메뉴 건너뛰기




Volumn 51, Issue 25, 2012, Pages 5022-5032

All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; APO-STATE; ATP-ASE ACTIVITY; BINDING FREE ENERGY; BINDING INTERFACE; FREE-ENERGY CALCULATIONS; HIGH QUALITY; KEY RESIDUES; KINESIN MOTORS; KINESINS; MICROTUBULES; MOLECULAR DYNAMICS SIMULATIONS; MOTOR PROTEINS; STRONG BINDING; STRUCTURAL CHANGE; STRUCTURAL INVESTIGATION; SUBDOMAIN; WEAK BINDING;

EID: 84862875366     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300362a     Document Type: Article
Times cited : (19)

References (100)
  • 1
    • 0032559260 scopus 로고    scopus 로고
    • Kinesin and dynein superfamily proteins and the mechanism of organelle transport
    • DOI 10.1126/science.279.5350.519
    • Hirokawa, N. (1998) Kinesin and dynein superfamily proteins and the mechanism of organelle transport Science 279, 519-526 (Pubitemid 28067273)
    • (1998) Science , vol.279 , Issue.5350 , pp. 519-526
    • Hirokawa, N.1
  • 3
    • 0031004776 scopus 로고    scopus 로고
    • Probing the kinesin-microtubule interaction
    • DOI 10.1074/jbc.272.14.9481
    • Tucker, C. and Goldstein, L. S. (1997) Probing the kinesin-microtubule interaction J. Biol. Chem. 272, 9481-9488 (Pubitemid 27154964)
    • (1997) Journal of Biological Chemistry , vol.272 , Issue.14 , pp. 9481-9488
    • Tucker, C.1    Goldstein, L.S.B.2
  • 4
    • 0034628619 scopus 로고    scopus 로고
    • Role of the kinesin neck linker and catalytic core in microtubule-based motility
    • DOI 10.1016/S0960-9822(00)00316-X
    • Case, R. B., Rice, S., Hart, C. L., Ly, B., and Vale, R. D. (2000) Role of the kinesin neck linker and catalytic core in microtubule-based motility Curr. Biol. 10, 157-160 (Pubitemid 30115748)
    • (2000) Current Biology , vol.10 , Issue.3 , pp. 157-160
    • Case, R.B.1    Rice, S.2    Hart, C.L.3    Ly, B.4    Vale, R.D.5
  • 6
    • 33846350208 scopus 로고    scopus 로고
    • To step or not to step? How biochemistry and mechanics influence processivity in Kinesin and Eg5
    • DOI 10.1016/j.ceb.2006.12.011, PII S095506740600192X
    • Valentine, M. T. and Gilbert, S. P. (2007) To step or not to step? How biochemistry and mechanics influence processivity in kinesin and Eg5 Curr. Opin. Cell. Biol. 19, 75-81 (Pubitemid 46127836)
    • (2007) Current Opinion in Cell Biology , vol.19 , Issue.1 , pp. 75-81
    • Valentine, M.T.1    Gilbert, S.P.2
  • 7
    • 0028985886 scopus 로고
    • Pathway of processive ATP hydrolysis by kinesin
    • Gilbert, S. P., Webb, M. R., Brune, M., and Johnson, K. A. (1995) Pathway of processive ATP hydrolysis by kinesin Nature 373, 671-676
    • (1995) Nature , vol.373 , pp. 671-676
    • Gilbert, S.P.1    Webb, M.R.2    Brune, M.3    Johnson, K.A.4
  • 8
    • 0031022509 scopus 로고    scopus 로고
    • Kinetic mechanism of a monomeric kinesin construct
    • DOI 10.1074/jbc.272.2.717
    • Ma, Y. Z. and Taylor, E. W. (1997) Kinetic mechanism of a monomeric kinesin construct J. Biol. Chem. 272, 717-723 (Pubitemid 27034555)
    • (1997) Journal of Biological Chemistry , vol.272 , Issue.2 , pp. 717-723
    • Ma, Y.-Z.1    Taylor, E.W.2
  • 9
    • 0032548491 scopus 로고    scopus 로고
    • Pathway of ATP hydrolysis by monomeric and dimeric kinesin
    • DOI 10.1021/bi9711184
    • Moyer, M. L., Gilbert, S. P., and Johnson, K. A. (1998) Pathway of ATP hydrolysis by monomeric and dimeric kinesin Biochemistry 37, 800-813 (Pubitemid 28060460)
    • (1998) Biochemistry , vol.37 , Issue.3 , pp. 800-813
    • Moyer, M.L.1    Gilbert, S.P.2    Johnson, K.A.3
  • 10
    • 3242776257 scopus 로고    scopus 로고
    • The kinetic mechanism of kinesin
    • DOI 10.1016/j.tibs.2004.04.010, PII S0968000404001033
    • Cross, R. A. (2004) The kinetic mechanism of kinesin Trends Biochem. Sci. 29, 301-309 (Pubitemid 38968762)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.6 , pp. 301-309
    • Cross, R.A.1
  • 11
    • 1542353988 scopus 로고
    • Kinesin ATPase: Rate-limiting ADP release
    • Hackney, D. D. (1988) Kinesin ATPase: rate-limiting ADP release Proc. Natl. Acad. Sci. U. S. A. 85, 6314-6318
    • (1988) Proc. Natl. Acad. Sci. U. S. A. , vol.85 , pp. 6314-6318
    • Hackney, D.D.1
  • 13
    • 3442876110 scopus 로고    scopus 로고
    • KIF1A alternately uses two loops to bind microtubules
    • DOI 10.1126/science.1096621
    • Nitta, R., Kikkawa, M., Okada, Y., and Hirokawa, N. (2004) KIF1A alternately uses two loops to bind microtubules Science 305, 678-683 (Pubitemid 39006759)
    • (2004) Science , vol.305 , Issue.5684 , pp. 678-683
    • Nitta, R.1    Kikkawa, M.2    Okada, Y.3    Hirokawa, N.4
  • 15
    • 53549086926 scopus 로고    scopus 로고
    • Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin
    • Nitta, R., Okada, Y., and Hirokawa, N. (2008) Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin Nat. Struct. Mol. Biol. 15, 1067-1075
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 1067-1075
    • Nitta, R.1    Okada, Y.2    Hirokawa, N.3
  • 16
    • 0343415156 scopus 로고    scopus 로고
    • The way things move: Looking under the hood of molecular motor proteins
    • Vale, R. D. and Milligan, R. A. (2000) The way things move: looking under the hood of molecular motor proteins Science 288, 88-95
    • (2000) Science , vol.288 , pp. 88-95
    • Vale, R.D.1    Milligan, R.A.2
  • 17
    • 0036830220 scopus 로고    scopus 로고
    • Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy
    • Sindelar, C. V., Budny, M. J., Rice, S., Naber, N., Fletterick, R., and Cooke, R. (2002) Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy Nat. Struct. Biol. 9, 844-848 (Pubitemid 35257785)
    • (2002) Nature Structural Biology , vol.9 , Issue.11 , pp. 844-848
    • Sindelar, C.V.1    Budny, M.J.2    Rice, S.3    Naber, N.4    Fletterick, R.5    Cooke, R.6
  • 18
    • 0028865659 scopus 로고
    • Mechanism of microtubule kinesin ATPase
    • Ma, Y. Z. and Taylor, E. W. (1995) Mechanism of microtubule kinesin ATPase Biochemistry 34, 13242-13251
    • (1995) Biochemistry , vol.34 , pp. 13242-13251
    • Ma, Y.Z.1    Taylor, E.W.2
  • 19
    • 0032495513 scopus 로고    scopus 로고
    • Structure of the αβ tubulin dimer by electron crystallography
    • DOI 10.1038/34465
    • Nogales, E., Wolf, S. G., and Downing, K. H. (1998) Structure of the alpha beta tubulin dimer by electron crystallography Nature 391, 199-203 (Pubitemid 28092482)
    • (1998) Nature , vol.391 , Issue.6663 , pp. 199-203
    • Nogales, E.1    Wolf, S.G.2    Downing, K.H.3
  • 20
    • 0033534629 scopus 로고    scopus 로고
    • High-resolution model of the microtubule
    • DOI 10.1016/S0092-8674(00)80961-7
    • Nogales, E., Whittaker, M., Milligan, R. A., and Downing, K. H. (1999) High-resolution model of the microtubule Cell 96, 79-88 (Pubitemid 29044155)
    • (1999) Cell , vol.96 , Issue.1 , pp. 79-88
    • Nogales, E.1    Whittaker, M.2    Milligan, R.A.3    Downing, K.H.4
  • 21
    • 0343811700 scopus 로고    scopus 로고
    • A model for the microtubule-Ncd motor protein complex obtained by cryo- electron microscopy and image analysis
    • DOI 10.1016/S0092-8674(00)80330-X
    • Sosa, H., Dias, D. P., Hoenger, A., Whittaker, M., Wilson-Kubalek, E., Sablin, E., Fletterick, R. J., Vale, R. D., and Milligan, R. A. (1997) A model for the microtubule-Ncd motor protein complex obtained by cryo-electron microscopy and image analysis Cell 90, 217-224 (Pubitemid 27329707)
    • (1997) Cell , vol.90 , Issue.2 , pp. 217-224
    • Sosa, H.1    Prabha Dias, D.2    Hoenger, A.3    Whittaker, M.4    Wilson-Kubalek, E.5    Sablin, E.6    Fletterick, R.J.7    Vale, R.D.8    Milligan, R.A.9
  • 22
    • 0032509950 scopus 로고    scopus 로고
    • A model of the microtubule-kinesin complex based on electron cryomicroscopy and X-ray crystallography
    • Kozielski, F., Arnal, I., and Wade, R. H. (1998) A model of the microtubule-kinesin complex based on electron cryomicroscopy and X-ray crystallography Curr. Biol. 8, 191-198 (Pubitemid 28126610)
    • (1998) Current Biology , vol.8 , Issue.4 , pp. 191-198
    • Kozielski, F.1    Arnal, I.2    Wade, R.H.3
  • 23
    • 0032550175 scopus 로고    scopus 로고
    • Image reconstructions of microtubules decorated with monomeric and dimeric kinesins: Comparison with x-ray structure and implications for motility
    • DOI 10.1083/jcb.141.2.419
    • Hoenger, A., Sack, S., Thormahlen, M., Marx, A., Muller, J., Gross, H., and Mandelkow, E. (1998) Image reconstructions of microtubules decorated with monomeric and dimeric kinesins: comparison with X-ray structure and implications for motility J. Cell Biol. 141, 419-430 (Pubitemid 28237090)
    • (1998) Journal of Cell Biology , vol.141 , Issue.2 , pp. 419-430
    • Hoenger, A.1    Sack, S.2    Thormahlen, M.3    Marx, A.4    Muller, J.5    Gross, H.6    Mandelkow, E.7
  • 24
    • 0344867017 scopus 로고    scopus 로고
    • Congruent docking of dimeric kinesin and ncd into three-dimensional electron cryomicroscopy maps of microtubule-motor ADP complexes
    • Hirose, K., Lowe, J., Alonso, M., Cross, R. A., and Amos, L. A. (1999) Congruent docking of dimeric kinesin and ncd into three-dimensional electron cryomicroscopy maps of microtubule-motor ADP complexes Mol. Biol. Cell 10, 2063-2074 (Pubitemid 29272650)
    • (1999) Molecular Biology of the Cell , vol.10 , Issue.6 , pp. 2063-2074
    • Hirose, K.1    Lowe, J.2    Alonso, M.3    Cross, R.A.4    Amos, L.A.5
  • 25
    • 0034695259 scopus 로고    scopus 로고
    • 15 A resolution model of the monomeric kinesin motor, KIF1A
    • Kikkawa, M., Okada, Y., and Hirokawa, N. (2000) 15 Å resolution model of the monomeric kinesin motor, KIF1A Cell 100, 241-252 (Pubitemid 30064912)
    • (2000) Cell , vol.100 , Issue.2 , pp. 241-252
    • Kikkawa, M.1    Okada, Y.2    Hirokawa, N.3
  • 26
    • 33748931452 scopus 로고    scopus 로고
    • High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations
    • DOI 10.1038/sj.emboj.7601299, PII 7601299
    • Kikkawa, M. and Hirokawa, N. (2006) High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations EMBO J. 25, 4187-4194 (Pubitemid 44435216)
    • (2006) EMBO Journal , vol.25 , Issue.18 , pp. 4187-4194
    • Kikkawa, M.1    Hirokawa, N.2
  • 27
    • 33748421625 scopus 로고    scopus 로고
    • Large Conformational Changes in a Kinesin Motor Catalyzed by Interaction with Microtubules
    • DOI 10.1016/j.molcel.2006.07.020, PII S109727650600517X
    • Hirose, K., Akimaru, E., Akiba, T., Endow, S. A., and Amos, L. A. (2006) Large conformational changes in a kinesin motor catalyzed by interaction with microtubules Mol. Cell 23, 913-923 (Pubitemid 44344516)
    • (2006) Molecular Cell , vol.23 , Issue.6 , pp. 913-923
    • Hirose, K.1    Akimaru, E.2    Akiba, T.3    Endow, S.A.4    Amos, L.A.5
  • 28
    • 34248200882 scopus 로고    scopus 로고
    • The beginning of kinesin's force-generating cycle visualized at 9-A resolution
    • DOI 10.1083/jcb.200612090
    • Sindelar, C. V. and Downing, K. H. (2007) The beginning of kinesin's force-generating cycle visualized in 9-Å resolution J. Cell Biol. 177, 377-385 (Pubitemid 46718267)
    • (2007) Journal of Cell Biology , vol.177 , Issue.3 , pp. 377-385
    • Sindelar, C.V.1    Downing, K.H.2
  • 29
    • 77749239756 scopus 로고    scopus 로고
    • An atomic-level mechanism for activation of the kinesin molecular motors
    • Sindelar, C. V. and Downing, K. H. (2010) An atomic-level mechanism for activation of the kinesin molecular motors Proc. Natl. Acad. Sci. U. S. A. 107, 4111-4116
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 4111-4116
    • Sindelar, C.V.1    Downing, K.H.2
  • 31
    • 0028952024 scopus 로고
    • Coordinated hydrolysis explains the mechanical behavior of kinesin
    • Peskin, C. S. and Oster, G. (1995) Coordinated hydrolysis explains the mechanical behavior of kinesin Biophys. J. 68, 202S-210S
    • (1995) Biophys. J. , vol.68
    • Peskin, C.S.1    Oster, G.2
  • 32
    • 84873411711 scopus 로고    scopus 로고
    • Discussion 210S-211S
    • Discussion 210S-211S.
  • 34
    • 17844411211 scopus 로고    scopus 로고
    • Normal-modes-based prediction of protein conformational changes guided by distance constraints
    • DOI 10.1529/biophysj.104.058453
    • Zheng, W. and Brooks, B. R. (2005) Normal-modes-based prediction of protein conformational changes guided by distance constraints Biophys. J. 88, 3109-3117 (Pubitemid 40586565)
    • (2005) Biophysical Journal , vol.88 , Issue.5 , pp. 3109-3117
    • Zheng, W.1    Brooks, B.R.2
  • 35
    • 34548304871 scopus 로고    scopus 로고
    • Protein conformational transitions explored by mixed elastic network models
    • DOI 10.1002/prot.21465
    • Zheng, W., Brooks, B. R., and Hummer, G. (2007) Protein conformational transitions explored by mixed elastic network models Proteins 69, 43-57 (Pubitemid 47339138)
    • (2007) Proteins: Structure, Function and Genetics , vol.69 , Issue.1 , pp. 43-57
    • Zheng, W.1    Brooks, B.R.2    Hummer, G.3
  • 36
    • 68149163617 scopus 로고    scopus 로고
    • Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
    • Zheng, W. and Tekpinar, M. (2009) Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model BMC Struct. Biol. 9, 45
    • (2009) BMC Struct. Biol. , vol.9 , pp. 45
    • Zheng, W.1    Tekpinar, M.2
  • 38
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • DOI 10.1038/nsb0902-646
    • Karplus, M. and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9, 646-652 (Pubitemid 34977295)
    • (2002) Nature Structural Biology , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 39
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • Mackerell, A. D., Jr. (2004) Empirical force fields for biological macromolecules: overview and issues J. Comput. Chem. 25, 1584-1604
    • (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
    • Mackerell Jr., A.D.1
  • 41
    • 79952822799 scopus 로고    scopus 로고
    • Exploring the intermediate states of ADP-ATP exchange: A simulation study on Eg5
    • Zhang, W. (2011) Exploring the intermediate states of ADP-ATP exchange: a simulation study on Eg5 J. Phys. Chem. B 115, 784-795
    • (2011) J. Phys. Chem. B , vol.115 , pp. 784-795
    • Zhang, W.1
  • 42
    • 79955020377 scopus 로고    scopus 로고
    • Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state
    • Naber, N., Larson, A., Rice, S., Cooke, R., and Pate, E. (2011) Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state J. Mol. Biol. 408, 628-642
    • (2011) J. Mol. Biol. , vol.408 , pp. 628-642
    • Naber, N.1    Larson, A.2    Rice, S.3    Cooke, R.4    Pate, E.5
  • 43
    • 37548999364 scopus 로고    scopus 로고
    • Force generation in kinesin hinges on cover-neck bundle formation
    • Hwang, W., Lang, M. J., and Karplus, M. (2008) Force generation in kinesin hinges on cover-neck bundle formation Structure 16, 62-71
    • (2008) Structure , vol.16 , pp. 62-71
    • Hwang, W.1    Lang, M.J.2    Karplus, M.3
  • 44
    • 55549115655 scopus 로고    scopus 로고
    • Interaction forces and interface properties of KIF1A kinesin-alphabeta tubulin complex assessed by molecular dynamics
    • Aprodu, I., Soncini, M., and Redaelli, A. (2008) Interaction forces and interface properties of KIF1A kinesin-alphabeta tubulin complex assessed by molecular dynamics J. Biomech. 41, 3196-3201
    • (2008) J. Biomech. , vol.41 , pp. 3196-3201
    • Aprodu, I.1    Soncini, M.2    Redaelli, A.3
  • 45
    • 80053602551 scopus 로고    scopus 로고
    • Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis
    • Li, M. H. and Zheng, W. J. (2011) Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis Biochemistry 50, 8645-8655
    • (2011) Biochemistry , vol.50 , pp. 8645-8655
    • Li, M.H.1    Zheng, W.J.2
  • 46
    • 38949092920 scopus 로고    scopus 로고
    • Protein Structure Fitting and Refinement Guided by Cryo-EM Density
    • DOI 10.1016/j.str.2007.11.016, PII S0969212608000130
    • Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W., and Sali, A. (2008) Protein structure fitting and refinement guided by cryo-EM density Structure 16, 295-307 (Pubitemid 351215215)
    • (2008) Structure , vol.16 , Issue.2 , pp. 295-307
    • Topf, M.1    Lasker, K.2    Webb, B.3    Wolfson, H.4    Chiu, W.5    Sali, A.6
  • 47
    • 41449099769 scopus 로고    scopus 로고
    • Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
    • Jolley, C. C., Wells, S. A., Fromme, P., and Thorpe, M. F. (2008) Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations Biophys. J. 94, 1613-1621
    • (2008) Biophys. J. , vol.94 , pp. 1613-1621
    • Jolley, C.C.1    Wells, S.A.2    Fromme, P.3    Thorpe, M.F.4
  • 48
    • 33745813129 scopus 로고    scopus 로고
    • Flexible Fitting in 3D-EM Guided by the Structural Variability of Protein Superfamilies
    • DOI 10.1016/j.str.2006.05.013, PII S0969212606002528
    • Velazquez-Muriel, J. A., Valle, M., Santamaria-Pang, A., Kakadiaris, I. A., and Carazo, J. M. (2006) Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies Structure 14, 1115-1126 (Pubitemid 44037421)
    • (2006) Structure , vol.14 , Issue.7 , pp. 1115-1126
    • Velazquez-Muriel, J.-A.1    Valle, M.2    Santamaria-Pang, A.3    Kakadiaris, I.A.4    Carazo, J.-M.5
  • 49
    • 46749096676 scopus 로고    scopus 로고
    • YUP.SCX: Coaxing atomic models into medium resolution electron density maps
    • Tan, R. K., Devkota, B., and Harvey, S. C. (2008) YUP.SCX: coaxing atomic models into medium resolution electron density maps J. Struct. Biol. 163, 163-174
    • (2008) J. Struct. Biol. , vol.163 , pp. 163-174
    • Tan, R.K.1    Devkota, B.2    Harvey, S.C.3
  • 50
    • 36749078686 scopus 로고    scopus 로고
    • Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution
    • DOI 10.1016/j.str.2007.09.021, PII S096921260700411X
    • Schroder, G. F., Brunger, A. T., and Levitt, M. (2007) Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement in low resolution Structure 15, 1630-1641 (Pubitemid 350213409)
    • (2007) Structure , vol.15 , Issue.12 , pp. 1630-1641
    • Schroder, G.F.1    Brunger, A.T.2    Levitt, M.3
  • 51
    • 4344716056 scopus 로고    scopus 로고
    • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
    • DOI 10.1016/j.jsb.2004.03.002, PII S1047847704000590
    • Tama, F., Miyashita, O., and Brooks, C. L., 3rd (2004) Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM J. Struct. Biol. 147, 315-326 (Pubitemid 39140738)
    • (2004) Journal of Structural Biology , vol.147 , Issue.3 , pp. 315-326
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 52
    • 33748351384 scopus 로고    scopus 로고
    • NORMA: A tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
    • DOI 10.1107/S090744490602244X
    • Suhre, K., Navaza, J., and Sanejouand, Y. H. (2006) NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps Acta Crystallogr. D Biol Crystallogr. 62, 1098-1100 (Pubitemid 44337384)
    • (2006) Acta Crystallographica Section D: Biological Crystallography , vol.62 , Issue.9 , pp. 1098-1100
    • Suhre, K.1    Navaza, J.2    Sanejouand, Y.-H.3
  • 53
    • 78751682350 scopus 로고    scopus 로고
    • Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization
    • Zheng, W. (2011) Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization Biophys. J. 100, 478-488
    • (2011) Biophys. J. , vol.100 , pp. 478-488
    • Zheng, W.1
  • 54
    • 42949089487 scopus 로고    scopus 로고
    • Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
    • DOI 10.1016/j.str.2008.03.005, PII S0969212608001330
    • Trabuco, L. G., Villa, E., Mitra, K., Frank, J., and Schulten, K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics Structure 16, 673-683 (Pubitemid 351615021)
    • (2008) Structure , vol.16 , Issue.5 , pp. 673-683
    • Trabuco, L.G.1    Villa, E.2    Mitra, K.3    Frank, J.4    Schulten, K.5
  • 55
    • 70349267547 scopus 로고    scopus 로고
    • Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
    • Trabuco, L. G., Villa, E., Schreiner, E., Harrison, C. B., and Schulten, K. (2009) Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography Methods 49, 174-180
    • (2009) Methods , vol.49 , pp. 174-180
    • Trabuco, L.G.1    Villa, E.2    Schreiner, E.3    Harrison, C.B.4    Schulten, K.5
  • 57
    • 0029989974 scopus 로고    scopus 로고
    • Crystal structure of the kinesin motor domain reveals a structural similarity to myosin
    • DOI 10.1038/380550a0
    • Kull, F. J., Sablin, E. P., Lau, R., Fletterick, R. J., and Vale, R. D. (1996) Crystal structure of the kinesin motor domain reveals a structural similarity to myosin Nature 380, 550-555 (Pubitemid 26110647)
    • (1996) Nature , vol.380 , Issue.6574 , pp. 550-555
    • Kull, F.J.1    Sablin, E.P.2    Lau, R.3    Fletterick, R.J.4    Vale, R.D.5
  • 58
    • 0035816597 scopus 로고    scopus 로고
    • Crystal structure of the mitotic spindle kinesin Eg5 reveals a novel conformation of the neck-linker
    • Turner, J., Anderson, R., Guo, J., Beraud, C., Fletterick, R., and Sakowicz, R. (2001) Crystal structure of the mitotic spindle kinesin Eg5 reveals a novel conformation of the neck-linker J. Biol. Chem. 276, 25496-25502
    • (2001) J. Biol. Chem. , vol.276 , pp. 25496-25502
    • Turner, J.1    Anderson, R.2    Guo, J.3    Beraud, C.4    Fletterick, R.5    Sakowicz, R.6
  • 59
    • 77949318844 scopus 로고    scopus 로고
    • ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism
    • Parke, C. L., Wojcik, E. J., Kim, S., and Worthylake, D. K. (2010) ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism J. Biol. Chem. 285, 5859-5867
    • (2010) J. Biol. Chem. , vol.285 , pp. 5859-5867
    • Parke, C.L.1    Wojcik, E.J.2    Kim, S.3    Worthylake, D.K.4
  • 60
    • 39649107974 scopus 로고    scopus 로고
    • X-ray structure and microtubule interaction of the motor domain of Neurospora crassa NcKin3, a kinesin with unusual processivity
    • DOI 10.1021/bi701483h
    • Marx, A., Muller, J., Mandelkow, E. M., Woehlke, G., Bouchet-Marquis, C., Hoenger, A., and Mandelkow, E. (2008) X-ray structure and microtubule interaction of the motor domain of Neurospora crassa NcKin3, a kinesin with unusual processivity Biochemistry 47, 1848-1861 (Pubitemid 351287111)
    • (2008) Biochemistry , vol.47 , Issue.7 , pp. 1848-1861
    • Marx, A.1    Muller, J.2    Mandelkow, E.-M.3    Woehlke, G.4    Bouchet-Marquis, C.5    Hoenger, A.6    Mandelkow, E.7
  • 62
    • 0033571450 scopus 로고    scopus 로고
    • The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations
    • DOI 10.1016/S0969-2126(00)80030-1
    • Kozielski, F., De Bonis, S., Burmeister, W. P., Cohen-Addad, C., and Wade, R. H. (1999) The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations Structure 7, 1407-1416 (Pubitemid 29529881)
    • (1999) Structure , vol.7 , Issue.11 , pp. 1407-1416
    • Kozielski, F.1    De Bonis, S.2    Burmeister, W.P.3    Cohen-Addad, C.4    Wade, R.H.5
  • 63
    • 0032558718 scopus 로고    scopus 로고
    • Direction determination in the minus-end-directed kinesin motor ncd
    • DOI 10.1038/27463
    • Sablin, E. P., Case, R. B., Dai, S. C., Hart, C. L., Ruby, A., Vale, R. D., and Fletterick, R. J. (1998) Direction determination in the minus-end-directed kinesin motor ncd Nature 395, 813-816 (Pubitemid 28485450)
    • (1998) Nature , vol.395 , Issue.6704 , pp. 813-816
    • Sablin, E.P.1    Case, R.B.2    Dai, S.C.3    Hart, C.L.4    Ruby, A.5    Vale, R.D.6    Fletterick, R.J.7
  • 65
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: visual molecular dynamics J. Mol. Graph. 14 (33-38) 27-38
    • (1996) J. Mol. Graph. , vol.14 , Issue.33-38 , pp. 27-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 68
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell, A. D., Jr., Feig, M., and Brooks, C. L., 3rd (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25, 1400-1415
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • Mackerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 69
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe, N. and MacKerell, A. D. (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 21, 86-104
    • (2000) J. Comput. Chem. , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, A.D.2
  • 70
    • 22244433235 scopus 로고    scopus 로고
    • How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines
    • DOI 10.1063/1.477414, PII S0021960698515425
    • Deserno, M. and Holm, C. (1998) How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines J. Chem. Phys. 109, 7678-7693 (Pubitemid 128678339)
    • (1998) Journal of Chemical Physics , vol.109 , Issue.18 , pp. 7678-7693
    • Deserno, M.1    Holm, C.2
  • 72
    • 48749137581 scopus 로고
    • Stochastic boundary-conditions for molecular-dynamics simulations of St2 water
    • Brunger, A., Brooks, C. L., and Karplus, M. (1984) Stochastic boundary-conditions for molecular-dynamics simulations of St2 water Chem. Phys. Lett. 105, 495-500
    • (1984) Chem. Phys. Lett. , vol.105 , pp. 495-500
    • Brunger, A.1    Brooks, C.L.2    Karplus, M.3
  • 73
    • 0000394907 scopus 로고    scopus 로고
    • Molecular dynamics algorithms for path integrals at constant pressure
    • Martyna, G. J., Hughes, A., and Tuckerman, M. E. (1999) Molecular dynamics algorithms for path integrals in constant pressure J. Chem. Phys. 110, 3275-3290 (Pubitemid 129615528)
    • (1999) Journal of Chemical Physics , vol.110 , Issue.7 , pp. 3275-3290
    • Martyna, G.J.1    Hughes, A.2    Tuckerman, M.E.3
  • 75
    • 78651543110 scopus 로고    scopus 로고
    • Hydrogen bonds and kinematic mobility of protein molecules
    • 021009
    • Shahbazi, Z., Ilies, H. T., and Kazerounian, K. (2010) Hydrogen bonds and kinematic mobility of protein molecules J. Mechan. Robot. 2 021009
    • (2010) J. Mechan. Robot. , vol.2
    • Shahbazi, Z.1    Ilies, H.T.2    Kazerounian, K.3
  • 76
    • 0031450506 scopus 로고    scopus 로고
    • Hydrogen bonds and salt bridges across protein-protein interfaces
    • Xu, D., Tsai, C. J., and Nussinov, R. (1997) Hydrogen bonds and salt bridges across protein-protein interfaces Protein Eng. 10, 999-1012 (Pubitemid 28004646)
    • (1997) Protein Engineering , vol.10 , Issue.9 , pp. 999-1012
    • Xu, D.1    Tsai, C.-J.2    Nussinov, R.3
  • 77
    • 0036840108 scopus 로고    scopus 로고
    • + channel: A computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles
    • Eriksson, M. A. and Roux, B. (2002) Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles Biophys. J. 83, 2595-2609 (Pubitemid 35265753)
    • (2002) Biophysical Journal , vol.83 , Issue.5 , pp. 2595-2609
    • Eriksson, M.A.L.1    Roux, B.2
  • 78
    • 0023899747 scopus 로고
    • Energetics of charge-charge interactions in proteins
    • Gilson, M. K. and Honig, B. H. (1988) Energetics of charge-charge interactions in proteins Proteins 3, 32-52
    • (1988) Proteins , vol.3 , pp. 32-52
    • Gilson, M.K.1    Honig, B.H.2
  • 79
    • 0032096837 scopus 로고    scopus 로고
    • Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
    • PII S0010465598000162
    • Im, W., Beglov, D., and Roux, B. (1998) Continuum Solvation Model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Comput. Phys. Commun. 111, 59-75 (Pubitemid 128400465)
    • (1998) Computer Physics Communications , vol.111 , Issue.1-3 , pp. 59-75
    • Im, W.1    Beglov, D.2    Roux, B.3
  • 80
    • 0040241932 scopus 로고    scopus 로고
    • The structure of the nucleotide-binding site of kinesin
    • DOI 10.1515/BC.1999.122
    • Muller, J., Marx, A., Sack, S., Song, Y. H., and Mandelkow, E. (1999) The structure of the nucleotide-binding site of kinesin Biol. Chem. 380, 981-992 (Pubitemid 29412759)
    • (1999) Biological Chemistry , vol.380 , Issue.7-8 , pp. 981-992
    • Muller, J.1    Marx, A.2    Sack, S.3    Song, Y.-H.4    Mandelkow, E.5
  • 81
    • 0344198646 scopus 로고    scopus 로고
    • Distinct conformations of the kinesin Unc104 neck regulate a monomer to dimer motor transition
    • DOI 10.1083/jcb.200308020
    • Al-Bassam, J., Cui, Y., Klopfenstein, D., Carragher, B. O., Vale, R. D., and Milligan, R. A. (2003) Distinct conformations of the kinesin Unc104 neck regulate a monomer to dimer motor transition J. Cell Biol. 163, 743-753 (Pubitemid 37517882)
    • (2003) Journal of Cell Biology , vol.163 , Issue.4 , pp. 743-753
    • Al-Bassam, J.1    Cui, Y.2    Klopfenstein, D.3    Carragher, B.O.4    Vale, R.D.5    Milligan, R.A.6
  • 82
  • 83
    • 39949083937 scopus 로고    scopus 로고
    • The role of microtubules in processive kinesin movement
    • Kikkawa, M. (2008) The role of microtubules in processive kinesin movement Trends Cell Biol. 18, 128-135
    • (2008) Trends Cell Biol. , vol.18 , pp. 128-135
    • Kikkawa, M.1
  • 84
    • 37249034254 scopus 로고    scopus 로고
    • A cool look at the structural changes in kinesin motor domains
    • DOI 10.1242/jcs.016931
    • Amos, L. A. and Hirose, K. (2007) A cool look at the structural changes in kinesin motor domains J. Cell Sci. 120, 3919-3927 (Pubitemid 350269398)
    • (2007) Journal of Cell Science , vol.120 , Issue.22 , pp. 3919-3927
    • Amos, L.A.1    Hirose, K.2
  • 85
    • 0030058832 scopus 로고    scopus 로고
    • Directional loading of the kinesin motor molecule as it buckles a microtubule
    • Gittes, F., Meyhofer, E., Baek, S., and Howard, J. (1996) Directional loading of the kinesin motor molecule as it buckles a microtubule Biophys. J. 70, 418-429 (Pubitemid 26021480)
    • (1996) Biophysical Journal , vol.70 , Issue.1 , pp. 418-429
    • Gittes, F.1    Meyhofer, E.2    Baek, S.3    Howard, J.4
  • 87
    • 0037306229 scopus 로고    scopus 로고
    • Equilibrium and transition between single- and double-headed binding of kinesin as revealed by single-molecule mechanics
    • Kawaguchi, K., Uemura, S., and Ishiwata, S. (2003) Equilibrium and transition between single- and double-headed binding of kinesin as revealed by single-molecule mechanics Biophys. J. 84, 1103-1113 (Pubitemid 36133434)
    • (2003) Biophysical Journal , vol.84 , Issue.2 , pp. 1103-1113
    • Kawaguchi, K.1    Uemura, S.2    Ishiwata, S.3
  • 88
    • 0030755709 scopus 로고    scopus 로고
    • Microtubule interaction site of the kinesin motor
    • DOI 10.1016/S0092-8674(00)80329-3
    • Woehlke, G., Ruby, A. K., Hart, C. L., Ly, B., Hom-Booher, N., and Vale, R. D. (1997) Microtubule interaction site of the kinesin motor Cell 90, 207-216 (Pubitemid 27329706)
    • (1997) Cell , vol.90 , Issue.2 , pp. 207-216
    • Woehlke, G.1    Ruby, A.K.2    Hart, C.L.3    Ly, B.4    Hom-Booher, N.5    Vale, R.D.6
  • 90
    • 0033563154 scopus 로고    scopus 로고
    • Motor proteins of the kinesin family. Structures, variations, and nucleotide binding sites
    • DOI 10.1046/j.1432-1327.1999.00341.x
    • Sack, S., Kull, F. J., and Mandelkow, E. (1999) Motor proteins of the kinesin family. Structures, variations, and nucleotide binding sites Eur. J. Biochem. 262, 1-11 (Pubitemid 29242602)
    • (1999) European Journal of Biochemistry , vol.262 , Issue.1 , pp. 1-11
    • Sack, S.1    Kull, F.J.2    Mandelkow, E.3
  • 91
    • 0030267349 scopus 로고    scopus 로고
    • Switches, latches, and amplifiers: Common themes of G proteins and molecular motors
    • Vale, R. D. (1996) Switches, latches, and amplifiers: common themes of G proteins and molecular motors J. Cell Biol. 135, 291-302
    • (1996) J. Cell Biol. , vol.135 , pp. 291-302
    • Vale, R.D.1
  • 92
    • 0029960235 scopus 로고    scopus 로고
    • X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 Å resolution
    • Smith, C. A. and Rayment, I. (1996) X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 Å resolution Biochemistry 35, 5404-5417
    • (1996) Biochemistry , vol.35 , pp. 5404-5417
    • Smith, C.A.1    Rayment, I.2
  • 94
    • 27744549807 scopus 로고    scopus 로고
    • Kinetic effects of kinesin switch I and switch II mutations
    • DOI 10.1074/jbc.M502985200
    • Auerbach, S. D. and Johnson, K. A. (2005) Kinetic effects of kinesin switch I and switch II mutations J. Biol. Chem. 280, 37061-37068 (Pubitemid 41587790)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.44 , pp. 37061-37068
    • Auerbach, S.D.1    Johnson, K.A.2
  • 95
    • 0035355208 scopus 로고    scopus 로고
    • A structural pathway for activation of the kinesin motor ATPase
    • DOI 10.1093/emboj/20.11.2611
    • Yun, M., Zhang, X., Park, C. G., Park, H. W., and Endow, S. A. (2001) A structural pathway for activation of the kinesin motor ATPase EMBO J. 20, 2611-2618 (Pubitemid 32938546)
    • (2001) EMBO Journal , vol.20 , Issue.11 , pp. 2611-2618
    • Yun, M.1    Zhang, X.2    Park, C.-G.3    Park, H.-W.4    Endow, S.A.5
  • 96
    • 34247237308 scopus 로고    scopus 로고
    • Multivariate Analysis of Conserved Sequence-Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain
    • DOI 10.1016/j.jmb.2007.02.049, PII S0022283607002306
    • Grant, B. J., McCammon, J. A., Caves, L. S., and Cross, R. A. (2007) Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain J. Mol. Biol. 368, 1231-1248 (Pubitemid 46617587)
    • (2007) Journal of Molecular Biology , vol.368 , Issue.5 , pp. 1231-1248
    • Grant, B.J.1    McCammon, J.A.2    Caves, L.S.D.3    Cross, R.A.4
  • 97
    • 77950546688 scopus 로고    scopus 로고
    • Key residues on microtubule responsible for activation of kinesin ATPase
    • Uchimura, S., Oguchi, Y., Hachikubo, Y., Ishiwata, S., and Muto, E. (2010) Key residues on microtubule responsible for activation of kinesin ATPase EMBO J. 29, 1167-1175
    • (2010) EMBO J. , vol.29 , pp. 1167-1175
    • Uchimura, S.1    Oguchi, Y.2    Hachikubo, Y.3    Ishiwata, S.4    Muto, E.5
  • 99
    • 0036150882 scopus 로고    scopus 로고
    • Kinesin: Switch I & II and the motor mechanism
    • Kull, F. J. and Endow, S. A. (2002) Kinesin: switch I & II and the motor mechanism J. Cell Sci. 115, 15-23 (Pubitemid 34105525)
    • (2002) Journal of Cell Science , vol.115 , Issue.1 , pp. 15-23
    • Kull, F.J.1    Endow, S.A.2
  • 100
    • 0032506523 scopus 로고    scopus 로고
    • Decoupling of nucleotide-and microtubule-binding sites in a kinesin mutant
    • DOI 10.1038/25153
    • Song, H. and Endow, S. A. (1998) Decoupling of nucleotide- and microtubule-binding sites in a kinesin mutant Nature 396, 587-590 (Pubitemid 28563721)
    • (1998) Nature , vol.396 , Issue.6711 , pp. 587-590
    • Song, H.1    Endow, S.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.