Shao Qing, Hall Carol K
Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh 27695, USA.
Found Mol Model Simul (2015). 2016;2016:1-20. doi: 10.1007/978-981-10-1128-3_1. Epub 2016 Jun 2.
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.
蛋白质-蛋白质相互作用在许多生物和工业过程中发挥着重要作用。在这项工作中，我们开发了一种每个残基两个珠子的模型，该模型使我们能够使用非连续分子动力学模拟来解释多蛋白质系统中的蛋白质-蛋白质相互作用。该模型采用非连续势来描述非键相互作用，并使用虚拟键来使蛋白质保持其天然状态。几何和能量参数源自侧链-侧链、侧链-主链和主链-主链对之间的平均力势。能量参数进行了缩放，目的是匹配实验中报道的溶菌酶的第二维里系数。我们还研究了几种键构建策略的性能。
