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Molecular dynamics simulation of Lewis blood groups and related oligosaccharides
Author(s) -
Mukhopadhyay Chaitali,
Bush C. Allen
Publication year - 1991
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360311408
Subject(s) - disaccharide , chemistry , glycosidic bond , trisaccharide , molecular dynamics , maxima and minima , carbohydrate conformation , dihedral angle , crystallography , oligosaccharide , folding (dsp implementation) , molecule , stereochemistry , computational chemistry , nuclear magnetic resonance spectroscopy , organic chemistry , hydrogen bond , mathematical analysis , mathematics , electrical engineering , enzyme , engineering
Molecular dynamics simulations without explicit inclusion of solvent molecules have been performed to study the motions of Lewis a and Lewis b blood group oligosaccharides, and two blood group A tetrasaccharides having type I and type II core chains. The blood group H trisaccharide has also been studied and compared with the blood group A type II core chain. The potential energy surface developed by Rasmussen and co‐workers was used with the molecular mechanics code CHARMM. The lowest energy minima of the component disaccharide fragments were obtained from conformational energy mapping. The lowest energy minima of these disaccharide fragments were used to build the tri‐ and tetrasaccharides that were further minimized before the actual heating/equilibration and dynamics simulations. The trajectories of the disaccharide fragments, e.g., Fuc α‐(1 → 4) GlcNAc, Gal β‐(1 → 4) GlcNAc, etc., show transitions among various minima. However, the oligosaccharides were found to be dynamically stable and no transitions to other minimum energy conformations were observed in the time series of the glycosidic dihedral angles even during trajectories as long as 300 ps. The stable conformations of the glycosidic linkages in the oligosaccharides are not necessarily the same as the minimum energy conformation of the corresponding isolated disaccharides. The average fluctuations of the glycosidic angles in the oligosaccharides were well within the range of ±15°. The results of these trajectory calculations were consistent with the relatively rigid single‐conformation models derived for these oligosaccharides from 1 H‐nmr data.