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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Conformational Dynamics of Trialanine in Water: A Molecular Dynamics Study
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Conformational Dynamics of Trialanine in Water: A Molecular Dynamics Study

机译：水中三丙氨酸的构象动力学：分子动力学研究

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摘要

Classical molecular dynamics (MD) studies of trialanine in aqueous solution are presented. The investigations have been inspired by recent 2D vibrational spectroscopy experiments of Woutersen and Hamm (J. Phys. Chem. B 2000, 104, 11316), who determined the structure and the conformational fluctuations of trialanine. The MD studies include various unbiased 20-ns simulations as well as umbrella sampling calculations of the potential of mean force along the central dihedral angles of trialanine. By employing the GROMOS96 force field, it is predicted that solvated trialanine is predomainantly (～80%) found in the extended conformations β and P_(II) and is also (～16) found in the helix conformation α_R. The results are explained by analyzing the free-energy contributions of intra- and intermolecular interactions, calculating the absolute entropy of the trialanine molecule, investigating the solvation and hydrogen bonding of the peptide, and studying the transitions between the extended and helix conformations. Moreover, the vibrational scross-relaxation rates associated with the two amide I modes of trialanine area calculated. The conformational structures and dynamics obtained from the MD studies are shown to be in good overall agreement with experimental data.
机译：介绍了在水溶液中的三氢嘌呤的经典分子动力学（MD）研究。该研究的灵感来自最近的Woutersen和Hamm的2D振动光谱实验（J. Phys。Chem。B 2000，104，11316），他们确定了三氢嘌呤的结构和构象波动。 MD研究包括各种无偏的20 ns模拟，以及沿三氢嘌呤中心二面角的平均力潜力的总括式采样计算。通过使用GROMOS96力场，可以预测，在扩展构象β和P_（II）中，溶剂化的三氢嘌呤主要存在（〜80％），在螺旋构型α_R中也存在（〜16）。通过分析分子内和分子间相互作用的自由能贡献，计算三氢嘌呤分子的绝对熵，研究肽的溶剂化和氢键以及研究延伸构象和螺旋构象之间的过渡来解释结果。此外，计算了与三氢嘌呤区的两种酰胺I模式相关的振动横向弛豫速率。从MD研究获得的构象结构和动力学显示出与实验数据具有良好的总体一致性。

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