Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations
Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations
复制标题
通过分子动力学模拟对嗜冷和嗜温枯草杆菌蛋白酶样丝氨酸蛋白酶进行比较热展开研究
DOI：
10.1080/07391102.2016.1188155
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发表时间：
2017-01-01
影响因子：
4.4
通讯作者：
Liu, Shu-Qun
中科院分区：
文献类型：
--
作者：
Du, Xing;Sang, Peng;Liu, Shu-Qun
来自嗜冷海洋细菌弧菌的枯草杆菌蛋白酶样丝氨酸蛋白酶 VPR 的分子动力学 (MD) 模拟。 PA-44 及其嗜温同源物蛋白酶 K (PRK) 在四种不同温度（300、373、473 和 573 K）下进行了 20 ns。 MD轨迹的比较分析表明，在几乎所有温度下，VPR都比PRK表现出更大的结构波动/偏差、更不稳定的规则二级结构元素和更高的全局灵活性。尽管这两种蛋白酶在高温下遵循相似的解折叠途径，但 VPR 在较低温度下启动解折叠，并且在相同高温下比 PRK 解折叠更快。这些观察结果共同表明，VPR 比 PRK 更不稳定且更不耐热。结构/几何性质分析表明，与PRK相比，VPR具有更大的回转半径（Rg）、更少的分子内接触和氢键（HBs）、更多的蛋白质溶剂HBs、以及更小的非极性区域埋藏和更大的极性区域暴露。这些表明，VPR 灵活性的增加很可能是由于其分子内相互作用的减少以及由于极性区域的较大暴露而产生的更有利的蛋白质-溶剂相互作用所致，而 PRK 的稳定性的增强可能归因于其因更好优化的疏水性而增加的分子内相互作用。还分析并确定了导致这两种蛋白酶局部灵活性显着差异的因素。这项研究提供了对适应不同温度的同源丝氨酸蛋白酶热稳定性的分子基础的见解。
Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.