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Structure and Dynamics of the Actin Filament |
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| Authors: | Jim Pfaendtner Edward Lyman Thomas D Pollard Gregory A Voth |
| Institution: | 1 Center for Biophysical Modeling and Simulation, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA 2 Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA 3 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA 4 Department of Cell Biology, Yale University, New Haven, CT 06520-8103, USA 5 Department Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA |
| Abstract: | We used all-atom molecular dynamics simulations to investigate the structure and properties of the actin filament, starting with either the recent Oda model or the older Holmes model. Simulations of monomeric and polymerized actin show that polymerization changes the nucleotide-binding cleft, bringing together the Q137 side chain and bound ATP in a way that may enhance the ATP hydrolysis rate in the filament. Simulations with different bound nucleotides and conformations of the DNase I binding loop show that the persistence length of the filament depends only on loop conformation. Computational modeling reveals how bound phalloidin stiffens actin filaments and inhibits the release of γ-phosphate from ADP-Pi actin. |
| Keywords: | MD molecular dynamics Arp actin-related protein DB loop DNase I binding loop Pi inorganic phosphate CG coarse-grained PDB Protein Data Bank |
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