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Biophys J. 2006 Mar 1;90(5):1572-82. Epub 2005 Dec 16.

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations.

Author information

1
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.

Abstract

A coarse-grained (CG) procedure that incorporates the information obtained from all-atom molecular dynamics (MD) simulations is presented and applied to actin filaments (F-actin). This procedure matches the averaged values and fluctuations of the effective internal coordinates that are used to define a CG model to the values extracted from atomistic MD simulations. The fluctuations of effective internal coordinates in a CG model are computed via normal-mode analysis (NMA), and the computed fluctuations are matched with the atomistic MD results in a self-consistent manner. Each actin monomer (G-actin) is coarse-grained into four sites, and each site corresponds to one of the subdomains of G-actin. The potential energy of a CG G-actin contains three bonds, two angles, and one dihedral angle; effective harmonic bonds are used to describe the intermonomer interactions in a CG F-actin. The persistence length of a CG F-actin was found to be sensitive to the cut-off distance of assigning intermonomer bonds. Effective harmonic bonds for a monomer with its third nearest neighboring monomers are found to be necessary to reproduce the values of persistence length obtained from all-atom MD simulations. Compared to the elastic network model, incorporating the information of internal coordinate fluctuations enhances the accuracy and robustness for a CG model to describe the shapes of low-frequency vibrational modes. Combining the fluctuation-matching CG procedure and NMA, the achievable time- and length scales of modeling actin filaments can be greatly enhanced. In particular, a method is described to compute the force-extension curve using the CG model developed in this work and NMA. It was found that F-actin is easily buckled under compressive deformation, and a writhing mode is developed as a result. In addition to the bending and twisting modes, this novel writhing mode of F-actin could also play important roles in the interactions of F-actin with actin-binding proteins and in the force-generation process via polymerization.

PMID:
16361345
PMCID:
PMC1367308
DOI:
10.1529/biophysj.105.073924
[Indexed for MEDLINE]
Free PMC Article

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