Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins. Issue 29 (5th September 2014)

• Record Type: Journal Article
• Authors: Pol‐Fachin, Laercio; Verli, Hugo; Lins, Roberto D.
• Is Part Of: Journal of computational chemistry. Volume 35:Issue 29(2014)
• Page Start: 2087
• Page End: 2095
• Publication Date: 2014-09-05
• Subjects: Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.23721
• Languages: English
• ISSNs: 0192-8651

Abstract

<abstract abstract-type="main"> <title> <x xml:space="preserve">Abstract</x> </title> <p>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.</p> </abstract>