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