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Extension and validation of the GROMOS 53A6 glyc parameter set for glycoproteins
Author(s) -
PolFachin Laercio,
Verli Hugo,
Lins Roberto D.
Publication year - 2014
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.23721
Subject(s) - glycoprotein , chemistry , monosaccharide , force field (fiction) , molecular dynamics , carbohydrate , glycosylation , biochemistry , computer science , computational chemistry , artificial intelligence
An extension of the GROMOS 53A6 GLYC force field for carbohydrates to encompass glycoprotein linkages is presented. The set includes new atomic charges and incorporates adequate torsional potential parameters for N‐, S‐, C‐, P‐, and O‐glycosydic linkages, offering compatibility with the GROMOS force field family for proteins. Validation included the description of glycosydic linkage geometries between amino acid and monosaccharide residues, comparison of NMR‐derived protein‐carbohydrate and carbohydrate–carbohydrate nuclear overhauser effect (NOE) signals for glycoproteins and the effects of glycosylation on protein flexibility and dynamics. © 2014 Wiley Periodicals, Inc.