500-picosecond molecular dynamics in water of the Man alpha 1----2Man alpha glycosidic linkage present in Asn-linked oligomannose-type structures on glycoproteins.
Molecular dynamics simulations of the Man alpha 1----2Man alpha glycosidic linkage found in the N-linked glycans of glycoproteins were performed in vacuo and in the presence of water. In the latter case significant dampening of the molecular fluctuations was found when compared to the in vacuo simulation. A 500-ps dynamics simulation in water showed only occasional short-lived deviations from the minimum-energy conformation, more consistent with carbohydrate "breathing" than flexibility. These studies add further evidence that oligosaccharides can maintain "fixed" geometries with relatively long lifetimes and are in agreement with experimental NMR-derived parameters for the same linkage in oligomannose structures.
Edge
C J
CJ
Department of Biochemistry, University of Oxford, U.K.
Singh
U C
UC
Bazzo
R
R
Taylor
G L
GL
Dwek
R A
RA
Rademacher
T W
TW
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D006023:Glycoproteins; D009682:Magnetic Resonance Spectroscopy; D008358:Mannose; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009844:Oligosaccharides; D013816:Thermodynamics; D014867:Water
D006023:Glycoproteins; D009844:Oligosaccharides; D014867:Water; D008358:Mannose