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2
Direct detection of molecular intermediates from first-passage times.通过首次通过时间直接检测分子中间体。
Sci Adv. 2020 May 1;6(18):eaaz4642. doi: 10.1126/sciadv.aaz4642. eCollection 2020 May.
3
Kinetics of Loop Closure in Disordered Proteins: Theory vs Simulations vs Experiments.无序蛋白质中闭环动力学:理论、模拟与实验对比
J Phys Chem B. 2020 Apr 30;124(17):3482-3493. doi: 10.1021/acs.jpcb.0c01437. Epub 2020 Apr 22.
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Memory effects in single-molecule force spectroscopy measurements of biomolecular folding.生物分子折叠的单分子力谱测量中的记忆效应。
Phys Chem Chem Phys. 2019 Nov 13;21(44):24527-24534. doi: 10.1039/c9cp04197d.
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Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors.通过反演观测到的牵连度从力谱实验中获得分子自由能分布。
J Chem Phys. 2019 Oct 21;151(15):154115. doi: 10.1063/1.5118362.
6
Probing microscopic conformational dynamics in folding reactions by measuring transition paths.通过测量转变途径来探测折叠反应中的微观构象动态。
Curr Opin Chem Biol. 2019 Dec;53:68-74. doi: 10.1016/j.cbpa.2019.07.006. Epub 2019 Aug 31.
7
Exact Solutions for Distributions of First-Passage, Direct-Transit, and Looping Times in Symmetric Cusp Potential Barriers and Wells.对称角形位垒和位阱中首通、直接穿越和循环时间分布的精确解。
J Phys Chem B. 2019 May 2;123(17):3786-3796. doi: 10.1021/acs.jpcb.9b01616. Epub 2019 Apr 23.
8
Measuring the average shape of transition paths during the folding of a single biological molecule.测量单个生物分子折叠过程中过渡路径的平均形状。
Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8125-8130. doi: 10.1073/pnas.1816602116. Epub 2019 Apr 5.
9
Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding.广义朗之万方程作为生物分子折叠中跨越势垒动力学的模型。
J Phys Chem B. 2019 Jan 31;123(4):802-810. doi: 10.1021/acs.jpcb.8b11137. Epub 2019 Jan 16.
10
Diffusion-limited association of disordered protein by non-native electrostatic interactions.无序蛋白质通过非天然静电相互作用的扩散限制缔合。
Nat Commun. 2018 Nov 9;9(1):4707. doi: 10.1038/s41467-018-06866-y.

宽分布的转变路径时间是潜在自由能景观多维性的特征。

Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes.

机构信息

Department of Chemistry, University of Texas at Austin, Austin, TX 78712.

Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892.

出版信息

Proc Natl Acad Sci U S A. 2020 Nov 3;117(44):27116-27123. doi: 10.1073/pnas.2008307117. Epub 2020 Oct 21.

DOI:10.1073/pnas.2008307117
PMID:33087575
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7959536/
Abstract

Recent single-molecule experiments have observed transition paths, i.e., brief events where molecules (particularly biomolecules) are caught in the act of surmounting activation barriers. Such measurements offer unprecedented mechanistic insights into the dynamics of biomolecular folding and binding, molecular machines, and biological membrane channels. A key challenge to these studies is to infer the complex details of the multidimensional energy landscape traversed by the transition paths from inherently low-dimensional experimental signals. A common minimalist model attempting to do so is that of one-dimensional diffusion along a reaction coordinate, yet its validity has been called into question. Here, we show that the distribution of the transition path time, which is a common experimental observable, can be used to differentiate between the dynamics described by models of one-dimensional diffusion from the dynamics in which multidimensionality is essential. Specifically, we prove that the coefficient of variation obtained from this distribution cannot possibly exceed 1 for any one-dimensional diffusive model, no matter how rugged its underlying free energy landscape is: In other words, this distribution cannot be broader than the single-exponential one. Thus, a coefficient of variation exceeding 1 is a fingerprint of multidimensional dynamics. Analysis of transition paths in atomistic simulations of proteins shows that this coefficient often exceeds 1, signifying essential multidimensionality of those systems.

摘要

最近的单分子实验观察到了转变路径,即在分子(特别是生物分子)克服激活障碍的短暂过程中被捕获的短暂事件。这些测量为生物分子折叠和结合、分子机器和生物膜通道的动力学提供了前所未有的机制见解。这些研究的一个关键挑战是从固有低维实验信号推断转变路径所经历的多维能量景观的复杂细节。一种常见的极简主义模型试图这样做,即沿着反应坐标的一维扩散,但它的有效性受到了质疑。在这里,我们表明,转变路径时间的分布(这是一个常见的实验可观测量)可用于区分由一维扩散模型描述的动力学与多维性至关重要的动力学。具体来说,我们证明,无论其潜在的自由能景观多么崎岖,从这个分布中获得的变异系数不可能超过 1 对于任何一维扩散模型:换句话说,该分布不能比单指数分布更宽。因此,变异系数超过 1 是多维动力学的特征。对蛋白质原子模拟中的转变路径的分析表明,该系数经常超过 1,表明这些系统的多维性至关重要。