HOW DOES NATURE FORM GLYCOSIDIC BONDS?

HOW DOES NATURE FORM
GLYCOSIDIC BONDS?
An ab initio molecular dynamics investigation
C
Carme
R i
Rovira
Universitat de Barcelona –
Parc Científic de Barcelona
Carbohydrates
50% of our daily
calorie intake comes
from carbohydrates
http://en wikipedia org/
http://en.wikipedia.org/
Carbohydrates are our “biological fuel “,
as well as the primary form of storage
and energy consumption in organisms
Introduction
The roles of carbohydrates
P l
Polysaccharides
h id
starch
cellulose
 Structural support
 Energy
E
storage
t
Glycoconjugates
 Cell-cell interaction
 Signal transduction
 Immune response
 Parasitic infections
carbohydrates
http://www.glycomicscentre.ca
GlcNAcMan5GlcNAc2
Deciphering
D
i h i mechanisms
h i
i which
in
hi h carbohydrates
b h d
are implicated
i li
d
is of enormous interest for the search of new therapeutic agents.
Introduction
Glicosidic bond
OH
glucose
HO
O
OH
O
glucose
OH
O
O
O
HO
OH
OH
glucose
glucose
O
HO
OH
O
O
OH
O
HO
HO
glycosidic bond:
C O bond between two sugar units
C-O
How do glycosidic bonds form?
Most glycosidic bonds are synthesized in nature from sugars that
are activated by a cofactor
Enzyme (glycoside transferase)
How do glycosidic bonds form?
The g
glycosidic
y
bond is formed upon
p transfer of a sugar
g molecule from
the donor (an activated sugar) to an acceptor molecule (typically another
sugar)
Enzyme (glycoside transferase)
Two modes of enzyme operation
Retention or inversion of the configuration of the anomeric carbon
retaining
t i i GT
The molecular mechanism of retaining GTs is very controversial
Palcic, Curr. Opin. Chem. Biol. 2011; Lee et al. Nat. Chem. Biol. 2011
Lairson et al. Annu. Rev. Biochem. 2008
Retention of the configuration of the anomeric carbon
retaining
t i i GT
high steric hindrance is expected
Possible mechanism for retaining enzymes
covalent glycosyl-enzyme intermediate
Possible mechanism for retaining enzymes
covalent glycosyl-enzyme intermediate
(double displacement,
~ retaining GHs)
retaining GHs
e.g. Biarnés et al. J. Am. Chem.
Soc. 133, 20301–09, 2011
Possible mechanism for retaining enzymes
covalent glycosyl-enzyme intermediate
(~ retaining GHs)
But
• All experimental attempts to isolate a glycosyl-enzyme
intermediate have failed
• Few GTs have a putative
Another possibility
+
-
The reaction takes place on
a single
g “face” of the sugar
g
“front-face attack”
B t
But
• High steric hindrance expected
• Little chemical precedence
Controversy
Two covalent bonds being
+
-
broken/formed in the
same region of the space
• Is
I the
th front-face
f
tf
reaction
ti feasible?
f
ibl ?
Simulation model
•Ab initio molecular dynamics
(to take into account the atomic
QM
and electronic motion at room temperature)
p
)
• QM/MM
MM
(Density Functional Theory/ AMBER)
• Metadynamics (Laio and Parrinello, PNAS 99, 12562-66, 2002)
(to model the chemical reaction)
Enzyme studied: trehalose-6-phosphate synthase
OH
HO
HO
OH
O
HO
HO
OH
O
O
O
N
+
OH
HO
O- O
enzyme
UDP-glucose
(donor)
OH
HO
O
OPO32O
HO
O
+
O
N
P
P
O
OH
O
O
OH
O-
OH
O
OH
HN
O
O
P
P
O
OH
HO
O
OH
O
OPO32-
-
O O
HN
OH
O
glucose-6P
(acceptor)
Enzyme
y
trehalose-6P
UDP
Trehalose is a natural disaccharide
used as food ingredient for its
sweet flavor and preservative
properties
O-
Enzyme·substrate complex
• Structure
St t
stable
t bl under
d molecular
l
l dynamics
d
i
• Good agreement with binary complexes structures
(Enzyme + UDP-Glc and Enzyme + UDP + Glc-6P)
Free energy landscape
~ 100 QM atoms
metastable intermediate
20 ps AIMD, 105 h MN
(64/128 procs).
lifetime ~ 2 ps
(dos milésimas de una milmillonésima de segundo!)
cleavage of phosphate-sugar bond
R
1
R
glycosidic
bond
formation
3
2
4
P
P
proton
transfer
Molecular mechanism of the front-face reaction
metadynamics
trajectory
Glucose-6P
UDP
Theory: Ardèvol & Rovira, Angew. Chem. Int. Ed. 50, 10897 –901, 2011
Experiment: Seung et al. Nat. Chem. Biol. 7, 631-38, 2011
Acknowledgments
Albert Ardèvol (ETH, Switzerland)
Discussions with:
Antoni Planas (Universitat Ramon Llull,
Llull Barcelona)
Seung Lee, Ben Davis (University of Oxford, UK)