title: Structural modeling and molecular dynamics simulation of the actin filament.
abstract: Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.
authors.affiliation: Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Splettstoesser
authors.forename: Kenneth C
authors.initials: KC
authors.lastname: Holmes
authors.forename: Frank
authors.initials: F
authors.lastname: Noé
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D008841:Actin Cytoskeleton / Q000737:chemistry* / Q000378:metabolism; D000244:Adenosine Diphosphate / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D008854:Microscopy, Electron; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D014961:X-Ray Diffraction
chemical_list: D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate