ArticleBiophysical journal2003
Simulation of F-actin filaments of several microns.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation.PloS one · 2013Article
- A mechanochemical model of actin filaments.Biophysical journal · 2012Article
- fSUB: normal mode analysis with flexible substructures.The journal of physical chemistry. B · 2012Article
- Response of an actin filament network model under cyclic stretching through a coarse grained Monte Carlo approach.Journal of theoretical biology · 2011Article
- Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives.Bioinformatics and biology insights · 2008Article
- Energetics and dynamics of constrained actin filament bundling.Biophysical journal · 2006Article
- Coarse-grained modeling of the actin filament derived from atomistic-scale simulations.Biophysical journal · 2006Article
- A New Method for Coarse-Grained Elastic Normal-Mode Analysis.Journal of chemical theory and computation · 2006Article
- The role of shape in determining molecular motions.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
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4 authors.
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Abstract
Here we report the results of applying substructure synthesis method to the simulation of F-actin filaments of several microns in length. The elastic deformational modes of long F-actin filaments were generated from the vibrational modes of the 13-subunit repeat of F-actin using a hierarchical synthesis scheme. The computationally synthesized deformational modes, in the very low-frequency regime, are in good agreement with theoretical solutions for long homogeneous elastic rods, which confirmed the usefulness of substructure synthesis method. Other low-frequency modes carry rich local deformational features that are unique to F-actins. All these modes thus provide a theoretical basis set for a description of spontaneously occurring thermal deformations, such as undulations, of the filaments. The results demonstrate that substructure synthesis method, as a method for computational modal analysis, is capable of scaling up the microscopic dynamic information, obtained from atomistic simulations, to a wide range of macroscopic length scale. Moreover, the combination of substructure synthesis method and hierarchical synthesis scheme provides an effective way in dealing with complex systems of periodic repeats that are abundant in cells.
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