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Free energy landscapes of peptides by enhanced conformational sampling

机译：通过增强的构象采样获得肽的自由能态

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The free energy landscapes of peptide conformations in water have been observed by the enhanced conformational sampling method, applying the selectively enhanced multicanonical molecular dynamics simulations. The conformations of the peptide dimers, -Gly-Gly-, -Gly-Ala-, -Gly-Ser-, -Ala-Gly-, -Asn-Gly-, -Pro-Gly-, -Pro-Ala-, and -Ala-Ala-, which were all blocked with N-terminal acetyl and C-terminal N-methyl groups, were individually sampled with the explicit TIP3P water molecules. From each simulation trajectory, we obtained the canonical ensemble at 300 K, from which the individual three-dimensional landscape was drawn by the potential of mean force using the three reaction coordinates: the backbone dihedral angle, psi, of the first amino acid, the backbone dihedral angle, phi, of the second amino acid, and the distance between the carbonyl oxygen of the N-terminal acetyl group and the C-terminal amide proton. The most stable state and several meta-stable states correspond to extended conformations and typical beta-turn conformations, and their free energy values were accounted for from the potentials of mean force at the states. In addition, the contributions from the intra-molecular energies of peptides and those from the hydration effects were analyzed. Consequently, the stable beta-turn conformations in the free energy landscape were consistent with the empirically preferred beta-turn types for each amino acid sequence. The thermodynamic values for the hydration effect were decomposed and they correlated well with the empirical values estimated from the solvent accessible surface area of each molecular conformation during the trajectories. The origin of the architecture of protein local fragments was analyzed from the viewpoint of the free energy and its decomposed factors. (C) 2000 Academic Press. [References: 66]
机译：通过使用选择性增强的多规范分子动力学模拟，通过增强的构象采样方法观察到了水中肽构象的自由能态。肽二聚体，-Gly-Gly-，-Gly-Ala-，-Gly-Ser-，-Ala-Gly-，-Asn-Gly-，-Pro-Gly-，-Pro-Ala-和-Ala-Ala-均被N-末端乙酰基和C-末端N-甲基封闭，分别用显性的TIP3P水分子采样。从每个模拟轨迹中，我们获得了300 K时的典范合奏，使用三个反应坐标：第一个氨基酸的骨架二面角psi，第二个氨基酸的骨架二面角phi和N末端乙酰基的羰基氧与C末端酰胺质子之间的距离。最稳定的状态和几个亚稳定状态对应于扩展构象和典型的β-转弯构象，并且它们的自由能值由该状态下的平均力势来解释。另外，分析了肽的分子内能量的贡献和水合作用的贡献。因此，在自由能图中稳定的β-转角构象与每个氨基酸序列的经验上优选的β-转角类型一致。分解水合效应的热力学值，并将其与根据轨迹中每个分子构象的溶剂可及表面积估算的经验值很好地相关。从自由能及其分解因素的角度分析了蛋白质局部片段结构的起源。 （C）2000学术出版社。 [参考：66]

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