Analysis of Molecular Dynamics Simulations of Protein Folding.
Analysis of Molecular Dynamics Simulations of Protein Folding.
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DOI：
10.1007/978-1-0716-1716-8_17
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发表时间：
2022-01-01
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影响因子：
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通讯作者：
Best, Robert B
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文献类型：
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作者：
Best, Robert B
蛋白质的无偏分子动力学模拟现在可以捕获自发折叠事件。这提供了反映折叠机制信息的大量数据，但提出了以有意义的方式解释它的挑战。在这里，我描述了如何使用此类模拟来识别用于描述折叠的反应状态和反应坐标，以及如何通过投影到这些坐标上来捕获折叠动力学。描述了用于量化对于定义折叠机制重要的相互作用的方法，以及用于将模拟与实验机制探针（例如 phi 值）进行比较的方法。
Unbiased molecular dynamics simulations of proteins can now capture spontaneous folding events. This provides a wealth of data reflecting information on folding mechanism, but raises the challenge of interpreting it in a meaningful way. Here, I describe how such simulations can be used to identify reactive states and reaction coordinates for describing folding, and how folding dynamics can be captured by projection onto those coordinates. Methods are described for quantifying the interactions important for defining the folding mechanism, and for comparison of simulations with experimental mechanistic probes, such as ϕ-values.