使用CHARMM对糖蛋白进行分子动力学模拟。
Molecular dynamics simulations of glycoproteins using CHARMM.
作者信息
Mallajosyula Sairam S, Jo Sunhwan, Im Wonpil, MacKerell Alexander D
机构信息
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD, 21201, USA.
出版信息
Methods Mol Biol. 2015;1273:407-29. doi: 10.1007/978-1-4939-2343-4_25.
Abstract
Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.
摘要
分子动力学模拟是研究碳水化合物和蛋白质的结构、动力学及热力学的有效工具。然而，由于缺乏合适的分子力场参数来描述碳水化合物与蛋白质区域之间的连接，以及缺乏用于为建模研究准备这些系统的工具，异质糖蛋白系统的模拟受到了限制。在这项工作中，我们概述了CHARMM碳水化合物力场在处理糖蛋白方面的最新进展，并详细描述了使用CHARMM-GUI聚糖阅读器构建糖蛋白几何结构所涉及的逐步程序。
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