A Discontinuous Potential Model for Protein-Protein Interactions.
A Discontinuous Potential Model for Protein-Protein Interactions.
复制标题
蛋白质-蛋白质相互作用的不连续电位模型。
DOI：
10.1007/978-981-10-1128-3_1
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
Hall,CarolK
中科院分区：
文献类型：
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作者：
Shao,Qing;Hall,CarolK
蛋白质-蛋白质相互作用在许多生物和工业过程中起着重要作用。在这项工作中，我们开发了一个两珠每残基模型，使我们能够考虑在多蛋白质系统中使用不连续的分子动力学模拟的蛋白质-蛋白质相互作用。该模型采用不连续势来描述非键相互作用和保持蛋白质天然状态的虚键。几何和能量参数来自侧链-侧链、侧链-主链和主链-主链对之间的平均力的势。能量参数的缩放与实验中报道的溶菌酶的第二维里系数相匹配的目的。我们还研究了几种债券建设策略的性能。
Protein–protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein–protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain–sidechain, sidechain–backbone, and backbone–backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.