Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 35, Issue 29, Pages 2087-2095Publisher
WILEY-BLACKWELL
DOI: 10.1002/jcc.23721
Keywords
carbohydrate; force field; glycosylation; molecular dynamics; sugar
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Funding
- CNPq
- NanoBiotec-BR
- FAPERGS
- FACEPE
- DCR-FACEPE [APQ-0398-1.06/13]
- nBioNet
- Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
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An extension of the GROMOS53A6(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 proteincarbohydrate and carbohydrate-carbohydrate nuclear overhauser effect (NOE) signals for glycoproteins and the effects of glycosylation on protein flexibility and dynamics. (c) 2014 Wiley Periodicals, Inc.
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