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Molecular dynamics simulations and the conformational mobility of blood group oligosaccharides
Author(s) -
Yan ZhenYi,
Bush C. Allen
Publication year - 1990
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.360290414
Subject(s) - chemistry , dihedral angle , glycosidic bond , molecular dynamics , nuclear overhauser effect , force field (fiction) , trisaccharide , fucose , crystallography , disaccharide , oligosaccharide , stereochemistry , computational chemistry , nuclear magnetic resonance spectroscopy , galactose , molecule , organic chemistry , hydrogen bond , artificial intelligence , computer science , enzyme
Molecular dynamics simulations were carried out without explicit consideration of solvent to explore the conformational mobility of blood group A and H oligosaccharides. The potential energy force field of Rasmussen and co‐workers was used with the CHARMM program on a number of disaccharide and trisaccharide models composed of fucose, galactose, glucose, N‐acetyl glucosamine, and N‐acetyl galactosamine chosen to represent various fragments of blood group oligosaccharides. In agreement with results of earlier studies, stable chair conformations were found for each pyranoside from which no transitions were detected in simulations as long as 800 ps. Exocyclic dihedral angles, including that of C5—C6, generally show numerous transitions on a time scale of approximately 5–30 ps. The dihedral angles of some but not all glycosidic linkages of blood group oligosaccharides show transitions on the time scale of 30–50 ps, implying that the extent of internal motion in blood group oligosaccharides depends strongly on linkage stereochemistry. For certain blood group A and H oligosaccharides that show limited internal motion in these simulations, we argue that the calculations are consistent with our previous analysis of 1 H nuclear Overhauser enhancement (NOE) data that imply single conformations over a wide range of temperature and solvent conditions. While the trajectories are consistent with 13 C T 1 values that have been interpreted as indicating rigid conformations, measurements of 13 C‐NOE and T 1 as a function of magnetic field strength are proposed as an improved method for experimental detection of the internal motion that is suggested for certain oligosaccharides in these simulations. The results of these simulations differ substantially from those of peptides of a similar molecular weight in that the oligosaccharides show much less internal motion.