Substructure synthesis method for simulating large molecular complexes

Dengming Ming, Yifei Kong, Yinghao Wu, Jianpeng Ma

Research output: Contribution to journalArticle

38 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)104-109
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume100
Issue number1
DOIs
Publication statusPublished - Jan 7 2003
Externally publishedYes

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Keywords

  • Conformational flexibility
  • Elastic deformation
  • Large conformational change
  • Normal mode analysis

ASJC Scopus subject areas

  • General

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