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首页> 外文期刊>Journal of Molecular Biology >Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles.
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Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles.

机译：用于比较多种分子动力学轨迹的分析方法：在蛋白质展开途径和变性集合体中的应用。

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摘要

In molecular dynamics simulations of protein unfolding, the pathway of one protein molecule is studied at a time. In contrast, experimental denaturation studies sample from large ensembles of molecules passing from the native to unfolded state. If reasonable comparisons with experiment are to be made, then the generality of the simulations needs to be confirmed by performing multiple unfolding simulations. Given that protein unfolding trajectories are very complicated functions of the proteins and the environment, comparing different trajectories, even under the same conditions, is not straightforward. Several methods are presented here that attempt to accomplish this task at different levels of complexity. The simpler methods are geometry based and make use of the root-mean-squared deviations between structures, while the more complicated methods are based on the time variation of the various properties of the system during the unfolding process. These methods are applied to multiple simulations of three different proteins, bovine pancreatic trypsin inhibitor, chymotrypsin inhibitor 2, and barnase. In general, for these three proteins protein unfolding proceeded via expansion of the core and fraying of secondary structure to yield the major transition state. Once past the transition state, the trajectories for a given protein diverged as the protein lost further secondary and tertiary structure by a variety of mechanisms. Although the unfolding pathways diverged, similar conformations were populated in the denatured state even when the unfolding occurred via different pathways. The multitude of different pathways leading to the denatured state agrees with the funnel description of protein folding. Although the pathways differed in conformational space, the physical properties of the conformations were often similar, highlighting the danger of assuming that similar observed properties imply similar conformations. In fact, there may be many different "conformational pathways" of unfolding that fit within a preferred "property space pathway". Copyright 1999 Academic Press.
机译：在蛋白质展开的分子动力学模拟中，一次研究一个蛋白质分子的途径。相比之下，实验性变性研究的样本来自从天然状态到未折叠状态的大分子分子。如果要与实验进行合理的比较，则需要通过执行多次展开模拟来确认模拟的普遍性。考虑到蛋白质的发展轨迹是蛋白质和环境的非常复杂的功能，即使在相同条件下，比较不同的轨迹也不是一件容易的事。这里介绍了几种方法，它们试图以不同的复杂度来完成此任务。比较简单的方法是基于几何的，并利用结构之间的均方根偏差，而比较复杂的方法是基于展开过程中系统各种属性的时间变化。这些方法适用于三种不同蛋白质的多重模拟，牛胰胰蛋白酶抑制剂，胰凝乳蛋白酶抑制剂2和Barnase。通常，对于这三种蛋白质，蛋白质的解折叠是通过核心的扩展和二级结构的磨损进行的，从而产生主要的过渡状态。一旦超过过渡状态，给定蛋白质的轨迹就会发散，因为该蛋白质通过各种机制失去了进一步的二级和三级结构。尽管展开途径不同，但即使通过不同途径发生了展开，在变性状态下仍存在相似的构象。导致变性状态的多种不同途径与蛋白折叠的漏斗描述一致。尽管构象空间中的途径不同，但构象的物理性质通常相似，突出了假设相似的观察性质暗示相似构象的危险。实际上，可能存在许多不同的展开“构象路径”，它们适合于优选的“财产空间路径”。版权所有1999，学术出版社。

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