“小提琴模型”：观察动态变构的社区网络。
The "violin model": Looking at community networks for dynamic allostery.
机构信息
Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave., Charleston, South Carolina 29425, USA.
Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, San Diego, California, 92093, USA.
出版信息
J Chem Phys. 2023 Feb 28;158(8):081001. doi: 10.1063/5.0138175.
Abstract
Allosteric regulation of proteins continues to be an engaging research topic for the scientific community. Models describing allosteric communication have evolved from focusing on conformation-based descriptors of protein structural changes to appreciating the role of internal protein dynamics as a mediator of allostery. Here, we explain a "violin model" for allostery as a contemporary method for approaching the Cooper-Dryden model based on redistribution of protein thermal fluctuations. Based on graph theory, the violin model makes use of community network analysis to functionally cluster correlated protein motions obtained from molecular dynamics simulations. This Review provides the theory and workflow of the methodology and explains the application of violin model to unravel the workings of protein kinase A.
摘要
变构调节蛋白仍然是科学界关注的热门研究课题。描述变构通讯的模型已经从关注蛋白质结构变化的构象描述符发展到认识到内部蛋白质动力学作为变构中介的作用。在这里，我们解释了一种变构的“小提琴模型”，这是一种基于蛋白质热波动再分配的当代方法，用于处理基于 Cooper-Dryden 模型的方法。基于图论，小提琴模型利用社区网络分析从分子动力学模拟中获得的功能上相关的蛋白质运动进行聚类。本综述提供了该方法的理论和工作流程，并解释了小提琴模型在揭示蛋白激酶 A 作用机制方面的应用。
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