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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Substructure synthesis method for simulating large molecular complexes
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Substructure synthesis method for simulating large molecular complexes

机译：模拟大分子配合物的亚结构合成方法

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This paper reports a computational method for describing the conformational flexibility of very large biomolecular complexes using a reduced number of degrees of freedom. It is called the substructure synthesis method, and the basic concept is to treat the motions of a given structure as a collection of those of an assemblage of substructures. The choice of substructures is arbitrary and sometimes quite natural, such as domains, subunits, or even large segments of biomolecular complexes. To start, a group of low-frequency substructure modes is determined, for instance by normal mode analysis, to represent the motions of the substructure. Next, a desired number of substructures are joined together by a set of constraints to enforce geometric compatibility at the interface of adjacent substructures, and the modes for the assembled structure can then be synthesized from the substructure modes by applying the Rayleigh-Ritz principle. Such a procedure is computationally much more desirable than solving the full eigenvalue problem for the whole assembled structure. Furthermore, to show the applicability to biomolecular complexes, the method is used to study F-actin, a large filamentous molecular complex involved in many cellular functions. The results demonstrate that the method is capable of studying the motions of very large molecular complexes that are otherwise completely beyond the reach of any conventional methods. [References: 35]
机译：本文报道了一种计算方法，该方法使用减少的自由度来描述非常大的生物分子复合物的构象柔性。这称为子结构综合方法，其基本概念是将给定结构的运动视为子结构集合的运动的集合。亚结构的选择是任意的，有时是很自然的，例如结构域，亚基，甚至是大分子的生物分子复合物。首先，确定一组低频子结构模式，例如通过常规模式分析，以表示子结构的运动。接下来，通过一组约束将所需数量的子结构连接在一起，以在相邻子结构的界面处强制实现几何兼容性，然后可以通过应用Rayleigh-Ritz原理从子结构模式中合成组装结构的模式。与解决整个组装结构的完整特征值问题相比，此过程在计算上更为可取。此外，为了显示对生物分子复合物的适用性，该方法用于研究F-肌动蛋白，F-肌动蛋白是一种参与许多细胞功能的大型丝状分子复合物。结果表明，该方法能够研究非常大的分子复合物的运动，而这些运动完全超出了任何常规方法的范围。 [参考：35]

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