Paper Citing NAMD - Abstract
Ghodsi, Hossein; Kazemi, M. T.
Elastic Properties of Actin Assemblies in Different States of Nucleotide Binding
CELLULAR AND MOLECULAR BIOENGINEERING, 5:1-13, MAR 2012
In this paper, the elastic properties of monomeric actin (G-actin) and the trimer nucleus (G-actin trimer) in different states of nucleotide binding are estimated using steered molecular dynamic (SMD) simulations. Three nucleotide binding states are considered: ADP- and ATP-bound actin and nucleotide-free actin assemblies. Our results show that nucleotide binding and the corresponding changes in structure have significant effects on the mechanical behaviors of actin assemblies. Simulations reveal that the deformation behavior of G-actin monomers is generally elastic up to engineering strains of 16 and 40% in the tension and shear tests, respectively. In addition, the G-actin trimers react linearly up to strains of 18%. The computed persistence lengths for G-actin monomers and trimers are in the range of 8-20 mu m, which are consistent with earlier experimental results. Our atomistic simulation results also reveal that formation and rupture of hydrogen bonds between actin nucleotide binding site and its nucleotide have significant role in response of actin assemblies to loading. This study provides more information about the relationship of actin nucleotide binding and mechanical properties of cytoskeleton.
