a Department of Zoology , Naihati Rishi Bankim Chandra College, West Bengal State University , Naihati , North 24 Parganas, West Bengal , India .
J Biomol Struct Dyn. 2014;32(6):928-49. doi: 10.1080/07391102.2013.799438. Epub 2013 Jun 24.
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.
已经对嗜热起源的海栖热袍菌趋化性蛋白“CheY”及其中温对应物沙门氏菌进行了 10 ns 每个在 300 和 350 K 以及 20 ns 每个在 400 和 450 K 的比较分子动力学模拟。轨迹根据不同的因素进行了分析，如均方根偏差、均方根波动、回转半径、溶剂可及表面积、氢键、盐桥含量和蛋白质-溶剂相互作用，这些因素表明了两者之间的明显差异。这两种蛋白质也遵循不同的解折叠途径。通过对角化协方差矩阵的迹计算得到的整体灵活性在接近最佳生长温度时显示出两种蛋白质具有相似的灵活性。然而，在较高温度下，中温蛋白质比其嗜热对应物显示出更高的整体灵活性。主成分分析也表明，在不同温度下模拟两种蛋白质时所探索的基本子空间不重叠，它们的运动方向明显不同。然而，在轨迹内存在显著的重叠，并且在 300 K 下两种蛋白质都观察到相似的运动方向。总体而言，中温蛋白质导致相空间构象采样增加，比其嗜热对应物更多。这是首次使用蛋白质动力学作为主要影响因素来研究 CheY 蛋白同源物的热稳定性。我们的研究可以作为研究来自两个生活在不同温度的生物体的两个同源蛋白质的热稳定性的分子基础的模型，它们之间的差异不太明显。
