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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations
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A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations

机译：分子动力学模拟分析的多尺度方法比较

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摘要

Molecular dynamics (MD) is the only technique available for obtaining dynamic protein data at atomic spatial resolution and picosecond or finer temporal resolution. In recent years, the cost of computational resources has decreased exponentially while the number of known protein structures, many of which are not characterized biochemically, has increased rapidly. These events have led to an increase in the use of MD in biological research, both to examine phenomena that cannot be resolved experimentally and to generate hypotheses that direct further experimental research. In fact, several databases of MD simulations have arisen in recent years. MD simulations, and especially MD simulation databases, contain massive amounts of data, yet interesting phenomena often occur over very short time periods and on the scale of only a few atoms, Analysis of such data must balance these fine-detail events with the global picture they create. Here, we address the multiscale nature of the problem by comparing several MD analysis methods to show their strengths and weaknesses at various scales using the wild-type and R282W mutant forms of the DNA-binding domain of protein p53..By leveraging these techniques together, we are able to pinpoint fine-detail and big picture differences between the protein's variants. Our analyses indicate that the R282W mutation of p53 destabilizes the L1 loop and loosens the H2 helix conformation, but the loosened LI loop can be rescued by residue H115, preventing the R282W mutation from completely destabilizing the protein or abolishing activity.
机译：分子动力学（MD）是在原子空间分辨率和皮秒或更精细的时间分辨率下获取动态蛋白质数据的唯一可用技术。近年来，计算资源的成本呈指数下降，而已知蛋白质结构的数量迅速增加，其中许多蛋白质没有生化特性。这些事件导致MD在生物学研究中的使用增加，既可以检查无法通过实验解决的现象，也可以产生指导进一步实验研究的假设。实际上，近年来已经出现了几种MD模拟数据库。 MD仿真，尤其是MD仿真数据库，包含大量数据，但是有趣的现象通常会在很短的时间内发生，并且只有几个原子的规模。对此类数据的分析必须使这些精细事件与全局图平衡他们创造。在这里，我们通过比较几种MD分析方法来解决该问题的多方面性质，这些方法使用蛋白质p53的DNA结合域的野生型和R282W突变体形式，以不同的规模显示了它们的优缺点。 ，我们能够查明蛋白质变体之间的细微差异和较大差异。我们的分析表明，p53的R282W突变使L1环不稳定并使H2螺旋构象松散，但松散的LI环可被残基H115挽救，从而阻止了R282W突变使蛋白质完全不稳定或废除活性。

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