Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K.
Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K.
复制标题
DOI：
10.3390/ijms17020254
复制
发表时间：
2016-02-19
影响因子：
5.6
通讯作者：
Liu SQ
中科院分区：
文献类型：
--
作者：
Sang P;Yang Q;Du X;Yang N;Yang LQ;Ji XL;Fu YX;Meng ZH;Liu SQ
为了获得有关溶剂温度对蛋白质动力学影响的详细信息，对丝氨酸蛋白酶K的溶质和溶剂在不同温度(300K或180K)耦合的多个长分子动力学(MD)进行了模拟。比较分析表明，酶K的内部柔韧性和流动性强烈依赖于溶剂温度，而弱依赖于蛋白质温度。在高溶剂温度下构建的自由能景观(FEL)比在低溶剂温度下构建的自由能景观(FEL)具有更坚固的表面、更宽的跨越范围和更高的最低自由能级。动态氢键(Hb)数的比较表明，较高的溶剂温度加剧了水分子与蛋白质表面原子之间的竞争Hb相互作用，进而加剧了蛋白质内部原子之间的竞争Hb相互作用，从而增强了构象灵活性，促进了蛋白质的集体运动。提出了一个改进的FEL模型来解释溶剂迁移率在促进原子和原子基团微观运动到蛋白质整体集体运动的级联放大中所起的作用。
To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD) simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K) have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs) at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB) numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein.