Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k.
Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k.
复制标题
单价离子结合对 S100 家族钙结合蛋白钙结合蛋白 D9k 分子动力学的影响。
DOI：
10.1002/jcc.25839
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发表时间：
2019
影响因子：
3
通讯作者：
Rance,Mark
中科院分区：
文献类型：
--
作者：
Thapa,Mahendra;Johnson,Eric;Rance,Mark
钙结合蛋白D9是EF-手型钙结合蛋白S100亚家族的成员，并已作为生物物理学研究的重要模型系统。无钙（apo）状态的快速时标动力学特征使用分子动力学模拟。骨架NH键矢量的序参数由模拟确定，并与实验得出的值进行比较，重点是钙结合位点I的动力学。在没有离子结合的情况下，位点I残基的模拟有序参数和实验有序参数之间存在显著差异。然而，它被发现在模拟中，Na+离子可以结合在网站I，并从模拟确定的顺序参数是在极好的协议与实验。与其他S100家族成员的X射线结构进行比较，其中观察到或建议Na+离子结合在位点I。© 2019 Wiley Periodicals，Inc.
Calbindin D9kis a member of the S100 subfamily of EF‐hand calcium binding proteins, and has served as an important model system for biophysical studies. The fast timescale dynamics of the calcium‐free (apo) state is characterized using molecular dynamics simulations. Order parameters for the backbone NH bond vectors are determined from the simulations and compared with experimentally derived values, with a focus on the dynamics of calcium‐binding site I. There is a significant discrepancy between simulated and experimental order parameters for site I residues in the case of no ion bound in site I. However, it was found in the simulations that a Na+ion can bind in site I, and the resulting order parameters determined from the simulations are in excellent agreement with experiment. Comparisons are made to X‐ray structures of other S100 family members in which Na+ions were observed or suggested to be bound in site I. © 2019 Wiley Periodicals, Inc.