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Biophysical Journal 85:27-35 (2003)
© 2003 The Biophysical Society

Simulation of F-Actin Filaments of Several Microns

Dengming Ming *, Yifei Kong {dagger}, Yinghao Wu {ddagger} and Jianpeng Ma * {dagger} {ddagger}

* Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas; {dagger} Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas; and {ddagger} Department of Bioengineering, Rice University, Houston, Texas

Correspondence: Address reprint requests to Jianpeng Ma, One Baylor Plaza, BCM-125, Baylor College of Medicine, Houston, TX 77030. Tel.: 713-798-8187; Fax: 713-796-9438; E-mail: jpma{at}bcm.tmc.edu.

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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