Toward Modular Analysis of Supramolecular Protein Assemblies

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• 作者：Jaehoon Kim ; Jin-Gyun Kim ; Giseok Yun ; Phill-Seung Lee ; Do-Nyun Kim
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：September 8, 2015
• 年：2015
• 卷：11
• 期：9
• 页码：4260-4272
• 全文大小：1157K
• ISSN：1549-9626

文摘

Despite recent advances in molecular simulation technologies, analysis of high-molecular-weight structures is still challenging. Here, we propose an automated model reduction procedure aiming to enable modular analysis of these structures. It employs a component mode synthesis for the reduction of finite element protein models. Reduced models may consist of real biological subunits or artificial partitions whose dynamics is described using the degrees of freedom at the substructural interfaces and a small set of dominant vibrational modes only. Notably, the proper number of dominant modes is automatically determined using a novel estimator for eigenvalue errors without calculating the reference eigensolutions of the full model. The performance of the proposed approach is thoroughly investigated by analyzing 50 representative structures including a crystal structure of GroEL and an electron density map of a ribosome.