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Biophys. J. BioFAST: First Published December 16, 2005. doi:10.1529/biophysj.105.073924
© 2005 by the Biophysical Society.

A more recent version of this article appeared on March 1, 2006.
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BIOPHYSICAL THEORY AND MODELING

Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations

Jhih-Wei Chu 1 and Gregory A. Voth 1*

1 University of Utah

* To whom correspondence should be addressed. E-mail: voth{at}chem.utah.edu.

Submitted on September 6, 2005
Revised on October 31, 2005
Accepted on 22 November 2005


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

Key Words: Coarse-graining, actin, cell motility, molecular dynamics, multiscale modeling, persistence length




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