title: Extension and validation of the GROMOS 53A6(GLYC) parameter set for glycoproteins.
abstract: An extension of the GROMOS 53A6GLYC 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.
authors.affiliation: Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil, 91500-970; Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil, 50670-540.
authors.forename: Laercio
authors.initials: L
authors.lastname: Pol-Fachin
authors.forename: Hugo
authors.initials: H
authors.lastname: Verli
authors.forename: Roberto D
authors.initials: RD
authors.lastname: Lins
mesh_terms: D002241:Carbohydrates / Q000737:chemistry*; D006023:Glycoproteins / Q000737:chemistry*; D006031:Glycosylation; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D054928:Validation Studies as Topic
chemical_list: D002241:Carbohydrates; D006023:Glycoproteins
keywords: carbohydrate; force field; glycosylation; molecular dynamics; sugar