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首页> 外文期刊>Journal of Molecular Biology >THERMODYNAMICS OF A REVERSE TURN MOTIF - SOLVENT EFFECTS AND SIDE-CHAIN PACKING
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THERMODYNAMICS OF A REVERSE TURN MOTIF - SOLVENT EFFECTS AND SIDE-CHAIN PACKING

机译：倒转母题的热力学-溶剂效应和侧链包装

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摘要

The linear pentapeptide, Ala-Tyr-cis-Pro-Tyr-Asp-NMA (AYPYD) is known to have a significant population of type VI turn conformers in aqueous solvent. We have carried out theoretical studies of the conformational energetics of this peptide using a potential of mean force (PMF) consisting of the AMBER/OPLS empirical potential energy function, a macroscopic electrostatic model of polar solvation, and a surface area-based model of non-polar solvation. Conformers were taken from molecular dynamics simulations reported elsewhere, or generated by a random search method reported here. The chain entropy of folding was calculated by a systematic search of accessible dihedral angle space. The intra-peptide component was found to strongly favor folding and was nearly cancelled by the polar solvation term which disfavored folding. The non-polar solvation term had Little effect. Fluctuations about the average value of the PMF were small and in accord with estimates from a simple harmonic model. When applied to conformers generated by a random search, the PMF selected a conformer close to the NMR-determined structure as the lowest energy conformer. The conformer with the second-lowest energy was extended, but was found to fold rapidly to the turn state in a subsequent molecular dynamics study, and may be an important state on the folding-unfolding pathway. Averages of the PMF were combined with the entropy estimates to provide an estimate of the free energy of folding that is in reasonable agreement with experimental results. Ln terms of the interplay between backbone electrostatic interactions and the packing of apolar side-chains, this peptide provides a model for the energetics of protein folding, and therefore makes a useful test case for calculations. (C) 1997 Academic Press Limited. [References: 64]
机译：已知线性五肽Ala-Tyr-顺式-Pro-Tyr-Asp-NMA（AYPYD）在水性溶剂中具有大量的VI型转角构象体。我们已经使用由AMBER / OPLS经验势能函数，极性溶剂化的宏观静电模型和基于表面积的非离子模型的平均力（PMF）对该肽的构象能量学进行了理论研究-极性溶剂化。合格者来自其他地方报道的分子动力学模拟，或通过此处报道的随机搜索方法生成。折叠的链熵是通过对可访问的二面角空间的系统搜索来计算的。发现肽内组分强烈有利于折叠，并且被不利于折叠的极性溶剂化术语几乎抵消。非极性溶剂化作用几乎没有。 PMF平均值的波动很小，符合简单谐波模型的估计。当将PMF应用于通过随机搜索生成的构象异构体时，它会选择与NMR确定的结构接近的构象异构体作为最低能量的构象异构体。具有第二低能量的构象异构体被扩展，但是在随后的分子动力学研究中被发现迅速折叠成转折状态，并且可能是折叠-展开途径中的重要状态。 PMF的平均值与熵估计值相结合，以提供与实验结果合理吻合的折叠自由能估计值。从主链静电相互作用和非极性侧链堆积之间的相互作用来看，该肽为蛋白质折叠的能量学提供了模型，因此为计算提供了有用的测试案例。 （C）1997 Academic Press Limited。 [参考：64]

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