Molecular dynamics simulations of evolved collective motions of atoms in the myosin motor domain upon perturbation of the ATPase pocket

Spudich, 1994, How molecular motors work, Nature, 372, 515, 10.1038/372515a0 Yanagida, 2000, Single-motor mechanics and models of the myosin motor, Philos. Trans. R. Soc. Lond., B, 355, 441, 10.1098/rstb.2000.0585 Rayment, 1993, Structure of the actin–myosin complex and its implications for muscle contraction, Science, 261, 58, 10.1126/science.8316858 Suzuki, 1998, Swing of the lever arm of a myosin motor at the isomerization and phosphate-release steps, Nature, 396, 380, 10.1038/24640 Houdusse, 1999, Atomic structure of scallop myosin subfragment S1 comlexed with MgADP: a novel conformation of the myosin head, Cell, 97, 459, 10.1016/S0092-8674(00)80756-4 Himmel, 2002, Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor, Proc. Natl. Acad. Sci., 99, 12645, 10.1073/pnas.202476799 Kitamura, 1999, A single myosin head moves along an actin filament with regular steps of 5.3 nanometres, Nature, 397, 129, 10.1038/16403 Minehardt, 2001, Molecular dynamics study of the energetic, mechanic, and structural implications of a closed phosphate tube in ncd, Biophys. J., 80, 1151, 10.1016/S0006-3495(01)76092-4 Lawson, 2004, Molecular dynamics analysis of structural factors influencing back door Pi release in myosin, Biophys. J., 86, 3794, 10.1529/biophysj.103.037390 Ishijima, 1998, Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin, Cell, 92, 161, 10.1016/S0092-8674(00)80911-3 Vale, 1990, Protein motors and Maxwell's demons: does mechanochemical transduction involve a thermal ratchet, Adv. Biophys., 26, 97, 10.1016/0065-227X(90)90009-I Case, 2002, vol. 7 Cornell, 1995, A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc., 117, 5179, 10.1021/ja00124a002 Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869 Ryckaert, 1977, Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5 Berendsen, 1984, Molecular dynamics with coupling to an external bath, J. Chem. Phys., 81, 3684, 10.1063/1.448118 Iwamoto, 2001, X-ray diffraction evidence for the lack of stereospecific protein interactions in highly activated actomyosin complex, J. Mol. Biol., 305, 863, 10.1006/jmbi.2000.4334 Ishiwata, 1987, Rotational motions of myosin heads in myofibril studied by phosphorescence anisotropy decay measurements, J. Biol. Chem., 262, 8314, 10.1016/S0021-9258(18)47565-5 Ramachandran, 1999, Rotational dynamics of the regulatory light chain in scallop muscle detected by time-resolved phosphorescence anisotropy, Biochemistry, 38, 9097, 10.1021/bi9902945 Roopnarine, 1998, Microsecond rotational dynamics of spin-labeled myosin regulatory light chain induced by relaxation and contraction of scallop muscle, Biochemistry, 37, 14428, 10.1021/bi9808363 Sugimoto, 1995, Conformational changes of the myosin heads during hydrolysis of ATP as analyzed by X-ray solution scattering, Biophys. J., 68, 29s Astumian, 1994, Fluctuation driven ratchets, Phys. Rev. Lett., 72, 1766, 10.1103/PhysRevLett.72.1766 Esaki, 2003, Model describing the biased Brownian movement of myosin, Proc. Jpn. Acad., Ser. B, 79, 9, 10.2183/pjab.79B.9 Go, 1990, A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis, Biophys. Chem., 35, 105, 10.1016/0301-4622(90)80065-F Kitao, 1991, The effects of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum, Chem. Phys., 158, 447, 10.1016/0301-0104(91)87082-7 Brooks, 1995, Harmonic analysis of large systems. I: methodology, J. Comput. Chem., 16, 1522, 10.1002/jcc.540161209 Higo, 2001, Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data, J. Comput. Chem., 22, 1983, 10.1002/jcc.1147 Tai, 2002, Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation, J. Am. Chem. Soc., 124, 6153, 10.1021/ja017310h Moritsugu, 2003, Temperature dependence of vibrational energy transfer in a protein molecule, J. Phys. Chem., B, 107, 3309, 10.1021/jp027823q