title: The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
abstract: The open nucleotide pocket conformation of actin in the profilin:actinCaATP x-ray structure has been hypothesized to be a crucial intermediate for nucleotide exchange in the actin depolymerization/polymerization cycle. The requirement for ancillary modification of actin for crystallization leads to ambiguities in this interpretation, however. We have used molecular dynamics simulations to model the thermodynamic properties of the actin x-ray structure, outside the crystal lattice, in an aqueous environment with profilin removed. Our simulations show that the open-nucleotide-pocket, profilin-free structure is actually unstable, and closes. The coordination of actin to the nucleotide in the molecular-dynamics-derived closed structure is virtually identical to that in the closed profilin:actinSrATP x-ray structure. Thus, there is currently no thermodynamically stable structure representing the open-nucleotide-pocket state of actin.
authors.affiliation: Department of Pharmaceutical Chemistry, and Cardiovascular Research Institute, University of California, San Francisco, California, USA.
authors.forename: T J
authors.initials: TJ
authors.lastname: Minehardt
authors.forename: P A
authors.initials: PA
authors.lastname: Kollman
authors.forename: R
authors.initials: R
authors.lastname: Cooke
authors.forename: E
authors.initials: E
authors.lastname: Pate
mesh_terms: D000199:Actins / Q000737:chemistry; D000255:Adenosine Triphosphate / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D001703:Biophysics / Q000379:methods*; D002118:Calcium / Q000737:chemistry; D002417:Cattle; D003198:Computer Simulation; D003285:Contractile Proteins / Q000737:chemistry; D003460:Crystallization; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008840:Microfilament Proteins / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D051304:Profilins / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D013997:Time Factors; D014965:X-Rays
chemical_list: D000199:Actins; D003285:Contractile Proteins; D008840:Microfilament Proteins; D009711:Nucleotides; D051304:Profilins; D000255:Adenosine Triphosphate; D002118:Calcium