GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations

被引：106

作者：

Pol-Fachin, Laercio ^{[1
]}

Fernandes, Claudia Lemelle ^{[1
]}

Verli, Hugo ^{[1
,2
]}

机构：

[1] Univ Fed Rio Grande do Sul, Ctr Biotechnol, BR-91500970 Porto Alegre, RS, Brazil

[2] Univ Fed Rio Grande do Sul, Fac Farm, BR-90610000 Porto Alegre, RS, Brazil

来源：

CARBOHYDRATE RESEARCH | 2009年 / 344卷 / 04期

关键词：

Glycoproteins; Molecular dynamics; Carbohydrates; Glycosidic linkage; GROMOS96; GLYCOSYLATED ADHESION DOMAIN; FREE ALPHA-SUBUNIT; N-GLYCOSYLATION; STATISTICAL-ANALYSIS; CRYSTAL PACKING; FORCE-FIELD; HEPARIN; OLIGOSACCHARIDES; FRAGMENT; SITES;

D O I：

10.1016/j.carres.2008.12.025

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Considering the small number of papers assessing the conformational profile of glycoproteins through molecular dynamics (MID) simulations, the current work reports on a systematic analysis of the performance of the GROMOS96 43a1 force field and Lowdin HF16-3(+) G(center dot center dot)-derived atomic charges in the conformational description of glycoproteins. The results substantiate the accuracy of the computational representation of glycoprotein conformational ensembles in aqueous solution based on their agreement to available experimental information, supporting further contributions Of Computational techniques, mainly MD, in future studies on the characterization of glycoprotein structure and function. (C) 2009 Elsevier Ltd. All rights reserved.

引用

页码：491 / 500

页数：10

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