Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations

The recovery stroke is a key step in the functional cycle of muscle motor protein myosin, during which pre‐recovery conformation of the protein is changed into the active post‐recovery conformation, ready to exersice force. We study the microscopic details of this transition using molecular dynamics simulations of atomistic models in implicit and explicit solvent. In more than 2 μs of aggregate simulation time, we uncover evidence that the recovery stroke is a two‐step process consisting of two stages separated by a time delay. In our simulations, we directly observe the first stage at which switch II loop closes in the presence of adenosine triphosphate at the nucleotide binding site. The resulting configuration of the nucleotide binding site is identical to that detected experimentally. Distribution of inter‐residue distances measured in the force generating region of myosin is in good agreement with the experimental data. The second stage of the recovery stroke structural transition, rotation of the converter domain, was not observed in our simulations. Apparently it occurs on a longer time scale. We suggest that the two parts of the recovery stroke need to be studied using separate computational models.

[1]  I. V. Negrashov,et al.  Structural kinetics of myosin by transient time-resolved FRET , 2011, Proceedings of the National Academy of Sciences.

[2]  Anne Houdusse,et al.  Structural and functional insights into the Myosin motor mechanism. , 2010, Annual review of biophysics.

[3]  D. Case,et al.  Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.

[4]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[5]  C. Brooks,et al.  Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.

[6]  C A Smith,et al.  X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution. , 1996, Biochemistry.

[7]  R. Cooke,et al.  Dynamics of the nucleotide pocket of myosin measured by spin-labeled nucleotides. , 2007, Biophysical journal.

[8]  T Shimada,et al.  Mutational Analysis of the Switch II Loop ofDictyostelium Myosin II* , 1998, The Journal of Biological Chemistry.

[9]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[10]  N. Okimoto,et al.  Behavior of water molecules in ATPase pocket of myosin , 2006 .

[11]  Junmei Wang,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..

[12]  R. Elber,et al.  Atomically detailed simulation of the recovery stroke in myosin by Milestoning , 2010, Proceedings of the National Academy of Sciences.

[13]  Jeremy C. Smith,et al.  The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. , 2007, Journal of molecular biology.

[14]  K C Holmes,et al.  Structural mechanism of muscle contraction. , 1999, Annual review of biochemistry.

[15]  E. Taylor,et al.  Mechanism of adenosine triphosphate hydrolysis by actomyosin. , 1971, Biochemistry.

[16]  Clive R. Bagshaw,et al.  Kinetic resolution of a conformational transition and the ATP hydrolysis step using relaxation methods with a Dictyostelium myosin II mutant containing a single tryptophan residue. , 2001, Biochemistry.

[17]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[18]  Haibo Yu,et al.  Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations , 2006, PLoS Comput. Biol..

[19]  H M Holden,et al.  X-ray structures of the myosin motor domain of Dictyostelium discoideum complexed with MgADP.BeFx and MgADP.AlF4-. , 1995, Biochemistry.

[20]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[21]  K. Fujiwara,et al.  Functional transitions in myosin: formation of a critical salt-bridge and transmission of effect to the sensitive tryptophan. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[22]  W. Jahn.  The association of actin and myosin in the presence of gamma-amido-ATP proceeds mainly via a complex with myosin in the closed conformation. , 2007, Biochemistry.

[23]  Clive R. Bagshaw,et al.  Analysis of Nucleotide Binding to DictyosteliumMyosin II Motor Domains Containing a Single Tryptophan Near the Active Site* , 2002, The Journal of Biological Chemistry.

[24]  I. Rayment,et al.  X-ray structures of the MgADP, MgATPgammaS, and MgAMPPNP complexes of the Dictyostelium discoideum myosin motor domain. , 1997, Biochemistry.

[25]  W. Stafford,et al.  Complexes of myosin subfragment-1 with adenosine diphosphate and phosphate analogs: probes of active site and protein conformation. , 1996, Biophysical chemistry.

[26]  M. Titus,et al.  Muscle and nonmuscle myosins probed by a spin label at equivalent sites in the force-generating domain , 2008, Proceedings of the National Academy of Sciences.

[27]  James A. Spudich,et al.  A myosin II mutation uncouples ATPase activity from motility and shortens step size , 2001, Nature Cell Biology.

[28]  K. Holmes,et al.  Role of the salt-bridge between switch-1 and switch-2 of Dictyostelium myosin. , 1999, Journal of molecular biology.

[29]  Eric J. Sorin,et al.  Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. , 2005, Biophysical journal.

[30]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[31]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[32]  Shuichi Nosé,et al.  Constant Temperature Molecular Dynamics Methods , 1991 .

[33]  D. Case,et al.  Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.

[34]  I. V. Negrashov,et al.  Structural dynamics of the myosin relay helix by time-resolved EPR and FRET , 2009, Proceedings of the National Academy of Sciences.

[35]  Stefan Fischer,et al.  Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke. , 2006, Journal of molecular biology.

[36]  Yang Yang,et al.  Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. , 2008, Journal of molecular biology.

[37]  H. Woo.  Exploration of the conformational space of myosin recovery stroke via molecular dynamics. , 2007, Biophysical chemistry.

[38]  Stefan Fischer,et al.  The structural coupling between ATPase activation and recovery stroke in the myosin II motor. , 2007, Structure.

[39]  J. Eccleston,et al.  Kinetics of the interaction of 2'(3')-O-(N-methylanthraniloyl)-ATP with myosin subfragment 1 and actomyosin subfragment 1: characterization of two acto-S1-ADP complexes. , 1991, Biochemistry.

[40]  Michael J. Harris,et al.  Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin , 2008, European Biophysics Journal.

[41]  C. Urbanke,et al.  A fluorescence temperature-jump study of conformational transitions in myosin subfragment 1. , 2001, The Biochemical journal.

[42]  Clive R. Bagshaw,et al.  The Mechanism of the Reverse Recovery Step, Phosphate Release, and Actin Activation of Dictyostelium Myosin II* , 2008, Journal of Biological Chemistry.

[43]  E. Taylor,et al.  Intermediate states of subfragment 1 and actosubfragment 1 ATPase: reevaluation of the mechanism. , 1978, Biochemistry.

[44]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[45]  Stefan Fischer,et al.  Structural mechanism of the recovery stroke in the myosin molecular motor. , 2005, Proceedings of the National Academy of Sciences of the United States of America.