, Le Coeur C, Bryche J-F, Tatou M, Zeghal M, Charpilienne A, et al. Norovirus capsid proteins self-assemble through biphasic kinetics via long-lived stave-like intermediates. J Am Chem Soc. 2013;135: 15373–81. doi:10.1021/ja403550f 147 Communication par affiche Poster P Identification and automated weighting of ensemble-averaged NOE restraints Silke Wieninger ∗ 1 , Beat Vögeli 2 , Nelly Morellet 3 , Benjamin Bardiaux 1 , Guillaume Bouvier 1 , Michael Nilges 1 1 3 Bioinformatique Structurale – Institut Pasteur de Paris – France 2 Laboratory of Physical Chemistry, ETH Zürich – Suisse Institut de Chimie des Substances Naturelles – Centre de Recherches de Gif – France NMR data represent a time and ensemble average. Accordingly, not all restraints derived from NMR experiments can be fulfilled by a single structure. To avoid introducing errors and to estimate the dynamical behavior of the protein, ensemble calculations are performed, which model a few conformations simultaneously. By treating only a subset of the NOEs as ensemble restraints instead of the full restraint set, we reduce the risk of data overfitting. We identify mutually incompatible restraints by generating a large set of conformations in a conventional ARIA run[1]. Clustering of the conformations using self-organizing maps[2,3] enables us to assign the restraints to different classes, which are weighted automatically during the ensemble ARIA run, based on the deviation of the atom distances from the NOE target distances[4]. Exemplary, we determine the structure of the 56-residue protein GB3, the third immunoglobulin binding domain of protein G, taking advantage of an extensive set of exact NOEs[5]. On another system, the piggyBac transposase, we show that the ensemble strategy allows to identify conformations which cannot be obtained using standard structure determination protocols. W Rieping, M Habeck, B Bardiaux, A Bernard, TE Malliavin, M Nilges (2007), Bioinformatics, 23:381-382. T Kohonen (2013), Neural Networks, 37:52-65. G Bouvier, N Duclert-Savatier, N Desdouits, D Meziane-Cherif, A Blondel, P Courvalin, M Nilges, TE Malliavin (2014), Chemical information and modeling, 54:289-301. M Habeck, W Rieping, M Nilges (2006), PNAS, 103:1756-1761. B Vögeli, S Kazemi, P Gntert, R Riek (2012), Nature structural and molecular biology, 19:10531057. ∗ Intervenant 148 Listes des auteurs Bouakouk-Chitti, Zohra, 106 Boukhenouna, Samia, 95 Boulard, Yves, 146 Bourg, Stéphane, 26, 100, 109 Bouvier, Guillaume, 76, 85, 148 Braka, Abdennour, 100 Branlant, Guy, 38, 91, 95 Bressanelli, Stéphane, 146 Broutin, Isabelle, 69 Brut, Marie, 102 Bui, Linh Chi, 90, 93 Bureau, Ronan, 53 Busca, Patricia, 55 Abdellatif, Nadhir, 83 Abi Hussein, Hiba, 59 Aci-Sèche, Samia, 34, 100 Agbulut, Onnik, 93 Aghajari, Nushin, 37 Allain, Fabrice, 74 Allouche, David, 45, 98 Alvarez, Pablo, 105 Amillastré, Emilie, 105 André, Isabelle, 45, 96, 98, 105 Andre-Leroux, Gwenaëlle, 130 Antonczak, Serge, 65, 113, 119 Archontis, Georgios, 103 Artemova, Svetlana, 83 Asencio Hernández, Julia, 39 Aubert, Marc, 83 Audit, Edouard, 103 Callebaut, Isabelle, 141 Cambon, Emmanuelle, 96 Camproux, Anne-Claude, 59, 121 Carrique, Loic, 37 Castaing, Bertrand, 26, 109 Cerdan, Rachel, 27 Charpentier, Emmanuelle, 119 Chatron, Nolan, 24 Chauvot De Beauchene, Isaure, 79 Chavatte, Philippe, 143 Chavent, Matthieu, 67 Cherfils, Jacqueline, 22 Cheron, Jean-Baptiste, 113, 119, 121 Chomienne, Christine, 90 Chomilier, Jacques, 145 Chrétien, Denis, 135 Clement, Nathalie, 143 Coadou, Gaël, 28 Colin, Sabrina, 30 Colloc’h, Nathalie, 89 Cools, Jan, 90 Cortes, Isidro, 85 Cortes, Juan, 114 Costa, Mauricio, 104, 123 Coste, Franck, 26, 109 Cragnolini, Tristan, 118 Crouzy, Serge, 115 Culard, Françoise, 26, 109 Czjzek, Mirjam, 135 Baaden, Marc, 117, 118, 135 Ballut, Lionel, 37 Baltus, Christine B., 132 Banarès, Jean-Louis, 123 Barakat, Fatima, 111 Barbault, Florent, 55 Barbe, Sophie, 45, 96, 98, 105 Bardiaux, Benjamin, 74, 148 Batista, Paulo R., 104 Baud, Stéphanie, 112 Bazgier, Václav, 132 Belloy, Nicolas, 119 Becker, Hubert F., 51 Ben Ouirane, Kaouther, 69 Bender, Andreas, 85 Benoit, Etienne, 24 Berka, Karel, 132 Bersweiler, Antoine, 38, 91 Best, Robert, 61 Bisch, Paulo M., 104 Blondel, Arnaud, 137 Blumberger, Jochen, 61 Boitard, Solène, 93 Bonnet, Pascal, 26, 34, 100 Borrel, Alexandre, 59 Bosc, Nicolas, 34 Boschi-Muller, Sandrine, 30, 88 Damian, Marjorie, 123 149 Gageat, Cédric, 118, 125 Gaillard, Thomas, 43 Garkavenko, Maria, 126 Garnier, Norbert, 26, 100, 109 Gate, Jocelyn, 83 Gelly, Jean-Christophe, 81 Geneix, Colette, 59 Ghouzam, Yassine, 81 Gloaguen, Céline, 53 Goffinont, Stéphane, 26, 109 Golebiowski, Jérôme, 65, 113, 119 Grudinin, Sergei, 77, 83, 126 Guca, Ewelina, 27 Gueroult, Marc, 105 Guichou, Jean-François, 27 Guidez, Fabien, 90 Guillaume, Jean-Luc, 143 Guyon, Frédéric, 57 Daniellou, Richard, 28 Dauchez, Manuel, 112, 119 David, Benoît, 63 De Brevern, Alexandre, 81 De Givry, Simon, 98 De March, Claire, 119 De Sancho, David, 61 De Vecchis, Dario, 117 De Vries, Sjoerd, 79 Debiec, Hanna, 107 Dejaegere, Annick, 52, 62 Delalande, Olivier, 134, 135 Delamar, Michel, 55 Delarue, Patrice, 111 Delsuc, Marc-André, 39 Dementin, Sébastien, 35, 94 Derreumaux, Philippe, 118, 125 Desdouits, Nathan, 137 Diharce, Julien, 65 Djaout, Kamel, 51 Dobbek, Holger, 94 Domnik, Lilith, 94 Donald, Bruce, 45 Douguet, Dominique, 50 Doutreligne, Sébastien, 118 Druart, Karen, 103 Duncan, Anna, 67 Duneau, Jean-Pierre, 70 Dupret, Jean-Marie, 90, 93 Duquesne, Sophie, 105 Durant, Laeticia, 90 Duval, Romain, 90 Hélie, Jean, 67 Hénin, Jérôme, 117 Hadj-Said, Jessica, 35, 94 Hilvert, Donald, 42 Hoh, François, 27 Hu, Rongjing, 55 Hubert, Jean-François, 134, 135 Iorga, Bogdan, 107, 144 Isenberg, Tobias, 73 Jacob, Christophe, 95 Jaillet, Léonard, 83, 139 Jockers, Ralf, 143 Jorda, Radek, 132 Eberhardt, Jérôme, 62 Emonard, Hervé, 119 Etchebest, Catherine, 69, 138 Etique Nicolas, 119 Katava, Marina, 128 Kauffmann, Brice, 29 Kazennov, Andrei, 126 Kellou-Taïri, Saf a, 106 Krebs, Fanny, 52 Kriznik, Alexandre, 38, 91 Kryštof, Vladimír, 132 Kubas, Adam, 61 Farce, Amaury, 143 Fehrentz, Jean-Alain, 123 Ferber, Mathias, 76 Ferey, Nicolas, 135 Fiorucci, Sébastien, 65, 113, 135 Flatters , Delphine, 121 Floquet, Nicolas, 104, 123 Fogha, Jade, 53 Fourmond, Vincent, 35, 94 Léger, Christophe, 35, 94 Lafite, Pierre, 28 Lambert, Eléonore, 112 Langenfeld, Florent, 24 150 Narth, Christophe, 71 Neveu, Emilie, 77 Ng Fuk Chong, Matthieu, 138 Nguyen, Khoa, 83 Nilges, Michael, 74, 76, 85, 137, 148 Lattard, Virginie, 24 Laurent, Marie Amandine, 145 Laurent, Xavier, 143 Laurin, Yoann, 129 Le Guen, Yann, 96 Le Rumeur, Elisabeth, 134, 135 Lec, Jean-Christophe, 30, 88 Legeai-Mallet, Laurence, 55 Li, Yan, 55 Licha, Raphael, 145 Limoges, Benoit, 29 Louet, Maxime, 66 Oulyadi, Hassan, 28 Overington, John P., 85 Pandélia, Maria-Eirini, 35 Panel, Nicolas, 43 Pasco-Brassart, Sylvie, 112 Pasquali, Samuela, 118, 125 Pathmanathan, Jananan, 145 Perahia, David, 104, 123 Petit, Emile, 90 Petitjean, Michel, 59 Piquemal, Jean-Philip, 71 Popov, Petr, 77 Postic, Guillaume, 81 Poulain, Laurent, 53 Prangé, Thierry, 89 Prestat, Guillaume, 55 Prevost, Chantal, 129, 135 Prié, Gildas, 132 Malliavin, Therese, 85 Manga, Khushdeep, 135 Mano, Nicolas, 29 Marie, Jacky, 123 Marot, Christophe, 132 Marques, Stéphanie, 28 Marroun, Sami, 28 Martinez, Jean, 104, 123 Martiny, Laurent, 119 Martiny, Virginie, 107 Marty, Alain, 105 Mary, Sophie, 123 Mathieu, Cécile, 90, 93 Maurel, François, 55 Mavre, François, 29 Mazon, Hortense, 30, 88, 91, 95 Menhart, Nick, 135 Mereu, Ilaria, 133 Merrouch, Meriem, 94 Meyer, Christophe, 34 Mias-Lucquin, Dominique, 134 Mignon, David, 43, 103 Molza, Anne-Elisabeth, 134, 135 Monet, Damien, 137 Montaut, Sabine, 28 Morellet, Nelly, 148 Mornon, Jean-Paul, 141 Moroy, Gautier, 57 Morris, May C., 104 Moulis, Claire, 96 Mulard, Laurence, 96 Munier-Lehmann, Hélène, 33 Myllykallio, Hannu, 51 Rahuel-Clermont, Sophie, 38, 91, 95 Rasolohery, Inès, 57 Raussin, Florent, 104 Rebehmed, Joseph, 141 Reddy, Tyler, 67 Redon, Stephane, 83, 139 Regad, Leslie, 59, 121 Remaud-Siméon, Magali, 96 Renault, Nicolas, 143 Renault, Pedro, 104 Rieux, Charlotte, 26, 109 Rinaldo, David, 48 Ritchie, Dave, 77 Robert, Charles, 129 Roberts, Kyle, 45 Rodrigues-Lima, Fernando, 90, 93 Rollin, Patrick, 28 Ronco, Pierre, 107 Sacquin-Mora, Sophie, 129 Salamone, Stéphane, 96 151 Sanejouand, Yves-Henri, 63 Sansom, Mark, 67 Santolini, Jérôme, 23 Savarin, Philippe, 129 Schiex, Thomas, 45, 98 Schuler, Marie, 28 Selwa, Edithe, 107, 144 Senac, Caroline, 121 Senet, Patrick, 111 Sidore, Marlon, 70 Simoncini, David, 98 Simonson, Thomas, 43 Sopkova-De-Oliveira Santos Jana, 53 Sterpone, Fabio, 128 Stines-Chaumeil, Claire, 29 Stote, Roland, 52, 62 Stratmann, Dirk, 145 Strick, Terence, 32 Sturgis, James, 70 Tellier, Charles, 63 Toledano, Michel, 95 Traore, Seydou, 45, 98 Tubiana, Thibault, 146 Talfournier, François, 30, 88 Taly, Antoine, 117, 118 Tatibouet, Arnaud, 28 Tchertanov, Luba, 24 Yengui, Mohamed, 83 Zacharias, Martin, 79 Zhang, Rhuizheng, 55 Vögeli, Beat, 148 Van Westen, Gerard J.P., 85 Verges, Alizée, 96 Verzeaux, Laurie, 119 Vial, Henri, 27 Viaud-Massuard, Marie-Claude, 132 Violot, Sébastien, 37 Viricel, Clément, 98 Voisin-Chiret, Anne Sophie, 53 Vos, Marten, 51 Wang, Po-Hung, 61 Wieninger, Silke, 148 Wroblowski, Berthold, 34 152 Liste des participants ABI HUSSEIN Hiba BARAKAT Fatima MTi – Inserm – UMR‐S 973 Université Paris Diderot‐Paris 7 Bât Lamarck A, 4e‐5e étage , Courrier 7113 35, rue Hélène Brion 75205 PARIS Cedex 13 France hiba.abihussein@univ‐paris‐diderot.fr Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 6303 CNRS – Université de Bourgogne 9, avenue A. Savary, BP 47870 21078 DIJON Cedex France fatima.barakat@u‐bourgogne.fr ACI‐SÈCHE Samia BARBAULT Florent Institut de Chimie organique et Analytique Université d'Orléans – Pôle de chimie Rue de Chartres ‐BP 6759 45067 ORLEANS Cedex 2 France samia.aci@cnrs‐orleans.fr ITODYS, UMR 7086 Université Paris Diderot 15, rue J‐A de Baïf 75205 PARIS France florent.barbault@univ‐paris‐diderot.fr ALLAIN Fabrice BARBE Sophie Unité de Bioinformatique Structurale CNRS UMR3528 Institut Pasteur 25‐28, rue du Docteur Roux 75015 PARIS France [email protected] Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) INSA/CNRS 5504 – UMR INSA/INRA 792 135, avenue de Rangueil 31077 TOULOUSE Cedex 04 France sophie.barbe@insa‐toulouse.fr ANDRE Isabelle BAUD Stéphanie Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) INSA/CNRS 5504 – UMR INSA/INRA 792 135, avenue de Rangueil 31077 TOULOUSE Cedex 04 France isabelle.andre@insa‐toulouse.fr SiRMa – UMR CNRS/URCA N° 7369 Plateau de Modélisation Moléculaire Multi‐ échelle – UFR Sciences Exactes et Naturelles, Moulin de la Housse 51687 REIMS Cedex 2 France stephanie.baud@univ‐reims.fr BAADEN Marc BELLOY Nicolas Laboratoire de Biochimie Théorique – CNRS UPR9080 Institut de Biologie Physico‐Chimique (IBPC) 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] Plateau de Modélisation Moléculaire Multi‐ échelle Université de Reims Champagne‐Ardenne UFR SEN, Campus Moulin de la Housse 51687 REIMS France nicolas.belloy@univ‐reims.fr 153 BEN OUIRANE Kaouther BRAKA Abdennour INSERM UMR_S 1134,DSIMB Université Paris Diderot‐ Paris 7 INTS 6, rue Alexandre Cabanel 75739 PARIS Cedex 15 France [email protected] Institut de Chimie Organique et Analytique Université d'Orléans – Pôle de chimie Rue de Chartres – BP 6759 45067 ORLEANS Cedex 2 France abdennour.braka@univ‐orleans.fr BLUMBERGER Jochen BRUT Marie Department of Physics and Astronomy University College London Gower Street LONDON WC1E 6BT, UK Grande‐Bretagne [email protected] Laboratoire analyse et architecture des systèmes (LAAS) – CNRS 7, avenue du Colonel Roche BP 54200 31031 TOULOUSE Cedex 4 France [email protected] BOSC Nicolas BUI Linh Chi Institut de Chimie Organique et Analytique Université d'Orléans Rue de Chartres 45067 ORLEANS France nicolas.bosc@univ‐orleans.fr Unité Biologie Fonctionnelle et Adaptative CNRS UMR 8251 – Université Paris Diderot Bâtiment Buffon – 3ème étage – Pièce 348A 4, rue Marie‐Andrée Lagroua Weill Hallé 75205 PARIS Cedex 13 France linh‐chi.bui@univ‐paris‐diderot.fr BOSCHI‐MULLER Sandrine BUSI Florent IMoPA UMR 7365 CNRS‐UL – Equipe Enzymologie Moléculaire – Université de Lorraine – Faculté de médecine 9, avenue de la Forêt de Haye – CS 50184 54506 VANDOEUVRE‐LES‐NANCY Cedex France sandrine.boschi@univ‐lorraine.fr Unité Biologie Fonctionnelle et Adaptative CNRS UMR 8251 – Équipe des RMCX Université Paris Diderot Paris 7 4, rue Marie Andrée Lagroua Weill Hallé 75205 PARIS Cedex 13 France florent.busi@univ‐paris‐diderot.fr BOUVIER Guillaume CARRIQUE Loïc Bioinformatique structurale Institut Pasteur Unité de Bioinformatique Structurale CNRS UMR 3528 – Département de Biologie Structurale et Chimie 75015 PARIS France [email protected] Biocrystallography and Structural Biology of Therapeutic Targets Group Institute for the Biology and Chemistry of Proteins 7, passage du Vercors 69367 LYON Cedex 07 France [email protected] 154 CASTAING Bertrand CHAVENT Matthieu Centre de Biophysique Moléculaire UPR4301 CNRS Rue Charles Sadron 45071 ORLEANS Cedex 2 France castaing@cnrs‐orleans.fr Biochemistry Department SBCB unit South Park Road OXFORD OX1 3QU Grande‐Bretagne [email protected] CERDAN Rachel CHERFILS Jacqueline Dynamique des Interactions Membranaires Normales et Pathologiques – UMR5235 CNRS‐Université de Montpellier Place Eugène Bataillon – Bât 24 – cc107 34095 MONTPELLIER Cedex 5 France rachel.cerdan@univ‐montp2.fr Laboratoire de Biologie et Pharmacologie Appliquée CNRS – Ecole Normale Supérieure Cachan 61, avenue du Président Wilson 94235 CACHAN cedex France jacqueline.cherfils@ens‐cachan.fr CHALOIN Laurent CHERON Jean‐Baptiste Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) CNRS – Université de Montpellier 1919, route de Mende 34293 MONTPELLIER Cedex 5 France [email protected] Institut de Chimie de Nice UMR 7272, Université de Nice‐Sophia Antipolis – CNRS Parc Valrose 06108 NICE Cedex 2 France [email protected] CHATRON Nolan COLLOC'H Nathalie CMLA CNRS UMR 8536 ENS Cachan Bât. Laplace, 1er étage 61, av. du président Wilson 94235 CACHAN Cedex France nchatron@ens‐cachan.fr ISTCT UMR 6301 CNRS Université de Caen Centre Cyceron Bd Becquerel 14074 CAEN France [email protected] CHAUVOT DE BEAUCHENE Isaure CORTES Isidro Theoretical biophysics – Molecular dynamics TUM JamesFranceanck Strasse 1 85748 GARCHING Allemagne [email protected] Unité de Bioinformatique Structurale Institut Pasteur 25‐28, rue du Dr. Roux 75015 PARIS France [email protected] 155 CORTES Juan DE VECCHIS Dario Laboratoire analyse et architecture des systèmes (LAAS) – CNRS 7, avenue du Colonel Roche BP 54200 31031 TOULOUSE Cedex 4 France [email protected] Laboratoire de Biochimie Théorique – UPR 9080 Institut de Biologie Physico‐Chimique (IBPC) 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] CROUZY Serge DEKIMECHE Katia Chimie et Biologie des Métaux CEA 17, rue des martyrs 38054 GRENOBLE Cedex 9 France [email protected] Schrödinger GmbH Dynamostr. 13 D‐68165 MANNHEIM Allemagne [email protected] DAUCHEZ Manuel DELALANDE Olivier CNRS UMR 7369 MEDyC, P3M‐MaSCA Université de Reims Champagne‐Ardenne UFR Sciences Exactes et Naturelles Moulin de la Housse – BP1039 51687 REIMS Cedex 2 France manuel.dauchez@univ‐reims.fr Institut de Génétique et Développement de Rennes (IGDR) Université de Rennes 1 2, avenue du Professeur Léon Bernard 35000 RENNES France olivier.delalande@univ‐rennes1.fr DAVID Benoît DELSUC Marc‐André UFIP, UMR CNRS 6286 Université de Nantes UFR SCIENCES ET TECHNIQUES 2, rue de la Houssinière 44322 NANTES Cedex 03 France [email protected]‐nantes.fr Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) CNRS 1, rue LaurentFranceies 67404 ILLKIRCH France [email protected] DE LAMOTTE Frédéric DEMENTIN Sébastien UMR Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales INRA Avenue Agropolis – TA A‐108/03 34398 MONTPELLIER Cedex 5 France [email protected] Bioénergétique et Ingénierie des Protéines BIP6 CNRS 31, chemin Joseph Aiguier 13402 MARSEILLE Cedex 20 France [email protected] 156 DIHARCE Julien DUNEAU Jean‐Pierre Institut de Chimie de Nice, ICN UMR CNRS 7272 28, avenue Valrose 06108 NICE Cedex 2 France [email protected] Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM) CNRS – Aix‐Marseille Université 31, chemin Joseph Aiguier 13402 MARSEILLE Cedex 20 France [email protected] DJAOUT Kamel DUPRET Jean‐Marie Laboratoire d'Optique et Biosciences (LOB) Ecole Polytechnique Route de Saclay 91128 PALAISEAU France [email protected] Unité de Biologie Fonctionnelle et Adaptative Université Paris Diderot – CNRS UMR 8251 Bâtiment Buffon, 3ème étage 4, rue Marie Andrée Lagroua Weill Hallé 75205 PARIS Cedex 13 France jean‐marie.dupret@univ‐paris‐diderot.fr DOUGUET Dominique DUVAL Romain Institut de Pharmacologie Moléculaire et Cellulaire CNRS UMR7275 660, route des lucioles 06560 VALBONNE France [email protected] Unité Biologie Fonctionnelle et Adaptative Université Paris Diderot – CNRS UMR 8251 Bâtiment Buffon 4, rue Marie Andrée Lagroua Weill‐Hallé 75013 PARIS France [email protected] DOUTRELIGNE Sébastien EBERHARDT Jérôme Laboratoire de Biochimie Théorique CNRS 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] Modélisation Moléculaire IGBMC 1, rue LaurentFranceies BP 10142 67404 ILLKIRCH Cedex France [email protected] DRUART Karen FARCE Amaury Laboratoire de Biochimie (BIOC) Ecole Polytechnique Route de Saclay 91128 PALAISEAU France [email protected] Therapeutic innovation targetting inflammation – LIRIC – UMR 995 Inserm Faculté de Médecine – Pôle Recherche Place Verdun 59045 LILLE Cedex France amaury.farce‐2@univ‐lille2.fr 157 FERBER Mathias GAGEAT Cédric Bio‐Informatique Structurale Institut Pasteur 25, rue du docteur Roux 75015 PARIS France [email protected] Institut de Biologie Physico‐Chimique (IBPC) CNRS 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] FIORUCCI Sébastien GAILLARD Thomas Institut de Chimie de Nice – UMR 7272 CNRS Université de Nice Sophia Antipolis ICN, UMR 7272 CNRS 28, avenue Valrose 06108 NICE Cedex 2 France [email protected] Laboratoire de Biochimie (BIOC) Ecole Polytechnique 91128 PALAISEAU Cedex France [email protected] FLATTERS Delphine GARNIER Norbert UMRS 973, MTi Université Paris Diderot 35, rue H. Brion Bât. Lamarck A (courrier 7113) 75205 PARIS Cedex 13 France delphine.flatters@univ‐paris‐diderot.fr Centre de Biophysique Moléculaire CNRS Rue Charles Sadron 45071 ORLEANS Cedex 2 France norbert.garnier@cnrs‐orleans.fr FLOQUET Nicolas GELLY Jean‐Christophe Institut des Biomolécules Max Mousseron (IBMM) – UMR5247 CNRS Faculté de Pharmacie 15, avenue Charles Flahault – BP 14491 34093 MONTPELLIER Cedex 05 France nicolas.floquet@univ‐montp1.fr INSERM UMR_S 1134,DSIMB, Université Paris Diderot‐ Paris 7,INTS 6, rue Alexandre Cabanel 75739 PARIS Cedex 15 France jean‐christophe.gelly@univ‐paris‐diderot.fr FORTUNE Antoine GOFFINONT Stéphane Département de Pharmacochimie Moléculaire UMR5063 CNRS / Université Joseph Fourier 470, avenue de la chimie 38400 SAINT MARTIN D'HERES France antoine.fortune@ujf‐grenoble.fr Centre de Biophysique Moléculaire – CNRS UPR 4301 Rue Charles Sadron CS 80054 45071 ORLEANS Cedex 2 France [email protected] 158 GRUDININ Sergei IORGA Bogdan LJK CNRS NANO – D Inria Minatec Campus 17, rue des Martyrs 38054 GRENOBLE France [email protected] Institut de Chimie des Substances Naturelles (ICSN) CNRS 1, avenue de la Terrasse Bât. 27 91198 GIF‐SUR‐YVETTE France [email protected] GUCA Ewelina ISENBERG Tobias Dynamique des Interactions Membranaires Normales et Pathologiques – UMR5235 CNRS‐Université de Montpellier Place Eugène Bataillon – Bât 24 – cc107 34095 MONTPELLIER Cedex 5 France [email protected] AVIZ research team Inria Saclay Université Paris‐Sud Bât. 660 91405 ORSAY France [email protected] Marc GUEROULT JAILLET Léonard LISBP INSA 135, avenue de Rangueil 31077 TOULOUSE France marc.gueroult@insa‐toulouse.fr NANO‐D Inria Rhône‐Alpes Bâtiment 51 C Minatec Campus 17, rue des Martyrs 38054 GRENOBLE Cedex France [email protected] HADJ‐SAID Jessica KAJAVA Andrey Bioénergétique et Ingénierie des Protéines ‐ UMR 7281 IMM 31, chemin Joseph Aiguier 13402 MARSEILLE Cedex 20 France [email protected] CRBM CNRS 1919, route de Mende 34293 MONTPELLIER France [email protected] HILVERT Donald KAPLAN Elise Laboratory of Organic Chemistry ETH Zurich HCI F339 Vladimir‐Prelog‐Weg 3 ZURICH Suisse [email protected] Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) CNRS – Université de Montpellier 1919, route de Mende 34090 MONTPELLIER Cedex 5 France [email protected] 159 KATAVA Marina LAFITE Pierre Laboratoire de Biochimie Théorique CNRS – UPR 9080 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] Institut de Chimie Organique et Analytique Université Orléans – CNRS UMR 7311 BP6759 Rue de Chartres 45067 ORLEANS Cedex 2 France pierre.lafite@univ‐orleans.fr KELLOU‐TAIRI Safia LAURIN Yoann Physico‐Chimie Théorique et Chimie Informatique Université des Sciences et de la Technologie Houari Boumediene – BP 32 El Alia ALGER Algérie [email protected] Laboratoire de Biochimie Théorique Institut de Biologie Physico‐Chimique (IBPC) 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] KREBS Fanny LEC Jean‐Christophe Biocomputing group Structural Biology & Genomics Dept. – IGBMC Université de Strasbourg 1, rue LaurentFranceies 67404 ILLKIRCH‐GRAFFENSTADEN Cedex France [email protected] UMR 7365 IMoPA – Equipe 3 / Enzymologie Moléculaire et Structurale 9, rue de la Forêt de Haye Bâtiment Biopole 54505 VANDOEUVRE‐LES‐NANCY France jean‐christophe.lec@univ‐lorraine.fr KRIZNIK Alexandre LEGENDRE Audrey UMR 7365 CNRS – Université de Lorraine Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA) –Campus Biologie Santé 9, avenue de la Forêt de Haye – CS 50184 54505 VANDOEUVRE LES NANCY Cedex France alexandre.kriznik@univ‐lorraine.fr Unité de Bioinformatique Structurale Institut Pasteur/CNRS 28, rue du Dr. Roux 75015 PARIS France [email protected] LABESSE Gilles LEGER Christophe Centre de Biochimie Structurale INSERM U1054 – CNRS UMR5048 – UM 29, rue de Navacelles 34090 MONTPELLIER Cedex France [email protected] Bioénergétique et Ingénierie des Protéines CNRS / AMU 31, chemin Joseph Aiguier, 13402 MARSEILLE Cedex 20 France [email protected] 160 LEROUX Gwenaëlle MARTINY Virginie Unité Mathématiques et Informatique Appliquées, du Génome à l'Environnement (MaIAGE) – INRA Domaine de Vilvert 78352 JOUY‐EN‐JOSAS France [email protected] Molecular Modelling and Structural Crystallography ICSN – CNRS UPR 2301, LabEx LERMIT Avenue de la Terrasse, Bât. 27, Bureau 310 91198 GIF‐SUR‐YVETTE France [email protected] LIONNE Corinne MATHIEU Cécile Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) CNRS – Université de Montpellier 1919, route de Mende 34293 MONTPELLIER Cedex 5 France [email protected] Unité Biologie Fonctionnelle et Adaptative Université Paris Diderot, CNRS UMR 8251 Bâtiment Buffon 4, rue M.A Lagroua Weill Hallé 75013 PARIS France [email protected] LOUET Maxime MEREU Ilaria Molécules Thérapeutiques in silico (MTi) Université Paris Diderot – Inserm UMR‐S 973 Bât Lamarck A, 4e et 5e étage , Courrier 7113 35, rue Hélène Brion 75205 PARIS Cedex 13 France [email protected] Multiscale Biomolecular Simulation Group Steinbuch Centre for Computing (SCC) Karlsruhe Institute of Technology (KIT) Hermann‐von‐Helmholtz‐Platz 1 76344 EGGENSTEIN‐LEOPOLDSHAFEN Allemagne [email protected] MANA Zohra MERROUCH Meriem Bio‐Logic SAS 1, rue de l'Europe 38640 CLAIX France zohra.mana@bio‐logic.net Laboratoire de Bioénergétiques et Ingénieries des Protéines UMR 72‐81 CNRS 31, chemin Joseph Aiguier 13402 MARSEILLE cedex 20 France [email protected] MAROT Christophe MIAS‐LUCQUIN Dominique UMR CNRS 7292 GICC – Equipe 4 Innovation Moléculaire et Thérapeutique UFR Sciences Pharmaceutiques Univ. Tours 31, avenue de Monge 37200 TOURS France Christophe.marot@univ‐orleans.fr Institut de Génétique et Développement de Rennes (IGDR) Université de Rennes 1 2, avenue du Professeur Léon BERNARD 35000 RENNES France [email protected]‐rennes1.fr 161 MOLZA Anne‐Elisabeth NEVEU Emilie Institut de Génétique et Développement de Rennes‐ Equipe Structure et Interactions Moléculaires (SIM) – Université de Rennes 1 2, avenue du Pr. Léon Bernard CS 34317 35043 RENNES Cedex France [email protected] NANO‐D – INRIA DRT/LETI/DACLE/ Bâtiment 51 C Minatec Campus 17, rue des Martyrs 38054 GRENOBLE Cedex France [email protected] MONET Damien NG FUK CHONG Matthieu Unité de Bioinformatique Structurale Institut Pasteur 25, rue du Docteur Roux 75015 PARIS France [email protected] INSERM UMR_S 1134 DSIMB 6, rue Alexandre Cabanel 75739 PARIS Cedex 15 France matthieu.ng‐fuk‐[email protected] MOROY Gautier NGUYEN Minh Khoa Molécules Thérapeutiques in silico (MTi) Université Paris Diderot – Inserm UMR‐S 973 35, rue Hélène Brion 75205 PARIS Cedex 13 France gautier.moroy@univ‐paris‐diderot.fr Laboratoire Jean Kuntzmann (LJK) INRIA Grenoble Minatec Campus 17, rue des Martyrs 38054 GRENOBLE France minh‐[email protected] MUNIER‐LEHMANN Hélène PETIT Emile Unité de Chimie et Biocatalyse Institut Pasteur, CNRS UMR3523 Unité de Chimie et Biocatalyse 28, rue du Dr Roux 75724 PARIS cedex 15 France [email protected] UMR 8251 Equipe RMCX Université Denis‐Diderot Bâtiment A 4, rue Lagroua Well Hallé 75013 PARIS France [email protected] NARTH Christophe RAHIMOVA Rahila Laboratoire de Chimie Théorique Université Pierre et Marie Currie Barre 12‐13 4ième étage – CC 137 4, place Jussieu 75252 PARIS France [email protected] Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) CNRS – Université de Montpellier 1919, route de Mende 34293 MONTPELLIER Cedex 5 France [email protected] 162 RAHUEL‐CLERMONT Sophie RENAULT Nicolas Laboratoire IMoPA – Equipe Enzymologie Moléculaire et Structurale UMR 7365 CNRS – Université de Lorraine 9, avenue de la Forêt de Haye, CS 50184 54505 VANDOEUVRE‐LES‐NANCY Cedex France sophie.rahuel@univ‐lorraine.fr Therapeutic innovation targetting inflammation – LIRIC – UMR 995 Inserm – Université Lille 2 / CHRU Lille Pôle Recherche, Place Verdun 59045 LILLE Cedex France nicolas.renault‐3@univ‐lille2.fr RASOLOHERY Inès RIEUX Charlotte Molécules Thérapeutiques in silico (MTi) Université Paris Diderot INSERM UMR‐S 973 Bât Lamarck A, 4e et 5e étage , Courrier 7113 35, rue Hélène Brion 75205 PARIS Cedex 13 France ines.rasolohery@univ‐paris‐diderot.fr Centre de Biophysique Moléculaire CNRS Rue Charles Sadron 45071 ORLEANS Cedex 2 France charlotte.rieux@cnrs‐orleans.fr REBEHMED Joseph RINALDO David IMPMC Université Pierre & Marie Curie Case 115 4, place Jussieu 75252 PARIS Cedex 05 France [email protected] Schrödinger GmbH Zeppelinstraße 73 81669 MÜNCHEN Allemagne [email protected] REDON Stéphane RODRIGUES‐LIMA Fernando NANO‐D – INRIA DRT/LETI/DACLE/ Bâtiment 51 C Minatec Campus 17, rue des Martyrs 38054 GRENOBLE Cedex France [email protected] Unité Biologie Fonctionnelle et Adaptative Université Paris Diderot – CNRS UMR 8251 4, rue MA Lagroua Weill Halle 75013 PARIS France fernando.rodrigues‐lima@univ‐paris‐ diderot.fr REMAUD‐SIMEON Magali SANTOLINI Jérôme LISBP‐INSAT Insa Toulouse 135, avenue de Rangueil 31077 TOULOUSE Cedex 4 France remaud@insa‐toulouse.fr UMR 8221 CEA/iBiTec‐S/SB2SM Bât. 532 CEA Saclay 91191 GIF‐SUR‐YVETTE Cedex France [email protected] 163 SELWA Edithe STRATMANN Dirk ICSN CNRS Avenue de la Terrasse Bâtiment 27 91198 GIF‐SUR‐YVETTE France [email protected] IMPMC – UPMC – Paris VI, UMR 7590 CNRS Campus Jussieu, Couloir 22/23, 4ème étage, Bureau 408 – Case courrier 115 4, place Jussieu 75252 PARIS Cedex 05 France [email protected] SENAC Caroline STRICK Terence Laboratoire d'imagerie biomédicale (LIB) UPMC CNRS INSERM 4, place Jussieu 75005 PARIS France [email protected] Equipe Nanomanipulation de Biomolécules Institut Jacques Monod 15, rue Hélène Brion 75013 PARIS France [email protected]‐paris‐diderot.fr SIDORE Marlon TALFOURNIER François Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM) CNRS/Université Aix‐Marseille 31, chemin Joseph Aiguier 13402 MARSEILLE Cedex 20 France [email protected] IMoPA UMR 7365 CNRS – Université de Lorraine 34, cours Léopold 54000 NANCY France francois.talfournier@univ‐lorraine.fr SOPKOVA‐DE OLIVEIRA SANTOS Jana TALY Antoine CERMN Université de Caen Basse‐Normandie Bd Becquerel 14032 CAEN France [email protected] Laboratoire de Biochimie Théorique UPR 9080 Institut de Biologie Physico‐Chimique (IBPC) 13, rue Pierre et Marie Curie 75005 PARIS France [email protected] STINES‐CHAUMEIL Claire TELLIER Charles Centre de Recherche Paul Pascal CNRS UPR 8641 115, avenue Albert Schweitzer 33600 PESSAC France stines@crpp‐bordeaux.cnrs.fr UFIP, UMR CNRS n°6286 Université de Nantes 2, rue de la Houssinière BP 92208 44322 NANTES Cedex 3 France charles.tellier@univ‐nantes.fr 164 THOMAS Aline VERZEAUX Laurie Département de Pharmacochimie Moléculaire CNRS – UFR de Pharmacie 470, rue de la Chimie – BP 53 38041 GRENOBLE Cedex 9 France aline.thomas@ujf‐grenoble.fr Laboratoire SiRMa UMR CNRS/URCA MEDyC n°7369 UFR SEN – Bâtiment 18 Chemin des rouliers 51687 REIMS Cedex 2 France [email protected] TINTILLIER Thibault WEIN‐GRATRAUD Sharon IBMM Faculté de Pharmacie 15, avenue Charles Flahault BP 14491 34093 MONTPELLIER Cedex 5 France thibault.tintillier@univ‐montp1.fr Dynamique des Interactions Membranaires Normales et Pathologiques – UMR5235 CNRS‐Université de Montpellier Place Eugène Bataillon – Bât 24 – cc107 34095 MONTPELLIER Cedex 5 France wein@univ‐montp2.fr TRAORE Seydou WIENINGER Silke CEA Saclay – IBITEC‐S/SB2SM/LBSR Point courrier 22 Bâtiment 144 91191 GIF‐SUR‐YVETTE Cedex France [email protected] Unité de Bioinformatique Structurale Institut Pasteur Paris 25‐28, rue du Dr Roux 75015 PARIS France [email protected] TUBIANA Thibault Institut de Biologie Intégrative de la Cellule I2BC CNRS CEA Saclay – Bât 532 91191 GIF‐SUR‐YVETTE Cedex France [email protected] 165 PROGRAMME Lundi 25 Mai Mardi 26 Mai Accueil Régulation et efficacité PLENIERE 2 Terence STRICK Hélène MUNIER‐LEHMANN Nicolas BOSC Jessica HADJ‐SAID Pause café 9h 10h 11h Loic CARRIQUE Sophie RAHUEL‐CLERMONT Marc‐André DELSUC Déjeuner 12h Déjeuner Mercredi 27 mai Enz. comme cibles thérap. PLENIERE 4 Dominique DOUGUET Flash n°4 Kamel DJAOUT Fanny KREBS Jana SOPKOVA‐DE OLIVEIRA Pause café Jeudi 28 Mai Visualisation et préd. struct. PLENIERE 6 Tobias ISENBERG Fabrice ALLAIN Mathias FERBER Emilie NEVEU I. CHAUVOT DE BEAUCHENE Pause café Flash n°5 Florent BARBAULT Inès RASOLOHERY Hiba ABI HUSSEIN Prix poster GT Enzymes Déjeuner Jean‐Christophe GELLY Stéphane REDON Prix GGMM Isidro CORTES Prix poster GGMM Déjeuner 13h 14h 15h 16h 17h 18h Bienvenue GGMM Bienvenue GT Enzymes Structures et mécanismes PLENIERE 1 Jacqueline CHERFILS Jérôme SANTOLINI Nolan CHATRON Bertrand CASTAING Pause café Pause café Flash n°1 Ewelina GUCA Pierre LAFITE Claire STINES‐CHAUMEIL Jean‐Christophe LEC Présentation Elsevier Apéritif de bienvenue Posters (1h30) Ingénierie enz., évol. dirigée PLENIERE 3 Donald HILVERT Flash n°2 Thomas GAILLARD Seydou TRAORE David RINALDO Flash n°3 Flash n°3 Pause café Posters (1h45) Rel. dynamique‐fonction PLENIERE 5 Jochen BLUMBERGER Jérôme EBERHARDT Benoît DAVID Julien DIHARCE Maxime LOUET Présentation Jeu "L'Expert" Pause café Pause café Matthieu CHAVENT Kaouther BEN OUIRANE Jean‐Pierre DUNEAU Christophe NARTH AG GGMM Apéritif Sétois Dégustation produits régionaux Posters (1h30) Diner Diner 19h Diner 20h Soirée festive 21h Jeu "L'Expert est dans la salle" Durées présentations Plénière : 45 min Flash : 1 min Com. orale : 15 min LEGENDE Présentations Enzymes Présentations communes Présentations communes Présentations GGMM Flash poster Sessions posters
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THESE Zaira E ARELLANO ANAYA original - thèse
infectées utilisent la machinerie cellulaire pour être constitutivement sécrétés en association
à des microvésicules d’origine endosomale (exosomes). L’efficacité avec laquelle les prions
sont secr...