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首页> 外文期刊>The Journal of Chemical Physics >Transition path times reveal memory effects and anomalous diffusion in the dynamics of protein folding
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Transition path times reveal memory effects and anomalous diffusion in the dynamics of protein folding

机译：过渡路径时间显示蛋白质折叠动态中的记忆效应和异常扩散

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摘要

Recent single-molecule experiments probed transition paths of biomolecular folding and, in particular, measured the time biomolecules spend while crossing their free energy barriers. A surprising finding from these studies is that the transition barriers crossed by transition paths, as inferred from experimentally observed transition path times, are often lower than the independently determined free energy barriers. Here we explore memory effects leading to anomalous diffusion as a possible origin of this discrepancy. Our analysis of several molecular dynamics trajectories shows that the dynamics of common reaction coordinates used to describe protein folding is subdiffusive, at least at sufficiently short times. We capture this effect using a one-dimensional fractional Brownian motion (FBM) model, in which the system undergoes a subdiffusive process in the presence of a potential of mean force, and show that this model yields much broader distributions of transition path times with stretched exponential long-time tails. Without any adjustable parameters, these distributions agree well with the transition path times computed directly from protein trajectories. We further discuss how the FBM model can be tested experimentally. Published by AIP Publishing.
机译：最近的单分子实验探测了生物分子折叠的过渡路径，特别是测量时间生物分子在穿过自由能屏障时花费。从这些研究中发现的令人惊讶的发现是从实验观察到的过渡路径时间推断出过渡路径交叉的过渡障碍通常低于独立确定的自由能屏障。在这里，我们探索记忆效应导致异常扩散作为这种差异的可能起源。我们对几个分子动力学轨迹的分析表明，用于描述蛋白质折叠的常见反应坐标的动态是沉重的，至少在足够短的时间内。我们使用一维分数褐色运动（FBM）模型捕获这种效果，其中系统在存在均值的潜在力的情况下经历沉屈的过程，并表明该模型产生了更广泛的过渡路径时间分布与拉伸指数长时间尾部。在没有任何可调节参数的情况下，这些分布很好地与直接从蛋白质轨迹计算的过渡路径时间很好。我们进一步讨论了如何通过实验测试FBM模型。通过AIP发布发布。

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