Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”

Comparative molecular dynamics simulations of chemotaxis protein “CheY” from thermophilic origin Thermotoga maritima and its mesophilic counterpart Salmonella enterica have been performed for 10 ns each at 300 and 350 K, and 20 ns each at 400 and 450 K. The trajectories were analyzed in terms of different factors like root-mean-square deviation, root-mean-square fluctuation, radius of gyration, solvent accessible surface area, H-bonds, salt bridge content, and protein–solvent interactions which indicate distinct differences between the two of them. The two proteins also follow dissimilar unfolding pathways. The overall flexibility calculated by the trace of the diagonalized covariance matrix displays similar flexibility of both the proteins near their optimum growth temperatures. However, at higher temperatures mesophilic protein shows increased overall flexibility than its thermophilic counterpart. Principal component analysis also indicates that the essential subspaces explored by the simulations of two proteins at different temperatures are nonoverlapping and they show significantly different directions of motion. However, there are significant overlaps within the trajectories and similar direction of motions are observed for both proteins at 300 K. Overall, the mesophilic protein leads to increased conformational sampling of the phase space than its thermophilic counterpart. This is the first ever study of thermostability of CheY protein homologs by using protein dynamism as a main impact. Our study might be used as a model for studying the molecular basis of thermostability of two homologous proteins from two organisms living at different temperatures with less visible differences.

本研究针对源自嗜热菌海栖热袍菌（Thermotoga maritima）的趋化蛋白CheY，及其嗜温同源物肠炎沙门氏菌（Salmonella enterica）的CheY蛋白，开展了对比分子动力学模拟：在300 K与350 K条件下，每组模拟时长均为10 ns；在400 K与450 K条件下，每组模拟时长均为20 ns。对所得模拟轨迹的分析涵盖多项关键表征参数，包括均方根偏差（root-mean-square deviation）、均方根波动（root-mean-square fluctuation）、回转半径（radius of gyration）、溶剂可及表面积（solvent accessible surface area）、氢键（H-bonds）、盐桥含量以及蛋白-溶剂相互作用，上述指标均证实两种蛋白间存在显著差异。两种蛋白的解折叠路径亦存在显著差异。通过对角化协方差矩阵的迹计算得到的整体柔性参数显示，在各自最适生长温度附近，两种蛋白的整体柔性水平相近。但在更高温度环境下，嗜温蛋白的整体柔性较其嗜热同源物有所提升。主成分分析（principal component analysis）结果同样表明，两种蛋白在不同温度下模拟所探索的核心子空间互不重叠，且运动方向存在显著差异。不过在300 K时，两种蛋白的模拟轨迹存在显著重叠，二者的运动方向也较为相似。总体而言，相较其嗜热同源物，嗜温蛋白能够实现相空间中更广泛的构象采样。本研究首次以蛋白动态特性为核心研究维度，探究CheY蛋白同源物的热稳定性机制。本研究可作为模型体系，用于研究两种生存于不同温度环境、表观差异较小的同源蛋白的热稳定性分子基础。