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Ramachandran‐type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field
Author(s) -
Salisburg Amanda M.,
Deline Ashley L.,
Lexa Katrina W.,
Shields George C.,
Kirschner Karl N.
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21099
Subject(s) - ramachandran plot , glycosidic bond , chemistry , disaccharide , force field (fiction) , molecular dynamics , computational chemistry , crystallography , oligosaccharide , stereochemistry , physics , protein structure , organic chemistry , biochemistry , quantum mechanics , enzyme
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 (α, ϕ, ψ) and (β, ϕ, ψ), whereas for three‐bond linkages, there are 54 possible regions that can be defined by (α, ϕ, ψ, ω) and (β, ϕ, ψ, ω). 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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009