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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >A COMPARATIVE ANALYSIS OF FOLDING PATHWAYS OF THERMOPHILIC AND MESOPHILIC PROTEINS BY MONTE CARLO SIMULATIONS
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A COMPARATIVE ANALYSIS OF FOLDING PATHWAYS OF THERMOPHILIC AND MESOPHILIC PROTEINS BY MONTE CARLO SIMULATIONS

机译：蒙特卡罗模拟对嗜热蛋白和中介蛋白折叠路径的比较分析

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In this work we have studied the folding pathways for four pairs of homologous proteins from thermophilic and mesophilic organisms from two different structural classes (class a, all-α proteins and class d, α + β proteins) using Monte Carlo simulations. We have obtained 50 trajectories for each protein and followed the free-energy profile and the order of folding of secondary structure elements between the last occurrence of the completely unfolded state and the first occurrence of the completely folded state. It turns out that the period of successful crossing of the free-energy barrier between unfolded and folded states for 40–45 trajectories (80–90%) makes 10% of the total folding time for four proteins (1tzvA, 1eyvA, 351c, and 1t4aA) and only 0.1% for two proteins (1dd3, 1ctf). This observation can be explained by a higher free-energy barrier for these proteins (1dd3, 1ctf) in comparison with other studied proteins. We have observed that folding pathways of thermophilic and mesophilic proteins may be the same, partly the same, and different. And similarity or difference between the folding pathways of thermophilic and mesophilic proteins does not depend on the structural class to which these proteins belong. Folding pathways for proteins from both classes correlate with the calculated folding nuclei for these proteins.
机译：在这项工作中，我们使用蒙特卡洛模拟研究了来自两个不同结构类别（a类，全α蛋白和d类，α+β蛋白）的嗜热和嗜温生物的四对同源蛋白的折叠途径。我们已经为每种蛋白质获得了50条轨迹，并遵循了自由能谱和二级结构元素在最后一次完全折叠状态与第一次完全折叠状态之间的折叠顺序。结果表明，在40-45个轨迹（80-90％）的折叠状态和折叠状态之间成功越过自由能垒的时间占四种蛋白质（1tzvA，1eyvA，351c和1t4aA）和两种蛋白质（1dd3、1ctf）的比例仅为0.1％。与其他研究过的蛋白质相比，这些蛋白质（1dd3、1ctf）具有更高的自由能垒可以解释这一现象。我们已经观察到嗜热和嗜温蛋白的折叠途径可能是相同的，部分相同的和不同的。嗜热蛋白和嗜温蛋白的折叠途径之间的相似性或差异并不取决于这些蛋白所属的结构类别。两种蛋白质的折叠路径与这些蛋白质的计算折叠核相关。

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