Effects of solvents on the intrinsic propensity of peptide backbone conformations
Effects of solvents on the intrinsic propensity of peptide backbone conformations
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溶剂对肽骨架构象固有倾向的影响
DOI：
10.1103/physreve.84.041933
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发表时间：
2011-10-28
影响因子：
2.4
通讯作者：
Wang, Wei
中科院分区：
文献类型：
--
作者：
Li, Wenfei;Qin, Meng;Wang, Wei
基于分子动力学模拟，我们研究了溶剂对肽骨架构象的内在倾向的影响。结果表明，与纯水相比，尿素水溶液降低了螺旋倾向。相比之下，甲醇降低了聚脯氨酸II（PPII）的倾向。这种溶剂依赖性的内在倾向的骨干构象与溶剂依赖性的水合的骨干基团和本地的肽内氢键的形成概率。尿素水溶液稳定局部肽内氢键的能力低，不利于螺旋构象。然而，具有低水合主链基团能力的甲醇不利于聚脯氨酸II构象。此外，溶剂效应可以通过肽的侧链进一步调节。在这项工作中观察到的肽骨架构象的内在倾向的溶剂效应表明，改变蛋白质骨架构象的内在倾向可以部分地有助于溶剂诱导的蛋白质结构和动力学变化。这些结果将有助于理解未折叠蛋白质或肽（或内在无序蛋白质）的构象分布的溶剂依赖性，其中全局三级相互作用不如折叠良好的蛋白质重要。
We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.