Pol-Fachin Laercio, Verli Hugo, Lins Roberto D
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.
J Comput Chem. 2014 Nov 5;35(29):2087-95. doi: 10.1002/jcc.23721. Epub 2014 Sep 5.
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.
本文提出了GROMOS 53A6GLYC碳水化合物力场的扩展，以涵盖糖蛋白连接。该集合包括新的原子电荷，并为N-、S-、C-、P-和O-糖苷键纳入了适当的扭转势参数，与蛋白质的GROMOS力场家族兼容。验证包括氨基酸和单糖残基之间糖苷键几何结构的描述、糖蛋白的核磁共振衍生的蛋白质-碳水化合物和碳水化合物-碳水化合物核Overhauser效应（NOE）信号的比较，以及糖基化对蛋白质灵活性和动力学的影响。
