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Synchronous and Asynchronous Response in Dynamically Perturbed Proteins
The Journal of Physical Chemistry B ( IF 3.3 ) Pub Date : 2021-01-19 , DOI: 10.1021/acs.jpcb.0c08409
Aysima Hacisuleyman 1 , Albert Erkip 2 , Batu Erman 3 , Burak Erman 1
Affiliation  

We present a dynamic perturbation-response model of proteins based on the Gaussian Network Model, where a residue is perturbed periodically, and the dynamic response of other residues is determined. The model shows that periodic perturbation causes a synchronous response in phase with the perturbation and an asynchronous response that is out of phase. The asynchronous component results from the viscous effects of the solvent and other dispersive factors in the system. The model is based on the solution of the Langevin equation in the presence of solvent, noise, and perturbation. We introduce several novel ideas: The concept of storage and loss compliance of the protein and their dependence on structure and frequency; the amount of work lost and the residues that contribute significantly to the lost work; new dynamic correlations that result from perturbation; causality, that is, the response of j when i is perturbed is not equal to the response of i when j is perturbed. As examples, we study two systems, namely, bovine rhodopsin and the class of nanobodies. The general results obtained are (i) synchronous and asynchronous correlations depend strongly on the frequency of perturbation, their magnitude decreases with increasing frequency, (ii) time-delayed mean-squared fluctuations of residues have only synchronous components. Asynchronicity is present only in cross correlations, that is, correlations between different residues, (iii) perturbation of loop residues leads to a large dissipation of work, (iv) correlations satisfy the hypothesis of pre-existing pathways according to which information transfer by perturbation rides on already existing equilibrium correlations in the system, (v) dynamic perturbation can introduce a selective response in the system, where the perturbation of each residue excites different sets of responding residues, and (vi) it is possible to identify nondissipative residues whose perturbation does not lead to dissipation in the protein. Despite its simplicity, the model explains several features of allosteric manipulation.

中文翻译:

动态扰动蛋白中的同步和异步响应

我们提出了基于高斯网络模型的蛋白质的动态摄动响应模型,其中一个残基被周期性地扰动,并确定其他残基的动态响应。该模型表明,周期性扰动会导致与扰动同相的同步响应,以及异相的异步响应。异步组分是由溶剂的粘性作用和系统中其他分散因素导致的。该模型基于存在溶剂,噪声和扰动的情况下的Langevin方程的解。我们介绍了几种新颖的思想:蛋白质的存储和损失顺应性概念及其对结构和频率的依赖性;丢失的工作量以及对丢失的工作有重大贡献的残留物;摄动产生新的动态相关性;因果关系,即i受到扰动时j的响应不等于j受扰动时i的响应。作为示例,我们研究了两个系统,即牛视紫红质和纳米抗体类别。获得的一般结果是:(i)同步和异步相关性在很大程度上取决于扰动的频率,其幅度随频率的增加而减小;(ii)残差的时滞均方波动仅具有同步分量。异步仅存在于互相关中,也就是说,不同残基之间存在相关性;(iii)循环残基的扰动会导致大量的工作耗散,(iv)相关性满足现有路径的假设,根据该假设,通过扰动进行的信息传递依赖于系统中已经存在的平衡相关性,(v)动态扰动会在系统中引入选择性响应,其中每个残基的扰动都会激发不同的响应残基集;以及(vi)可以识别其干扰不会导致蛋白质耗散的非耗散残基。尽管简单,但是该模型解释了变构操纵的几个特征。(vi)可以鉴定其干扰不会导致蛋白质耗散的非耗散残基。尽管简单,但是该模型解释了变构操纵的几个特征。(vi)可以鉴定其干扰不会导致蛋白质耗散的非耗散残基。尽管简单,但是该模型解释了变构操纵的几个特征。
更新日期:2021-01-28
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