核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

doi:10.11944/j.issn.1000-0518.2018.10.170342

摘要/Abstract

摘要：

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。

关键词: 核糖核酸酶Sa, 停留时间相关函数, 偶极-偶极时间相关函数, 分子动力学模拟

Abstract:

Extensive molecular dynamics simulations were performed to study the distribution and dynamics of water and urea in the hydration shell of ribonuclease Sa(RNase Sa) under different urea concentrations. It is found that urea molecules have stronger interactions with protein than water molecules and are enriched on the surface of RNase Sa by displacing water molecules. Urea molecules prefer to interact with hydrophobic residues and form hydrogen bonds with the backbone of RNase Sa. The transitional and rotational dynamics of urea molecules are much slower than those of water molecules. Besides, the increased urea concentrations can slow down the transitional and rotational dynamics of water molecules, but have no regular influences on the dynamics of urea molecules. Our results can help understanding the different influences of urea and water molecules on the stability of proteins.

Key words: ribonuclease Sa, survival time correlation function, rotational time correlation function, molecular dynamics simulations

杨科成, 崔凤超, 李云琦. 核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟[J]. 应用化学, 2018, 35(10): 1243-1248.

YANG Kecheng, CUI Fengchao, LI Yunqi. Distribution and Dynamics of Water and Urea in Hydration Shell of Ribonuclease Sa:A Molecular Dynamics Simulation Study[J]. Chinese Journal of Applied Chemistry, 2018, 35(10): 1243-1248.

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