Fitting of high-resolution structures into electron microscopy reconstruction images

Structure

Volumn 13, Issue 3, 2005, Pages 389-400

  Fabiola, Felcy ^a   Chapman, Michael S ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ELECTRON MICROSCOPY; IMAGE ANALYSIS; IMAGE QUALITY; METHODOLOGY; OPTICAL RESOLUTION; PRIORITY JOURNAL; STEREOCHEMISTRY;

EID: 14844311200     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.01.007     Document Type: Article

References (65)

1. T.S. Baker, and J.E. Johnson Low resolution meets high: towards a resolution continuum from cells to atoms Curr. Opin. Struct. Biol. 6 1996 585 594
2. D.M. Belnap, B.M. McDermott Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, and A.C. Steven Three-dimensional structure of poliovirus receptor bound to poliovirus Proc. Natl. Acad. Sci. USA 97 2000 73 78
3. E. Blanc, and M.S. Chapman RSRef: interactive real-space refinement with stereochemical restraints for use during model-building J. Appl. Crystallogr. 30 1997 566 567
4. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swamithan, and M. Karplus CHARMM: a program for macromolecular energy minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
5. A.T. Brünger X-Plor Version 3.1: A System for X-ray Crystallography and NMR 1992 Yale University Press New Haven, CT
6. A.T. Brünger The free R value: a more objective statistic for crystallography Methods Enzymol. 277 1997 366 396
7. A.T. Brünger, and L.M. Rice Crystallographic refinement by simulated annealing: methods and applications Methods Enzymol. 277 1997 243 269
8. A.T. Brünger, J. Kuriyan, and M. Karplus Crystallographic R factor refinement by molecular dynamics Science 235 1987 458 460
9. A.T. Brünger, A. Krukowski, and J. Erickson Slow-cooling protocols for crystallographic refinement by simulated annealing Acta Crystallogr. A46 1990 585 593
10. A.T. Brünger, P.D. Adams, G.M. Clore, P. Gros, R.W. Gross-Kunstleve, J.-S. Jiang, J. Kurzewski, M. Nilges, N.S. Pannu, and R.J. Read Crystallography and NMR system: a new software system for macromolecular structure determination Acta Crystallogr. D54 1998 905 921
11. A.T. Brünger, P.D. Adams, and L.M. Rice Recent developments for the efficient crystallographic refinement of macromolecular structures Curr. Opin. Struct. Biol. 8 1998 606 611
12. A.T. Brünger, P.D. Adams, and L.M. Rice Annealing in crystallography: a powerful optimization tool Prog. Biophys. Mol. Biol. 72 1999 135 155
13. F.T. Burling, W.I. Weis, K.M. Flaherty, and A. Brünger Direct observation of protein solvation and discrete disorder using experimental crystallographic phases Science 271 1996 72 77
14. P. Chacon, and W. Wriggers Multi-resolution contour-based fitting of macromolecular structures J. Mol. Biol. 317 2002 375 384
15. M.S. Chapman Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron density function Acta Crystallogr. A51 1995 69 80
16. M.S. Chapman, and E. Blanc Potential use of real space refinement in protein structure determination Acta Crystallogr. D53 1997 203 206
17. M.S. Chapman, and M.G. Rossmann Structural refinement of the DNA-containing capsid of canine parvovirus using RSRef, a resolution-dependent stereochemically restrained real-space refinement method Acta Crystallogr. D52 1996 129 142
18. Z. Chen, E. Blanc, and M.S. Chapman Real space molecular dynamics refinement Acta Crystallogr. D55 1999 464 468
19. L.F. Chen, E. Blanc, M.S. Chapman, and K.A. Taylor Real space refinement of acto-myosin structures from sectioned muscle J. Struct. Biol. 133 2001 221 232
20. J.Z. Chen, J. Furst, M.S. Chapman, and N. Grigorieff Low-resolution structure refinement in electron microscopy J. Struct. Biol. 144 2003 144 151
21. J.M. Cowley Scattering factors for the diffraction of electrons by crystalline solids A.J.C. Wilson International Tables for Crystallography 1995 Kluwer Boston 4.3.1
22. W.L. DeLano The PyMOL Molecular Graphics System 2002 DeLano Scientific San Carlso, CA
23. R. Diamond A real-space refinement procedure for proteins Acta Crystallogr. A27 1971 436 452
24. R. Dominguez, Y. Freyzon, K.M. Trybus, and C. Cohen Crystal structure of a vertebrate smooth muscle myosin motor domain and its complex with the essential light chain: visualization of the pre-power stroke state Cell 94 1998 559 571
25. P.A. Doyle, and P.S. Turner Relativistic Hartree-Fock X-ray and electron scattering factors Acta Crystallogr. A24 1968 390 397
26. P.S. Furcinitti, J. van Oostrum, and R.M. Burnett Adenovirus polypeptide IX revealed as capsid cement by difference images from electron microscopy and crystallography EMBO J. 8 1989 3563 3570
27. H. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. Van Roey, R.K. Agrawal, S.C. Harvey, and A. Sali Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement Cell 113 2003 789 801
28. Y. He, V.D. Bowman, S. Mueller, C.M. Bator, J. Bella, X. Peng, T.S. Baker, E. Wimmer, R.J. Kuhn, and M.G. Rossmann Interaction of the poliovirus receptor with poliovirus Proc. Natl. Acad. Sci. USA 97 2000 79 84
29. A. Hodel, S.-H. Kim, and A.T. Brünger Model bias in macromolecular crystallography Acta Crystallogr. A48 1992 851 858
30. T.A. Jones, and L. Liljas Crystallographic refinement of macromolecules having non-crystallographic symmetry Acta Crystallogr. A 40 1984 50 57
31. J.M. Kenney, J. Hantula, S.D. Fuller, L. Mindich, P.M. Ojala, and D.H. Bamford Bacteriophage φ6 envelope elucidated by chemical cross-linking, immunodetection and cryoelectron microscopy Virology 190 1992 635 644
32. G.J. Kleywegt, and A. Brünger Cross-validation in crystallography: practice and applications Structure 4 1996 897 904
33. J.A. Kovacs, and W. Wriggers Fast rotational matching Acta Crystallogr. D Biol. Crystallogr. 58 2002 1282 1286
34. J. Liu, D.W. Taylor, and K.A. Taylor A 3-D reconstruction of smooth muscle alpha-actinin by CryoEm reveals two different conformations at the actin-binding region J. Mol. Biol. 338 2004 115 125
35. J. Liu, T. Wendt, D. Taylor, and K. Taylor Refined model of the 10S conformation of smooth muscle myosin by cryo-electron microscopy 3D image reconstruction J. Mol. Biol. 329 2003 963 972
36. J. Navaza, J. Lepault, F.A. Rey, C. Alvarez-Rua, and J. Borge On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation Acta Crystallogr. D Biol. Crystallogr. 58 2002 1820 1825
37. N. Olson, P. Kolatkar, M.A. Oliveira, R.H. Cheng, J.M. Greve, A. McClelland, T.S. Baker, and M.G. Rossmann Structure of a human rhinovirus complexed with its receptor molecule Proc. Natl. Acad. Sci. USA 90 1993 507 511
38. B.V. Prasad, J.W. Burns, E. Marietta, M.K. Estes, and W. Chiu Localization of VP4 neutralization sites in rotavirus by three-dimensional cryo-electron microscopy Nature 343 1990 476 479
39. I. Rayment, H.M. Holden, M. Whittaker, C.B. Yohn, M. Lorenz, K.C. Holmes, and R.A. Milligan Structure of the actin-myosin complex and its implications for muscle contraction Science 261 1993 58 65
40. I. Rayment, W.R. Rypniewsky, K. Schmidt-Bäse, R. Smith, D.R. Tomchick, M.M. Benning, D.A. Winkelmann, G. Wesenberg, and H.M. Holden Three-dimensional structure of myosin subfragment-1: a molecular motor Science 261 1993 50 58
41. L.M. Rice, and A.T. Brünger Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement Proteins 19 1994 277 290
42. A.M. Roseman Docking structures of domains into maps from cryo-electron microscopy using local correlation Acta Crystallogr. D Biol. Crystallogr. 56 2000 1332 1340
43. M.G. Rossmann Fitting atomic models into electron-microscopy maps Acta Crystallogr. D Biol. Crystallogr. 56 2000 1341 1349
44. M.G. Rossmann, R. Bernal, and S.V. Pletnev Combining electron microscopic with x-ray crystallographic structures J. Struct. Biol. 136 2001 190 200
45. R.R. Schröder, D.J. Manstein, J. Werner, H. Holden, I. Rayment, K.C. Holmes, and J.A. Spudich Three-dimensional atomic model of F-actin decorated with Dictoselium myosin S1 Nature 364 1993 171 174
46. T.J. Smith, N.H. Olson, R.H. Cheng, E.S. Chase, and T.S. Baker Structure of a human rhinovirus-bivalently bound antibody complex: implications for viral neutralization and antibody flexibility Proc. Natl. Acad. Sci. USA 90 1993 7015 7018
47. T.J. Smith, N.H. Olson, R.H. Cheng, H. Liu, E.S. Chase, W.M. Lee, D.M. Leippe, A.G. Mosser, R.R. Rueckert, and T.S. Baker Structure of human rhinovirus complexed with Fab fragments from a neutralizing antibody J. Virol. 67 1993 1148 1158
48. P.K. Stewart, S.D. Fuller, and R.M. Burnett Bridging the resolution gap between X-ray crystallography and electron microscopy EMBO J. 12 1993 2589 2599
49. P.L. Stewart, S.D. Fuller, and R.M. Burnett Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy EMBO J. 12 1993 2589 2599
50. F. Tama, W. Wriggers, and C.L. Brooks 3rd. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory J. Mol. Biol. 321 2002 297 305
51. F. Tama, O. Miyashita, and C.L. Brooks 3rd. 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
52. F. Tama, O. Miyashita, and C.L. Brooks 3rd. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM J. Struct. Biol. 147 2004 315 326
53. E. Thouvenin, and E. Hewat When two into one won't go: fitting in the presence of steric hindrance and partial occupancy Acta Crystallogr. D Biol. Crystallogr. 56 2000 1350 1357
54. D.E. Tronrud Conjugate-direction minimization: an improved method for the refinement of macromolecules Acta Crystallogr. A48 1992 912 916
55. D.E. Tronrud, L.F. Ten Eyck, and B.W. Matthews An efficient general-purpose least-squares refinement program for macromolecular structures Acta Crystallogr. A43 1987 489 501
56. N. Volkmann, and D. Hanein Quantitative fitting of atomic models into observed densities derived by electron microscopy J. Struct. Biol. 125 1999 176 184
57. N. Volkmann, and D. Hanein Docking of atomic models into reconstructions from electron microscopy Methods Enzymol. 374 2003 204 225
58. N. Volkmann, G. Ouyang, K.M. Trybus, D.J. DeRosier, S. Lowey, and D. Hanein Myosin isoforms show unique conformations in the actin-bound state Proc. Natl. Acad. Sci. USA 100 2003 3227 3232
59. G. Wang, C. Porta, Z. Chen, T. Baker, and J.E. Johnson Identification of a Fab interaction footprint site on an icosahedral virus by cryoelectron microscopy and X-ray crystallography Nature 355 1992 275 278
60. W.I. Weis, R. Kahn, R. Fourne, K. Drickamer, and W.A. Hendrickson Structure of the calcium-dependent lectin domain from a rat nannose-binding protein determined by MAD phasing Science 254 1991 1608 1615
61. T. Wendt, D. Taylor, K.M. Trybus, and K. Taylor 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
62. W. Wriggers, and S. Birmanns Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data J. Struct. Biol. 133 2001 193 202
63. W. Wriggers, and P. Chacon Modeling tricks and fitting techniques for multiresolution structures Structure (Camb.) 9 2001 779 788
64. W. Wriggers, R.A. Milligan, and J.A. McCammon Situs: a package for docking crystal structures into low-resolution maps from electron microscopy J. Struct. Biol. 125 1999 185 195
65. X. Wu, J.L. Milne, M.J. Borgnia, A.V. Rostapshov, S. Subramaniam, and B.R. Brooks 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