Multiscale Coarse-Graining via Normal Mode Analysis

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• 作者：Fei Xia ; Lanyuan Lu
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2012
• 出版时间：November 13, 2012
• 年：2012
• 卷：8
• 期：11
• 页码：4797-4806
• 全文大小：480K
• 年卷期：v.8,no.11(November 13, 2012)
• ISSN：1549-9626

文摘

A multiscale coarse-graining method called the normal-mode analysis based fluctuation matching (NMA-FM) is developed for constructing coarse-grained models of biomolecular systems. In the framework of normal-mode analysis, an arbitrary fine-grained model can be systematically converted to a more coarse-grained model, while the crucial low-frequency motions of the fine-grained system are able to be reproduced in the coarse-grained modeling. The method relies on the technique of fluctuation matching that has been devised earlier for parametrizing heterogeneous elastic network models based on data from atomistic molecular dynamics simulations. The new approach is quite efficient since it avoids expensive atomistic molecular dynamics simulations and can start from already coarse-grained elastic network models. In the practical aspect, the method is suitable for conformational analyses of large biomacromolecules and calculations of mechanical properties of biomaterials, which is demonstrated by the studied systems including an amyloid dimer, lysozyme and adenylate kinase proteins, and the S2 subdomain of myosin.