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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
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Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

机译：用于通过模拟和动力学实验探测生物分子动力学中单个松弛过程的动力学指纹

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摘要

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is "dynamical fingerprints" which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
机译：在他们对复杂生物分子系统动力学的看法上，动力学实验和模拟之间存在差距。尽管实验通常仅显示出一些易于辨别的指数松弛，但模拟通常表明复杂的多态行为。在这里，提出了一个协调这两种方法的理论框架。中心概念是“动态指纹”，其中包含在动态过程的时间尺度上的峰值，该峰值与由实验可观察到的幅度有关。指纹可以从实验和模拟数据中生成，并且通过匹配峰进行比较可以将模拟中存在的结构变化分配给实验观察到的松弛过程。该方法在这里应用于测试案例，该案例用分子动力学模拟解释了一组荧光肽上的单分子荧光相关光谱实验。这些肽表现出复杂的动力学，显示出与实验数据的明显简单性相一致。此外，指纹方法可用于设计具有特定位置标记的新实验，该标记可最佳地探测所研究分子中的特定动力学过程。

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    Frank Noe; Sooren Doose; Isabella Daidone; Marc Loollmann; Markus Sauer; John D. Chodera; Jeremy C. Smith;

  • 作者单位

    Research Center Matheon, FU Berlin, Arnimallee 6,14159 Berlin, Germany;

    Department of Biotechnology and Biophysics, Julius-Maximilians University,Am Hubland / Biozentrum, 97074 Wuurzburg, Germany;

    Dipartimento di Chimica, University of L'Aquila, Via Vetoio (Coppito 1), 67010 Coppito (AQ),Italy;

    Applied Laser Physics and Laser Spectroscopy, Bielefeld University, Universitatsstrasse 25, 33615 Bielefeld, Germany;

    Department of Biotechnology and Biophysics, Julius-Maximilians University,Am Hubland / Biozentrum, 97074 Wuurzburg, Germany;

    California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720-3220;

    Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831-6255;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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  • 正文语种 eng
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