Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field.
The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (alpha, phi, psi) and (beta, phi, psi), whereas for three-bond linkages, there are 54 possible regions that can be defined by (alpha, phi, psi, omega) and (beta, phi, psi, omega). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.
Salisburg
Amanda M
AM
Chemistry Department, Center for Molecular Design, Hamilton College Clinton, New York 13323, USA.
Deline
Ashley L
AL
Lexa
Katrina W
KW
Shields
George C
GC
Kirschner
Karl N
KN
D000596:Amino Acids / Q000737:chemistry*; D002241:Carbohydrates / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004187:Disaccharides / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D012984:Software; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D002241:Carbohydrates; D004187:Disaccharides; D014867:Water