ArticleProceedings of the National Academy of Sciences of the United States of America2003
Substructure synthesis method for simulating large molecular complexes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 46 citations in OpenAlex.
- COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS.Multiscale modeling & simulation : a SIAM interdisciplinary journal · 2014Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- fSUB: normal mode analysis with flexible substructures.The journal of physical chemistry. B · 2012Article
- Group theory and biomolecular conformation: I. Mathematical and computational models.Journal of physics. Condensed matter : an Institute of Physics journal · 2010Review
- Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations.Journal of molecular biology · 2008Article
- Atomistic simulation approach to a continuum description of self-assembled beta-sheet filaments.Biophysical journal · 2006Article
- A New Method for Coarse-Grained Elastic Normal-Mode Analysis.Journal of chemical theory and computation · 2006Article
- Comparison of tRNA motions in the free and ribosomal bound structures.Biophysical journal · 2005Article
- Rigid-cluster models of conformational transitions in macromolecular machines and assemblies.Biophysical journal · 2005Article
- New advances in normal mode analysis of supermolecular complexes and applications to structural refinement.Current protein & peptide science · 2004Review
- Refinement of F-actin model against fiber diffraction data by long-range normal modes.Biophysical journal · 2004Article
- Small-world communication of residues and significance for protein dynamics.Biophysical journal · 2004Article
- Simulation of F-actin filaments of several microns.Biophysical journal · 2003Article
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Authors and funding
4 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
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.
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