BACKGROUND The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. RESULTS The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. CONCLUSIONS The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

中文翻译：

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来自海洋深水和浅水火球菌属物种的 Nip7 蛋白的分子动力学模拟。

背景鉴定蛋白质结构适应极端环境条件的机制是结构生物学的一项具有挑战性的任务。我们对参与来自浅水 (P. furiosus) 和深水 (P. abyssi) 海洋高热古菌在不同温度（300 和 373 K）和压力下的 RNA 加工的 Nip7 蛋白进行了分子动力学 (MD) 模拟（0.1、50 和 100 兆帕）。目的是揭示不同温度和压力下深海和浅海蛋白质模型之间的异同。结果 目前的结果表明，在所有压力和温度检查值下，这两种蛋白质的 3D 模型是紧凑、稳定的，并且与 P. abyssi Nip7 的已知晶体结构相似。MD 模拟过程中多肽链的结构偏差和波动在环区域中最为明显，对于两种蛋白质的 C 端结构域，它们的幅度更大。蛋白质球可能参与蛋白质-蛋白质相互作用的许多高度移动的片段被鉴定出来。鉴定了在深水和浅水蛋白质之间具有显着构象动力学差异的多肽链区域。结论我们的分析结果表明，在所检查的温度和压力范围内，温度升高对蛋白质球动态特性变化的影响大于压力升高。在升高温度和压力下，深海和浅海蛋白质模型的构象变化是不均匀的。我们目前的结果表明，浅水和深水蛋白质之间的氨基酸替换仅对两种蛋白质的整体稳定性产生轻微影响。相反，它们可能会影响 Nip7 蛋白与其蛋白质或 RNA 伙伴的相互作用。