利用单分子时间序列数据来优化分子模拟中的构象动力学。
Use of single-molecule time-series data for refining conformational dynamics in molecular simulations.
机构信息
Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; RIKEN Cluster for Pioneering Research, Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan; RIKEN Center for Biosystems Dynamics Research, Laboratory for Biomolecular Function Simulation, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047 Japan.
出版信息
Curr Opin Struct Biol. 2020 Apr;61:153-159. doi: 10.1016/j.sbi.2019.12.022. Epub 2020 Jan 28.
Atomically detailed description of conformational dynamics in biomolecules is often essential to understand biological functions. Combining experimental measurements with molecular simulations significantly improves the outcome. Ensemble refinements, where the simulations are utilized to refine ensemble averaged data in NMR, SAXS, or cryo-EM, are a popular approach in integrative structural biology. Single-molecule time-series data contain rich temporal information of biomolecular dynamics. However, direct usage of the time-series data together with molecular simulations is just beginning. Here, we review data-assimilation approaches linking molecular simulations with experimental time-series data and discuss current limitations and potential applications of this approach in integrative structural biology.
原子细节描述生物分子的构象动力学对于理解生物功能通常是至关重要的。将实验测量与分子模拟相结合可以显著提高结果的准确性。在整合结构生物学中，集合精修是一种很受欢迎的方法，它利用模拟来精修 NMR、SAXS 或 cryo-EM 中的集合平均数据。单分子时间序列数据包含丰富的生物分子动力学时间信息。然而，直接使用时间序列数据和分子模拟才刚刚开始。在这里，我们回顾了将分子模拟与实验时间序列数据相结合的数据同化方法，并讨论了这种方法在整合结构生物学中的当前局限性和潜在应用。
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