how does nature form glycosidic bonds? - bsc
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HOW DOES NATURE FORM HOW DOES NATURE FORM
GLYCOSIDIC BONDS?GLYCOSIDIC BONDS?An ab initio molecular dynamics investigation
C R i
An ab initio molecular dynamics investigation
Carme RoviraUniversitat de Barcelona –Parc Científic de BarcelonaParc Científic de Barcelona
Carbohydrates
50% of our dailycalorie intake comes from carbohydrates
http://en wikipedia org/
Carbohydrates are our “biological fuel “,
http://en.wikipedia.org/
as well as the primary form of storageand energy consumption in organisms
IntroductionThe roles of carbohydrates
P l h id starchPolysaccharides Structural support
E t
starchcellulose
Glycoconjugates
Energy storage
Glycoconjugates Cell-cell interaction
Signal transduction Signal transduction
Immune response
Parasitic infections carbohydrates Parasitic infectionsGlcNAcMan5GlcNAc2
carbohydrates
http://www.glycomicscentre.ca
D i h i h i i hi h b h d i li dDeciphering mechanisms in which carbohydrates are implicatedis of enormous interest for the search of new therapeutic agents.
IntroductionGlicosidic bond
OOH
OOH
OH
OHO
O
HO
O
O
HO OH
OH
OH
O
HO
OO
glucose glucose glucose glucose
HOO
HO
glycosidic bond: C O bond between two sugar unitsC-O bond between two sugar units
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 glycosidic bond is formed upon transfer of a sugar molecule from g y p gthe 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
t i i GTretaining GT
The molecular mechanism of retaining GTs is very controversial
Palcic, Curr. Opin. Chem. Biol. 2011; Lee et al. Nat. Chem. Biol. 2011Lairson et al. Annu. Rev. Biochem. 2008
Retention of the configuration of the anomeric carbon
t i i GTretaining 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 GHse.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 ona single “face” of the sugar
“front-face attack”
g g
B t• High steric hindrance expected
But
• Little chemical precedence
Controversy
Two covalent bonds beingbroken/formed in the+
-
broken/formed in thesame region of the space
I th f t f ti f ibl ?• Is the front-face reaction feasible?
Simulation model
•Ab initio molecular dynamics
(to take into account the atomic
and electronic motion at room temperature)QM
p )
• QM/MM
(Density Functional Theory/ AMBER)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
O
OHOPO 2-
OHO
HO
OH
OHOOH OH
OO
O
PO-
O
O
+O
OH OH
NP
O-
O
O
+HOHO
HO
OHO
OH
OHOPO3
OH
HOHO
OHO
OH
O OPO32-
OH
PO-
O
OO
N
HN
O
O
PO-
O
Oenzyme
O
UDP-glucose(donor)
glucose-6P(acceptor)
N
HN
O
O
OO
trehalose-6P UDP
O
Enzyme Trehalose is a natural disaccharidey Trehalose is a natural disaccharideused as food ingredient for itssweet flavor and preservativepropertiesproperties
Enzyme·substrate complex
St t t bl d l l d i• Structure stable under molecular dynamics• Good agreement with binary complexes structures
(Enzyme + UDP-Glc and Enzyme + UDP + Glc-6P)(Enzyme + UDP-Glc and Enzyme + UDP + Glc-6P)
Free energy landscape
metastable intermediate~ 100 QM atoms
20 ps AIMD, 105 h MN
(64/128 procs).
lifetime ~ 2 ps
(dos milésimas de una milmillonésima de segundo!)
Rcleavage of phosphate-sugar bond
glycosidic bondformation
11
2
33R
formation4
P
PP
protontransfer
Molecular mechanism of the front-face reaction
metadynamicsmetadynamics trajectory
Glucose-6P
UDPUDP
Theory: Ardèvol & Rovira, Angew. Chem. Int. Ed. 50, 10897 –901, 2011Experiment: Seung et al. Nat. Chem. Biol. 7, 631-38, 2011
Acknowledgments
Albert Ardèvol (ETH, Switzerland)
Discussions with:Antoni Planas (Universitat Ramon Llull Barcelona)Antoni Planas (Universitat Ramon Llull, Barcelona)Seung Lee, Ben Davis (University of Oxford, UK)