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Volumn 147, Issue 3, 2004, Pages 315-326

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM

Author keywords

Electron density; Flexible docking; Gaussian networks; X ray structure

Indexed keywords

BACTERIAL RNA; ELONGATION FACTOR; RNA POLYMERASE;

EID: 4344716056     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.03.002     Document Type: Article
Times cited : (214)

References (53)
  • 1
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:1997;173-181
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 2
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: Normal mode and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B.R., Karplus M. Harmonic dynamics of proteins: normal mode and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA. 80:1983;6571-6575
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 6571-6575
    • Brooks, B.R.1    Karplus, M.2
  • 3
    • 0022111715 scopus 로고
    • Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
    • Brooks B.R., Karplus M. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA. 82:1985;4995-4999
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 4995-4999
    • Brooks, B.R.1    Karplus, M.2
  • 7
    • 0036297629 scopus 로고    scopus 로고
    • Multi-resolution contour-based fitting of macromolecular structures
    • Chacon P., Wriggers W. Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 317:2002;375-384
    • (2002) J. Mol. Biol. , vol.317 , pp. 375-384
    • Chacon, P.1    Wriggers, W.2
  • 8
    • 0037436340 scopus 로고    scopus 로고
    • Mega-Dalton biomolecular motion captured from electron microscopy reconstructions
    • Chacon P., Tama F., Wriggers W. Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326:2003;485-492
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 9
    • 0001832403 scopus 로고
    • Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function
    • Chapman M.S. Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr. A. 51:1995;69-80
    • (1995) Acta Crystallogr. a , vol.51 , pp. 69-80
    • Chapman, M.S.1
  • 11
    • 0036077875 scopus 로고    scopus 로고
    • Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
    • Delarue M., Sanejouand Y.H. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol. 320:2002;1011-1024
    • (2002) J. Mol. Biol. , vol.320 , pp. 1011-1024
    • Delarue, M.1    Sanejouand, Y.H.2
  • 12
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • Doruker P., Jernigan R.L., Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:2002;119-127
    • (2002) J. Comput. Chem. , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 13
    • 0028454915 scopus 로고
    • New approach for determining low-frequency normal-modes in macromolecules
    • Durand P., Trinquier G., Sanejouand Y.H. New approach for determining low-frequency normal-modes in macromolecules. Biopolymers. 34:1994;759-771
    • (1994) Biopolymers , vol.34 , pp. 759-771
    • Durand, P.1    Trinquier, G.2    Sanejouand, Y.H.3
  • 14
    • 0034691576 scopus 로고    scopus 로고
    • A ratchet-like inter-subunit reorganization of the ribosome during translocation
    • Frank J., Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 406:2000;318-322
    • (2000) Nature , vol.406 , pp. 318-322
    • Frank, J.1    Agrawal, R.K.2
  • 16
    • 0025066772 scopus 로고
    • Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
    • Gibrat J.F., Go N. Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins. 8:1990;258-279
    • (1990) Proteins , vol.8 , pp. 258-279
    • Gibrat, J.F.1    Go, N.2
  • 17
    • 0020771265 scopus 로고
    • Dynamics of a small globular proteins in terms of low-frequency vibrational modes
    • Go N., Noguti T., Nishikawa T. Dynamics of a small globular proteins in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:1983;3696-3700
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 18
    • 0021701376 scopus 로고
    • Variational calculation of the normal modes of a large macromolecule: Methods and some initial results
    • Harrison W. Variational calculation of the normal modes of a large macromolecule: methods and some initial results. Biopolymers. 23:1984;2943-2949
    • (1984) Biopolymers , vol.23 , pp. 2943-2949
    • Harrison, W.1
  • 19
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:1998;417-429
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 21
    • 0035906702 scopus 로고    scopus 로고
    • Bridging the information gap: Computational tools for intermediate resolution structure interpretation
    • Jiang W., Baker M.L., Ludtke S.J., Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308:2001;1033-1044
    • (2001) J. Mol. Biol. , vol.308 , pp. 1033-1044
    • Jiang, W.1    Baker, M.L.2    Ludtke, S.J.3    Chiu, W.4
  • 22
    • 0025294520 scopus 로고
    • Refinement of protein dynamic structure - Normal mode refinement
    • Kidera A., Go N. Refinement of protein dynamic structure - normal mode refinement. Proc. Natl. Acad. Sci. USA. 87:1990;3718-3722
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 3718-3722
    • Kidera, A.1    Go, N.2
  • 25
    • 0037764817 scopus 로고    scopus 로고
    • Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data
    • Liu H.J., Qu C.X., Johnson J.E., Case D.A. Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data. J. Struct. Biol. 142:2003;356-363
    • (2003) J. Struct. Biol. , vol.142 , pp. 356-363
    • Liu, H.J.1    Qu, C.X.2    Johnson, J.E.3    Case, D.A.4
  • 26
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • Ming D., Kong Y.F., Lambert M.A., Huang Z., Ma J.P. How to describe protein motion without amino acid sequence and atomic coordinates. Proc. Natl. Acad. Sci. USA. 99:2002;8620-8625
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.F.2    Lambert, M.A.3    Huang, Z.4    Ma, J.P.5
  • 27
    • 0037062479 scopus 로고    scopus 로고
    • Domain movements in human fatty acid synthase by quantized elastic deformational model
    • Ming D.M., Kong Y.F., Wakil S.J., Brink J., Ma J.P. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc. Natl. Acad. Sci. USA. 99:2002;7895-7899
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 7895-7899
    • Ming, D.M.1    Kong, Y.F.2    Wakil, S.J.3    Brink, J.4    Ma, J.P.5
  • 28
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • Miyashita O., Onuchic J.N., Wolynes P.G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Natl. Acad. Sci. USA. 100:2003;12570-12575
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 29
    • 0029937635 scopus 로고    scopus 로고
    • Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary T-like, quaternary R-like intermediate structures
    • Mouawad L., Perahia D. Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. J. Mol. Biol. 258:1996;393-410
    • (1996) J. Mol. Biol. , vol.258 , pp. 393-410
    • Mouawad, L.1    Perahia, D.2
  • 30
    • 0029374782 scopus 로고
    • Computation of low-frequency normal-modes in macromolecules - Improvements to the method of diagonalization in a mixed basis and application to hemoglobin
    • Perahia D., Mouawad L. Computation of low-frequency normal-modes in macromolecules - improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Comput. Chem. 19:1995;241-246
    • (1995) Comput. Chem. , vol.19 , pp. 241-246
    • Perahia, D.1    Mouawad, L.2
  • 33
    • 0033780164 scopus 로고    scopus 로고
    • Fitting atomic models into electron-microscopy maps
    • Rossmann M.G. Fitting atomic models into electron-microscopy maps. Acta Crystallogr. D. 56:2000;1341-1349
    • (2000) Acta Crystallogr. D , vol.56 , pp. 1341-1349
    • Rossmann, M.G.1
  • 34
    • 0035783056 scopus 로고    scopus 로고
    • Combining electron microscopic with X-ray crystallographic structures
    • Rossmann M.G., Bernal R., Pletnev S.V. Combining electron microscopic with X-ray crystallographic structures. J. Struct. Biol. 136:2001;190-200
    • (2001) J. Struct. Biol. , vol.136 , pp. 190-200
    • Rossmann, M.G.1    Bernal, R.2    Pletnev, S.V.3
  • 35
    • 0033813317 scopus 로고    scopus 로고
    • Conformational changes studied by cryo-electron microscopy
    • Saibil H.R. Conformational changes studied by cryo-electron microscopy. Nat. Struct. Biol. 7:2000;711-714
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 711-714
    • Saibil, H.R.1
  • 36
    • 0025109873 scopus 로고
    • Deoxymyoglobin studied by the conformational normal mode analysis 1. Dynamics of globin and the heme-globin interaction
    • Seno Y., Go N. Deoxymyoglobin studied by the conformational normal mode analysis 1. Dynamics of globin and the heme-globin interaction. J. Mol. Biol. 216:1990;95-109
    • (1990) J. Mol. Biol. , vol.216 , pp. 95-109
    • Seno, Y.1    Go, N.2
  • 37
    • 0029643791 scopus 로고
    • Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryoelectron microscopy
    • Speir J.A., Munshi S., Wang G.J., Baker T.S., Johnson J.E. Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryoelectron microscopy. Structure. 3:1995;63-78
    • (1995) Structure , vol.3 , pp. 63-78
    • Speir, J.A.1    Munshi, S.2    Wang, G.J.3    Baker, T.S.4    Johnson, J.E.5
  • 38
    • 0036307741 scopus 로고    scopus 로고
    • The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
    • Tama F., Brooks III C.L. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J. Mol. Biol. 318:2002;733-747
    • (2002) J. Mol. Biol. , vol.318 , pp. 733-747
    • Tama, F.1    Brooks III, C.L.2
  • 39
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F., Sanejouand Y.H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:2001;1-6
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 40
    • 1642355235 scopus 로고    scopus 로고
    • Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
    • Tama F., Miyashita O., Brooks III C.L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337:2004;985-999
    • (2004) J. Mol. Biol. , vol.337 , pp. 985-999
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 41
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Tama F., Wriggers W., Brooks III C.L. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:2002;297-305
    • (2002) J. Mol. Biol. , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks III, C.L.3
  • 43
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • Tama F., Valle M., Frank J., Brooks III C.L. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:2003;9319-9323
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks III, C.L.4
  • 45
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1996;1905-1908
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 47
    • 0032779888 scopus 로고    scopus 로고
    • Quantitative fitting of atomic models into observed densities derived by electron microscopy
    • Volkmann N., Hanein D. Quantitative fitting of atomic models into observed densities derived by electron microscopy. J. Struct. Biol. 125:1999;176-184
    • (1999) J. Struct. Biol. , vol.125 , pp. 176-184
    • Volkmann, N.1    Hanein, D.2
  • 49
    • 0035836733 scopus 로고    scopus 로고
    • Three-dimensional image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2
    • Wendt T., Taylor D., Trybus K.M., Taylor K. Three-dimensional image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2. Proc. Natl. Acad. Sci. USA. 98:2001;4361-4366
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 4361-4366
    • Wendt, T.1    Taylor, D.2    Trybus, K.M.3    Taylor, K.4
  • 50
    • 0035783173 scopus 로고    scopus 로고
    • Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data
    • Wriggers W., Birmanns S. Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data. J. Struct. Biol. 133:2001;193-202
    • (2001) J. Struct. Biol. , vol.133 , pp. 193-202
    • Wriggers, W.1    Birmanns, S.2
  • 51
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    • Wriggers W., Milligan R.A., McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125:1999;185-195
    • (1999) J. Struct. Biol. , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 52
    • 0037285752 scopus 로고    scopus 로고
    • A core-weighted fitting method for docking atomic structures into low-resolution maps: Application to cryo-electron microscopy
    • Wu X.W., Milne J.L.S., Borgnia M.J., Rostapshov A.V., Subramaniam S., Brooks B.R. A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J. Struct. Biol. 141:2003;63-76
    • (2003) J. Struct. Biol. , vol.141 , pp. 63-76
    • Wu, X.W.1    Milne, J.L.S.2    Borgnia, M.J.3    Rostapshov, A.V.4    Subramaniam, S.5    Brooks, B.R.6
  • 53
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 angstrom resolution
    • Zhang G.Y., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 angstrom resolution. Cell. 98:1999;811-824
    • (1999) Cell , vol.98 , pp. 811-824
    • Zhang, G.Y.1    Campbell, E.A.2    Minakhin, L.3    Richter, C.4    Severinov, K.5    Darst, S.A.6


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