Paper Citing NAMD - Abstract
Matsushita, Shinji; Inoue, Yasuhiro; Adachi, Taiji
Quantitative analysis of extension-torsion coupling of actin filaments
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 420:710-713, APR 20 2012
Actin filaments have a double-helix structure consisting of globular actin molecules. In many mechanical cellular activities, such as cell movement, division, and shape control, modulation of the extensional and torsional dynamics of the filament has been linked to regulatory actin-binding protein functions. Therefore, it is important to quantitatively evaluate extension-torsion coupling of filament to better understand the actin filament dynamics. In the present study, the extension-torsion coupling was investigated using molecular dynamics simulations. We constructed a model for the actin filament consisting of 14 actin subunits in an ionic solvent as a minimal functional unit, and analyzed longitudinal and twisting Brownian motions of the filament. We then derived the expected value of energy associated with extension and torsion at equilibrium, and evaluated the extension-torsion stiffness of the filament from the thermal fluctuations obtained from the MD simulations. The results demonstrated that as the analyzed sampling-window duration was increased, the extension-torsion coupling stiffness evaluated on a nanosecond scale tended to converge to a value of 7.6 x 10(-11) N. The results obtained from this study will contribute to the understanding of biomechanical events, under mechanical tension and torque, involving extension-torsion coupling of filaments. (C) 2012 Elsevier Inc. All rights reserved.
