A conformational transition in the myosin VI converter contributes to the variable step size.
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M Karplus | M. Karplus | E. Vanden-Eijnden | M. Cecchini | M Cecchini | V. Ovchinnikov | V Ovchinnikov | E Vanden-Eijnden | V. Ovchinnikov
[1] Jürgen Schlitter,et al. Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in Insulin , 1993 .
[2] V. Pande,et al. On the transition coordinate for protein folding , 1998 .
[3] R. Zwanzig. High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .
[4] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[5] A. Fersht. Structure and mechanism in protein science , 1998 .
[6] E Weinan,et al. Transition pathways in complex systems: Reaction coordinates, isocommittor surfaces, and transition tubes , 2005 .
[7] Toshio Ando,et al. Video imaging of walking myosin V by high-speed atomic force microscopy , 2010, Nature.
[8] Michelle Peckham,et al. The Predicted Coiled-coil Domain of Myosin 10 Forms a Novel Elongated Domain That Lengthens the Head* , 2005, Journal of Biological Chemistry.
[9] Ivan Rayment,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 .
[10] Eric Vanden-Eijnden,et al. Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. , 2011, The Journal of chemical physics.
[11] Eric Vanden-Eijnden,et al. Simplified and improved string method for computing the minimum energy paths in barrier-crossing events. , 2007, The Journal of chemical physics.
[12] Eric Vanden-Eijnden,et al. Markovian milestoning with Voronoi tessellations. , 2009, The Journal of chemical physics.
[13] H. Sweeney,et al. Kinetic Mechanism and Regulation of Myosin VI* , 2001, The Journal of Biological Chemistry.
[14] M Karplus,et al. The missing link between thermodynamics and structure in F1-ATPase , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[15] Eric Vanden-Eijnden,et al. Transition-path theory and path-finding algorithms for the study of rare events. , 2010, Annual review of physical chemistry.
[16] Rasmus R. Schröder,et al. Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide , 2003, Nature.
[17] W. E,et al. Towards a Theory of Transition Paths , 2006 .
[18] K. Holmes,et al. The structural basis of muscle contraction. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[19] M Karplus,et al. Calculation of free-energy differences by confinement simulations. Application to peptide conformers. , 2009, The journal of physical chemistry. B.
[20] M. Karplus,et al. Pi release from myosin: a simulation analysis of possible pathways. , 2010, Structure.
[21] Amedeo Caflisch,et al. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water , 1999 .
[22] Eric Vanden-Eijnden,et al. Revisiting the finite temperature string method for the calculation of reaction tubes and free energies. , 2009, The Journal of chemical physics.
[23] Klaus Schulten,et al. Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain. , 2010, Structure.
[24] Jeffrey G. Reifenberger,et al. Myosin VI undergoes a 180° power stroke implying an uncoupling of the front lever arm , 2009, Proceedings of the National Academy of Sciences.
[25] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[26] Eric Vanden-Eijnden. Transition Path Theory , 2006 .
[27] E. Vanden-Eijnden,et al. On-the-fly string method for minimum free energy paths calculation , 2007 .
[28] Amber L. Wells,et al. Myosin VI is a processive motor with a large step size , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[29] Clara Franzini-Armstrong,et al. Myosin VI dimerization triggers an unfolding of a three-helix bundle in order to extend its reach. , 2009, Molecular cell.
[30] A. Mehta,et al. Myosin-V stepping kinetics: a molecular model for processivity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[31] H. Sweeney,et al. The Structural Basis for the Large Powerstroke of Myosin VI , 2007, Cell.
[32] Paul R Selvin,et al. Myosin VI Steps via a Hand-over-Hand Mechanism with Its Lever Arm Undergoing Fluctuations when Attached to Actin* , 2004, Journal of Biological Chemistry.
[33] Philipp Metzner,et al. Illustration of transition path theory on a collection of simple examples. , 2006, The Journal of chemical physics.
[34] Matthias Rief,et al. The myosin coiled-coil is a truly elastic protein structure , 2002, Nature materials.
[35] M. Karplus,et al. Stochastic boundary conditions for molecular dynamics simulations of ST2 water , 1984 .
[36] P. Knight. Dynamic behaviour of the head-tail junction of myosin. , 1996, Journal of molecular biology.
[37] P. Tavan,et al. Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force , 1996, Science.
[38] László Nyitray,et al. Visualization of an unstable coiled coil from the scallop myosin rod , 2003, Nature.
[39] B. Brooks,et al. Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .
[40] Michael Whittaker,et al. A 35-Å movement of smooth muscle myosin on ADP release , 1995, Nature.
[41] S. Rosenfeld,et al. How myosin VI coordinates its heads during processive movement , 2007, The EMBO journal.
[42] Carl A. Morris,et al. The structure of the myosin VI motor reveals the mechanism of directionality reversal , 2005, Nature.
[43] K. Homma,et al. Myosin VI walks "wiggly" on actin with large and variable tilting. , 2007, Molecular cell.
[44] Daniel Safer,et al. Myosin VI is an actin-based motor that moves backwards , 1999, Nature.
[45] Kenneth C Holmes,et al. The actin-myosin interface , 2010, Proceedings of the National Academy of Sciences.
[46] K C Holmes,et al. The structure of the rigor complex and its implications for the power stroke. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[47] Martin Karplus,et al. Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase. , 2003, Advances in protein chemistry.
[48] Richard B Sessions,et al. An efficient, path-independent method for free-energy calculations. , 2006, The journal of physical chemistry. B.
[49] Urs Haberthür,et al. FACTS: Fast analytical continuum treatment of solvation , 2008, J. Comput. Chem..
[50] Anne Houdusse,et al. Three myosin V structures delineate essential features of chemo‐mechanical transduction , 2004, The EMBO journal.
[51] P. Selvin,et al. Full-length myosin VI dimerizes and moves processively along actin filaments upon monomer clustering. , 2006, Molecular cell.
[52] Clara Franzini-Armstrong,et al. A flexible domain is essential for the large step size and processivity of myosin VI. , 2005, Molecular cell.
[53] G. Ciccotti,et al. String method in collective variables: minimum free energy paths and isocommittor surfaces. , 2006, The Journal of chemical physics.
[54] C. Dellago,et al. Transition Path Sampling , 2005 .
[55] Roberto Dominguez,et al. Structure of the light chain-binding domain of myosin V. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[56] P. Selvin,et al. The unique insert at the end of the myosin VI motor is the sole determinant of directionality , 2007, Proceedings of the National Academy of Sciences.
[57] Sebastian Doniach,et al. Long single α-helical tail domains bridge the gap between structure and function of myosin VI , 2008, Nature Structural &Molecular Biology.
[58] J. Sleep,et al. Exchange between inorganic phosphate and adenosine 5'-triphosphate in the medium by actomyosin subfragment 1. , 1980, Biochemistry.
[59] K. Trybus,et al. Coiled-coil unwinding at the smooth muscle myosin head-rod junction is required for optimal mechanical performance. , 2001, Biophysical journal.
[60] H E Huxley,et al. The Mechanism of Muscular Contraction , 1965, Scientific American.
[61] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[62] H. Sweeney,et al. The motor mechanism of myosin V: insights for muscle contraction. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[63] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[64] W. Kabsch,et al. Atomic model of the actin filament , 1990, Nature.
[65] P. Selvin,et al. Holding two heads together: Stability of the myosin II rod measured by resonance energy transfer between the heads , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[66] John Trinick,et al. Two-headed binding of a processive myosin to F-actin , 2000, Nature.