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Computer Simulations of Intrinsically Disordered Proteins
Annual Review of Physical Chemistry ( IF 14.7 ) Pub Date : 2017-05-02 00:00:00 , DOI: 10.1146/annurev-physchem-052516-050843
Song-Ho Chong 1 , Prathit Chatterjee 1 , Sihyun Ham 1
Affiliation  

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

中文翻译:


固有紊乱蛋白的计算机模拟

内在无序蛋白(IDP)的研究是结构和分子生物学的新领域,需要一种新的范例来将结构障碍与功能联系起来。分子动力学模拟和统计热力学可能为这类迷人的蛋白质的原子级表征和热力学描述提供理想的工具,从而补充实验研究。但是,IDP对潜在的分子力学力场中的误差显示出敏感性。因此,通过仿真实现IDP的准确结构表征是一个挑战。在IDP采样的异质结构体上进行构型空间整合以提取,尤其是提取蛋白质构型熵,也是一项艰巨的任务。在这篇评论中,我们总结了最近在力场发展方面所做的努力以及在将其应用于国内流离失所者时对其性能进行的严格评估。我们还调查了蛋白质构型熵计算方法的最新进展,旨在提供结构紊乱和蛋白质活性之间的热力学联系。

更新日期:2017-05-02
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