메뉴 건너뛰기




Volumn 2, Issue 3, 2009, Pages 366-374

Coarse-grained structural modeling of molecular motors using multibody dynamics

Author keywords

Molecular simulation; Myosin V; Open source software; Protein kinematics

Indexed keywords

ACTIN; MOLECULAR MOTOR; MYOSIN V;

EID: 70349531201     PISSN: 18655025     EISSN: 18655033     Source Type: Journal    
DOI: 10.1007/s12195-009-0084-4     Document Type: Review
Times cited : (18)

References (45)
  • 2
    • 0036175994 scopus 로고    scopus 로고
    • Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase
    • RA Bockmann H Grubmuller 2002 Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase Nat. Struct. Biol 9 198 202
    • (2002) Nat. Struct. Biol , vol.9 , pp. 198-202
    • Bockmann, R.A.1    Grubmuller, H.2
  • 4
    • 0002133110 scopus 로고    scopus 로고
    • MBO(N)D: A multibody method for long-time molecular dynamics simulations
    • 10.1002/(SICI)1096-987X(200002)21:3<159::AID-JCC1>3.0.CO;2-J
    • HM Chun, et al. 2000 MBO(N)D: a multibody method for long-time molecular dynamics simulations J. Comput. Chem 21 159 184 10.1002/(SICI)1096-987X(200002) 21:3<159::AID-JCC1>3.0.CO;2-J
    • (2000) J. Comput. Chem , vol.21 , pp. 159-184
    • Chun, H.M.1
  • 7
    • 10644225267 scopus 로고    scopus 로고
    • Three myosin V structures delineate essential features of chemo-mechanical transduction
    • DOI 10.1038/sj.emboj.7600458
    • PD Coureux HL Sweeney A Houdusse 2004 Three myosin V structures delineate essential features of chemo-mechanical transduction EMBO J. 23 4527 4537 10.1038/sj.emboj.7600458 (Pubitemid 39657853)
    • (2004) EMBO Journal , vol.23 , Issue.23 , pp. 4527-4537
    • Coureux, P.-D.1    Sweeney, H.L.2    Houdusse, A.3
  • 8
    • 39749143266 scopus 로고    scopus 로고
    • Least action principles and their application to constrained and task-level problems in robotics and biomechanics
    • 05262314 10.1007/s11044-007-9097-8
    • V De Sapio O Khatib S Delp 2008 Least action principles and their application to constrained and task-level problems in robotics and biomechanics Multib. Syst. Dyn. 19 303 322 05262314 10.1007/s11044-007-9097-8
    • (2008) Multib. Syst. Dyn , vol.19 , pp. 303-322
    • De Sapio, V.1    Khatib, O.2    Delp, S.3
  • 9
    • 33847680889 scopus 로고    scopus 로고
    • Dynamics of the unbound head during myosin V processive translocation
    • DOI 10.1038/nsmb1206, PII NSMB1206
    • AR Dunn JA Spudich 2007 Dynamics of the unbound head during myosin V processive translocation Nat. Struct. Biol 14 246 248 10.1038/nsmb1206 (Pubitemid 46355576)
    • (2007) Nature Structural and Molecular Biology , vol.14 , Issue.3 , pp. 246-248
    • Dunn, A.R.1    Spudich, J.A.2
  • 10
    • 0037468838 scopus 로고    scopus 로고
    • Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization
    • DOI 10.1038/nature01529
    • JN Forkey ME Quinlan M Alexander Shaw JET Corrie YE Goldman 2003 Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization Nature 422 399 404 10.1038/nature01529 (Pubitemid 36411387)
    • (2003) Nature , vol.422 , Issue.6930 , pp. 399-404
    • Forkey, J.N.1    Quinlan, M.E.2    Shaw, M.A.3    Corrie, J.E.T.4    Goldman, Y.E.5
  • 11
    • 0345528058 scopus 로고    scopus 로고
    • Crystal Structure of Scallop Myosin S1 in the Pre-Power Stroke State to 2. 6 A Resolution: Flexibility and Function in the Head
    • DOI 10.1016/j.str.2003.10.013
    • S Gourinath, et al. 2003 Crystal structure of scallop myosin S1 in the pre-power stroke state to 2.6 Å resolution: flexibility and function in the head Structure 11 1621 1627 10.1016/j.str.2003.10.013 (Pubitemid 37510360)
    • (2003) Structure , vol.11 , Issue.12 , pp. 1621-1627
    • Gourinath, S.1    Himmel, D.M.2    Brown, J.H.3    Reshetnikova, L.4    Szent-Gyorgyi, A.G.5    Cohen, C.6
  • 13
    • 0033766762 scopus 로고    scopus 로고
    • A myosin family tree
    • T Hodge MJ Cope 2000 A myosin family tree J. Cell Sci. 113 3353 3354
    • (2000) J. Cell Sci , vol.113 , pp. 3353-3354
    • Hodge, T.1    Cope, M.J.2
  • 14
    • 0141843643 scopus 로고    scopus 로고
    • Elechron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide
    • DOI 10.1038/nature02005
    • KC Holmes I Angert F Jon Kull W Jahn RR Schroder 2003 Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide Nature 425 423 427 10.1038/nature02005 (Pubitemid 37187274)
    • (2003) Nature , vol.425 , Issue.6956 , pp. 423-427
    • Holmes, K.C.1    Angert, I.2    Kull, F.J.3    Jahn, W.4    Schroder, R.R.5
  • 16
    • 37548999364 scopus 로고    scopus 로고
    • Force generation in Kinesin Hinges on cover-neck bundle formation
    • 10.1016/j.str.2007.11.008
    • W Hwang MJ Lang M Karplus 2008 Force generation in Kinesin Hinges on cover-neck bundle formation Structure 16 62 71 10.1016/j.str.2007.11.008
    • (2008) Structure , vol.16 , pp. 62-71
    • Hwang, W.1    Lang, M.J.2    Karplus, M.3
  • 18
    • 21244502885 scopus 로고    scopus 로고
    • Dynamics of myosin-V processivity
    • DOI 10.1529/biophysj.104.047662
    • G Lan SX Sun 2005 Dynamics of myosin-V processivity Biophys. J. 88 999 1008 10.1529/biophysj.104.047662 (Pubitemid 40975933)
    • (2005) Biophysical Journal , vol.88 , Issue.2 , pp. 999-1008
    • Lan, G.1    Sun, S.X.2
  • 19
    • 34249894142 scopus 로고    scopus 로고
    • Small-angle X-ray scattering from RNA, proteins, and protein complexes
    • DOI 10.1146/annurev.biophys.36.040306.132655
    • J Lipfert S Doniach 2007 Small-angle X-ray scattering from RNA, proteins, and protein complexes Annu. Rev. Biophys. Biomol. Struct. 36 307 10.1146/annurev.biophys.36.040306.132655 (Pubitemid 46998121)
    • (2007) Annual Review of Biophysics and Biomolecular Structure , vol.36 , pp. 307-327
    • Lipfert, J.1    Doniach, S.2
  • 21
    • 84976783589 scopus 로고
    • Algorithm 550: Solid polyhedron measures
    • 10.1145/355873.355885
    • AM Messner GQ Taylor 1980 Algorithm 550: solid polyhedron measures ACM Trans. Math. Softw. 6 121 130 10.1145/355873.355885
    • (1980) ACM Trans. Math. Softw , vol.6 , pp. 121-130
    • Messner, A.M.1    Taylor, G.Q.2
  • 23
    • 36749068925 scopus 로고    scopus 로고
    • How kinesin waits between steps
    • DOI 10.1038/nature06346, PII NATURE06346
    • T Mori RD Vale M Tomishige 2007 How kinesin waits between steps Nature 450 750 754 10.1038/nature06346 (Pubitemid 350207692)
    • (2007) Nature , vol.450 , Issue.7170 , pp. 750-754
    • Mori, T.1    Vale, R.D.2    Tomishige, M.3
  • 24
    • 56949097193 scopus 로고    scopus 로고
    • Substructured molecular dynamics using multibody dynamics algorithms
    • 10.1016/j.ijnonlinmec.2008.04.003
    • RM Mukherjee PS Crozier SJ Plimpton KS Anderson 2008 Substructured molecular dynamics using multibody dynamics algorithms Int. J. Non. Linear Mech. 43 1040 1055 10.1016/j.ijnonlinmec.2008.04.003
    • (2008) Int. J. Non. Linear Mech , vol.43 , pp. 1040-1055
    • Mukherjee, R.M.1    Crozier, P.S.2    Plimpton, S.J.3    Anderson, K.S.4
  • 25
    • 33644548665 scopus 로고    scopus 로고
    • Structural basis for myosin V discrimination between distinct cargoes
    • DOI 10.1038/sj.emboj.7600965, PII 7600965
    • N Pashkova Y Jin S Ramaswamy LS Weisman 2006 Structural basis for myosin V discrimination between distinct cargoes EMBO J. 25 693 700 10.1038/sj.emboj.7600965 (Pubitemid 43292432)
    • (2006) EMBO Journal , vol.25 , Issue.4 , pp. 693-700
    • Pashkova, N.1    Jin, Y.2    Ramaswamy, S.3    Weisman, L.S.4
  • 27
    • 33847175935 scopus 로고    scopus 로고
    • High performance computing in biology: Multimillion atom simulations of nanoscale systems
    • DOI 10.1016/j.jsb.2006.10.023, PII S104784770600308X, Advanced in Molecular Dynamics Simulations
    • KY Sanbonmatsu CS Tung 2007 High performance computing in biology: multimillion atom simulations of nanoscale systems J. Struct. Biol 157 470 480 10.1016/j.jsb.2006.10.023 (Pubitemid 46304255)
    • (2007) Journal of Structural Biology , vol.157 , Issue.3 , pp. 470-480
    • Sanbonmatsu, K.Y.1    Tung, C.-S.2
  • 28
    • 33745418309 scopus 로고    scopus 로고
    • Multibody dynamics in computational mechanics and engineering applications
    • DOI 10.1016/j.cma.2005.04.024, PII S0045782505005293
    • W Schiehlen N Guse R Seifried 2006 Multibody dynamics in computational mechanics and engineering applications Comput. Meth. Appl. Mech. Eng 195 5509 5522 1119.70007 10.1016/j.cma.2005.04.024 2243316 (Pubitemid 43942210)
    • (2006) Computer Methods in Applied Mechanics and Engineering , vol.195 , Issue.41-43 , pp. 5509-5522
    • Schiehlen, W.1    Guse, N.2    Seifried, R.3
  • 29
    • 70349534997 scopus 로고    scopus 로고
    • Schliwa, M. (ed.) Weinheim: Wiley
    • Schliwa, M. (ed.) Molecular Motors. Weinheim: Wiley, 2003, 604 pp.
    • (2003) Molecular Motors , pp. 604
  • 30
    • 30844455998 scopus 로고    scopus 로고
    • Walking with myosin V
    • DOI 10.1016/j.ceb.2005.12.014, PII S0955067405001924, Cell Structure and Dynamics
    • JR Sellers C Veigel 2006 Walking with myosin V Curr. Opin. Cell Biol 18 68 73 10.1016/j.ceb.2005.12.014 (Pubitemid 43107610)
    • (2006) Current Opinion in Cell Biology , vol.18 , Issue.1 , pp. 68-73
    • Sellers, J.R.1    Veigel, C.2
  • 32
    • 34249948276 scopus 로고    scopus 로고
    • Myosin V walks by lever action and Bownian motion
    • DOI 10.1126/science.1140468
    • K Shiroguchi K Kinosita Jr 2007 Myosin V walks by lever action and Brownian motion Science 316 1208 1212 10.1126/science.1140468 (Pubitemid 46877486)
    • (2007) Science , vol.316 , Issue.5828 , pp. 1208-1212
    • Shiroguchi, K.1    Kinosita Jr., K.2
  • 33
    • 38849181099 scopus 로고    scopus 로고
    • Development of generic multibody road vehicle models for crashworthiness
    • DOI 10.1007/s11044-007-9093-z
    • L Sousa P Veríssimo J Ambrósio 2008 Development of generic multibody road vehicle models for crashworthiness Multib. Syst. Dyn. 19 133 158 05277394 10.1007/s11044-007-9093-z (Pubitemid 351189577)
    • (2008) Multibody System Dynamics , vol.19 , Issue.1-2 , pp. 133-158
    • Sousa, L.1    Verissimo, P.2    Ambrosio, J.3
  • 36
    • 56349092606 scopus 로고    scopus 로고
    • Microscopes for fluorimeters: The era of single molecule measurements
    • 10.1016/j.cell.2008.11.009
    • RD Vale 2008 Microscopes for fluorimeters: the era of single molecule measurements Cell 135 779 785 10.1016/j.cell.2008.11.009
    • (2008) Cell , vol.135 , pp. 779-785
    • Vale, R.D.1
  • 37
    • 58749103193 scopus 로고    scopus 로고
    • Biomolecular simulation and modelling: Status, progress and prospects
    • 10.1098/rsif.2008.0105.focus
    • MW van der Kamp KE Shaw CJ Woods AJ Mulholland 2008 Biomolecular simulation and modelling: status, progress and prospects J. R. Soc. Interface 5 173 190 10.1098/rsif.2008.0105.focus
    • (2008) J. R. Soc. Interface , vol.5 , pp. 173-190
    • Van Der Kamp, M.W.1    Shaw, K.E.2    Woods, C.J.3    Mulholland, A.J.4
  • 38
    • 0036144267 scopus 로고    scopus 로고
    • The gated gait of the processive molecular motor, myosin V
    • DOI 10.1038/ncb732
    • C Veigel F Wang ML Bartoo JR Sellers JE Molloy 2002 The gated gait of the processive molecular motor, myosin V Nat. Cell Biol 4 59 65 10.1038/ncb732 (Pubitemid 34071981)
    • (2002) Nature Cell Biology , vol.4 , Issue.1 , pp. 59-65
    • Veigel, C.1    Wang, F.2    Bartoo, M.L.3    Sellers, J.R.4    Molloy, J.E.5
  • 39
    • 26944449015 scopus 로고    scopus 로고
    • Load-dependent kinetics of myosin-V can explain its high processivity
    • DOI 10.1038/ncb1287, PII N1287
    • C Veigel S Schmitz F Wang JR Sellers 2005 Load-dependent kinetics of myosin-V can explain its high processivity Nat. Cell Biol 7 861 869 10.1038/ncb1287 (Pubitemid 41486286)
    • (2005) Nature Cell Biology , vol.7 , Issue.9 , pp. 861-869
    • Veigel, C.1    Schmitz, S.2    Wang, F.3    Sellers, J.R.4
  • 40
    • 22244472947 scopus 로고    scopus 로고
    • Elastic lever-arm model for myosin V
    • DOI 10.1529/biophysj.104.046763
    • A Vilfan 2005 Elastic lever-arm model for myosin V Biophys. J. 88 3792 3805 10.1529/biophysj.104.046763 (Pubitemid 40991095)
    • (2005) Biophysical Journal , vol.88 , Issue.6 , pp. 3792-3805
    • Vilfan, A.1
  • 41
    • 0032547899 scopus 로고    scopus 로고
    • 1 motor of ATP synthase
    • DOI 10.1038/24409
    • H Wang G Oster 1998 Energy transduction in the F1 motor of ATP synthase Nature 396 279 282 10.1038/24409 (Pubitemid 28541394)
    • (1998) Nature , vol.396 , Issue.6708 , pp. 279-282
    • Wang, H.1    Oster, G.2
  • 42
    • 0035912221 scopus 로고    scopus 로고
    • 1-ATPase
    • DOI 10.1038/35073513
    • R Yasuda H Noji M Yoshida K Kinosita H Itoh 2001 Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase Nature 410 898 904 10.1038/35073513 (Pubitemid 32335828)
    • (2001) Nature , vol.410 , Issue.6831 , pp. 898-904
    • Yasuda, R.1    Noji, H.2    Yoshida, M.3    Kinosita Jr., K.4    Itoh, H.5
  • 43
    • 0037832404 scopus 로고    scopus 로고
    • Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization
    • DOI 10.1126/science.1084398
    • A Yildiz, et al. 2003 Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization Science 300 2061 2065 10.1126/science.1084398 (Pubitemid 36760126)
    • (2003) Science , vol.300 , Issue.5628 , pp. 2061-2065
    • Yildiz, A.1    Forkey, J.N.2    McKinney, S.A.3    Ha, T.4    Goldman, Y.E.5    Selvin, P.R.6
  • 44
    • 33847278350 scopus 로고    scopus 로고
    • Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations
    • DOI 10.1371/journal.pcbi.0030021
    • H Yu L Ma Y Yang Q Cui 2007 Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations PLoS Comput. Biol 3 e21 10.1371/journal.pcbi.0030021 (Pubitemid 46318381)
    • (2007) PLoS Computational Biology , vol.3 , Issue.2 , pp. 0199-0213
    • Yu, H.1    Ma, L.2    Yang, Y.3    Cui, Q.4
  • 45
    • 41949099222 scopus 로고    scopus 로고
    • Towards atomic resolution structural determination by single-particle cryo-electron microscopy
    • 10.1016/j.sbi.2008.03.004
    • ZH Zhou 2008 Towards atomic resolution structural determination by single-particle cryo-electron microscopy Curr. Opin. Struct. Biol 18 218 228 10.1016/j.sbi.2008.03.004
    • (2008) Curr. Opin. Struct. Biol , vol.18 , pp. 218-228
    • Zhou, Z.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.