title: CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase.
abstract: Adenosine triphosphate (ATP) is an indispensable energy source in cells. In a wide variety of biological phenomena like glycolysis, muscle contraction/relaxation, and active ion transport, chemical energy released from ATP hydrolysis is converted to mechanical forces to bring about large-scale conformational changes in proteins. Investigation of structure-function relationships in these proteins by molecular dynamics (MD) simulations requires modeling of ATP in solution and ATP bound to proteins with accurate force-field parameters. In this study, we derived new force-field parameters for the triphosphate moiety of ATP based on the high-precision quantum calculations of methyl triphosphate. We tested our new parameters on membrane-embedded sarcoplasmic reticulum Ca(2+)-ATPase and four soluble proteins. The ATP-bound structure of Ca(2+)-ATPase remains stable during MD simulations, contrary to the outcome in shorter simulations using original parameters. Similar results were obtained with the four ATP-bound soluble proteins. The new force-field parameters were also tested by investigating the range of conformations sampled during replica-exchange MD simulations of ATP in explicit water. Modified parameters allowed a much wider range of conformational sampling compared with the bias toward extended forms with original parameters. A diverse range of structures agrees with the broad distribution of ATP conformations in proteins deposited in the Protein Data Bank. These simulations suggest that the modified parameters will be useful in studies of ATP in solution and of the many ATP-utilizing proteins.
authors.affiliation: Graduate School of Science and Engineering, Chuo University , 1-13-27, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan.|RIKEN Theoretical Molecular Science Laboratory , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.|RIKEN Advanced Institute for Computational Science, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Yasuaki
authors.initials: Y
authors.lastname: Komuro
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Suyong
authors.initials: S
authors.lastname: Re
authors.affiliation: RIKEN Advanced Institute for Computational Science, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Chigusa
authors.initials: C
authors.lastname: Kobayashi
authors.affiliation: Graduate School of Science and Engineering, Chuo University , 1-13-27, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan.
authors.forename: Eiro
authors.initials: E
authors.lastname: Muneyuki
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.|RIKEN Advanced Institute for Computational Science, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.|RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.|RIKEN iTHES , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita