Abstract
Actin filaments represent a truly multiscale physical system in which changes at the chemical reaction level (ATP hydrolysis) affect the conformation of actin subunits which in turn affect the binding affinity of actin-binding proteins and the stability of actin filaments. Connecting information between these scales and understanding the physical basis of these changes is a significant and challenging problem. We present a coarse-grained (CG) model and analysis of molecular dynamics simulations of actin filaments in the ATP and ADP-bound states to understand the large scale changes in structure and dynamics based on nucleotide state. Because the CG model is based on the underlying protein structure, changes in the distribution and stability of CG sites highlight specific areas in the filament that may respond to the nucleotide state, and which should be analyzed further at the atomistic scale. These CG models are essential to allow simulation of actin filaments at a network level and to characterize how nucleotide state affects the emergent properties of the network.
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