Free energy landscapes of peptides by enhanced conformational sampling.
Free energy landscapes of peptides by enhanced conformational sampling.
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通过增强构象采样获得肽的自由能景观。
DOI：
10.1006/jmbi.1999.3440
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发表时间：
2000
影响因子：
5.6
通讯作者：
Haruki Nakamura
中科院分区：
文献类型：
--
作者：
N. Nakajima;J. Higo;A. Kidera;Haruki Nakamura
用增强构象采样方法，应用选择性增强多峰分子动力学模拟方法，观察了多肽在水中构象的自由能景观。用显性的TIP3P水分子分别对N端乙酰基和C端N-甲基封闭的-Gly-Gly-，-Gly-Ala-，-Gly-Ser-，-Ala-Gly-，-Asn-Gly-，-Pro-Gly-，-Pro-Ala-和-Ala-Ala-进行了构象分析。从每个模拟轨迹得到300K下的正则系综图，利用三个反应坐标：第一个氨基酸的主链二面角psi、第二个氨基酸的主链二面角Phi和N-端乙酰基上的羰基氧与C-端酰胺质子之间的距离，通过平均作用力势绘制出个体的三维景观。最稳定态和几个亚稳定态对应于扩展构象和典型的β转角构象，它们的自由能值由这些态处的平均力势来计算。此外，还分析了多肽分子内能量的贡献和水合作用的贡献。因此，自由能格局中稳定的β转角构象与每个氨基酸序列的经验首选的贝塔转角类型是一致的。对水合效应的热力学数值进行了分解，并与轨迹过程中由各分子构象的溶剂可及表面积估算的经验值进行了良好的关联。从自由能及其分解因子的角度分析了蛋白质局部碎片构型的起源。
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.
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影响因子：
5.6
作者：
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影响因子：
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作者：
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影响因子：
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作者：
PRIVALOV, PL;MAKHATADZE, GI
通讯作者：
MAKHATADZE, GI