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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
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Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions

机译：原始自然动力学的分层组织是通过竞争直接相互作用和水介导的相互作用而形成的

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摘要

The native state dynamics of the small globular serine protease inhibitor eglin c has been studied in a long 336 ns computer simulation in explicit solvent. We have elucidated the energy landscape explored during the course of the simulation by using Principal Component Analysis. We observe several basins in the energy landscape in which the system lingers for extended periods. Through an iterative process we have generated a tree-like hierarchy of states describing the observed dynamics. We observe a range of divergent contact types including salt bridges, hydrogen bonds, hydrophilic interactions, and hydrophobic interactions, pointing to the frustration between competing interactions. Additionally, we find evidence of competing water-mediated interactions. Divergence in water-mediated interactions may be found to supplement existing direct contacts, but they are also found to be independent of such changes. Water-mediated contacts facilitate interactions between residues of like charge as observed in the simulation. Our results provide insight into the complexity of the dynamic native state of a globular protein and directly probe the residual frustration in the native state.
机译：小球状丝氨酸蛋白酶抑制剂eglin c的自然状态动力学已在336 ns的计算机模拟中在显性溶剂中进行了长期研究。我们已经使用主成分分析阐明了在仿真过程中探索的能源格局。我们观察到能源景观中的几个盆地，其中系统持续了很长时间。通过迭代过程，我们生成了描述所观察到的动态的树状状态层次。我们观察到一系列不同的接触类型，包括盐桥，氢键，亲水性相互作用和疏水性相互作用，这表明竞争性相互作用之间的挫败感。此外，我们发现了竞争性水介导相互作用的证据。可以发现水介导的相互作用的差异补充了现有的直接接触，但也发现它们与这种变化无关。如在仿真中观察到的，水介导的接触促进了类似电荷的残基之间的相互作用。我们的结果提供了对球状蛋白动态天然状态的复杂性的见解，并直接探测了天然状态下的残留挫折感。

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