Refinement of protein structures by iterative comparative modeling and cryoEM density fitting

Journal of Molecular Biology

Volumn 357, Issue 5, 2006, Pages 1655-1668

  Topf, Maya ^a   Baker, Matthew L ^b   Marti Renom, Marc A ^a   Chiu, Wah ^b   Sali, Andrej ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Comparative modeling; Cryo electron microscopy; Density fitting; Homology modeling; Protein structure prediction

Indexed keywords

CAPSID PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; ATOM; BLUETONGUE ORBIVIRUS; CRYOELECTRON MICROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN TARGETING; QUALITY CONTROL;

BLUETONGUE VIRUS; MIRIDAE; RICE DWARF VIRUS;

EID: 33645075435     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.01.062     Document Type: Article

References (67)

1. A. Sali, R. Glaeser, T. Earnest, and W. Baumeister From words to literature in structural proteomics Nature 422 2003 216 225
2. R.B. Russell, F. Alber, P. Aloy, F.P. Davis, D. Korkin, and M. Pichaud A structural perspective on protein-protein interactions Curr. Opin. Struct. Biol. 14 2004 313 324
3. B. Alberts The cell as a collection of protein machines: preparing the next generation of molecular biologists Cell 92 1998 291 294
4. H.R. Saibil Macromolecular structure determination by cryo-electron microscopy Acta Crystallog. sect. D 56 2000 1215 1222
5. J. Frank Single-particle imaging of macromolecules by cryo-electron microscopy Annu. Rev. Biophys. Biomol. Struct. 31 2002 303 319
6. R. Henderson Realizing the potential of electron cryo-microscopy Quart. Rev. Biophys. 37 2004 3 13
7. W. Chiu, M.L. Baker, W. Jiang, M. Dougherty, and M.F. Schmid Electron cryomicroscopy of biological machines at subnanometer resolution Structure (Camb) 13 2005 363 372
8. W. Jiang, M.L. Baker, S.J. Ludtke, and W. Chiu Bridging the information gap: computational tools for intermediate resolution structure interpretation J. Mol. Biol. 308 2001 1033 1044
9. F. Fabiola, and M.S. Chapman Fitting of high-resolution structures into electron microscopy reconstruction images Structure (Camb) 13 2005 389 400
10. R. Beckmann, C.M. Spahn, N. Eswar, J. Helmers, P.A. Penczek, and A. Sali Architecture of the protein-conducting channel associated with the translating 80S ribosome Cell 107 2001 361 372
11. J.A. Davis, Y. Takagi, R.D. Kornberg, and F.A. Asturias Structure of the yeast RNA polymerase II holoenzyme: mediator conformation and polymerase interaction Mol. Cell. 10 2002 409 415
12. K.C. Holmes, I. Angert, F.J. Kull, W. Jahn, and R.R. Schroder Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide Nature 425 2003 423 427
13. M.M. Golas, B. Sander, C.L. Will, R. Luhrmann, and H. Stark Molecular architecture of the multiprotein splicing factor SF3b Science 300 2003 980 984
14. V.A. Kostyuchenko, P.G. Leiman, P.R. Chipman, S. Kanamaru, M.J. van Raaij, and F. Arisaka Three-dimensional structure of bacteriophage T4 baseplate Nature Struct. Biol. 10 2003 688 693
15. D.S. Shin, L. Pellegrini, D.S. Daniels, B. Yelent, L. Craig, and D. Bates Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2 EMBO J. 22 2003 4566 4576
16. D. Ming, Y. Kong, M.A. Lambert, Z. Huang, and J. Ma How to describe protein motion without amino acid sequence and atomic coordinates Proc. Natl Acad. Sci. USA 99 2002 8620 8625
17. F. Tama, W. Wriggers, and C.L. Brooks III Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory J. Mol. Biol. 321 2002 297 305
18. M.F. Schmid, M.B. Sherman, P. Matsudaira, and W. Chiu Structure of the acrosomal bundle Nature 431 2004 104 107
19. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
20. D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96
21. M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 29 2000 291 325
22. M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, B. John, U. Pieper, and R. Karchin Comparative protein structure modeling J.M. Walker The Proteomics Protocols Handbook 2005 Humana Press Inc. Totowa, NJ 831 860
23. K. Ginalski, N.V. Grishin, A. Godzik, and L. Rychlewski Practical lessons from protein structure prediction Nucl. Acids Res. 33 2005 1874 1891
24. B. Wallner, and A. Elofsson All are not equal: a benchmark of different homology modeling programs Protein Sci. 14 2005 1315 1327
25. A. Bairoch, R. Apweiler, C.H. Wu, W.C. Barker, B. Boeckmann, and S. Ferro The Universal Protein Resource (UniProt) Nucl. Acids Res. 33 2005 D154 D159
26. U. Pieper, N. Eswar, F. Davis, H. Braberg, M.S.P. Madhusudhan, and A. Rossi MODBASE, a database of annotated comparative protein structure models, and associated resources Nucl. Acids Res. 34 2006 D291 D295
27. A. Sali, and J. Kuriyan Challenges at the frontiers of structural biology Trends Cell. Biol. 9 1999 M20 M24
28. G. Wang, and R.L. Dunbrack Jr Scoring profile-to-profile sequence alignments Protein Sci. 13 2004 1612 1626
29. M.A. Marti-Renom, M.S. Madhusudhan, and A. Sali Alignment of protein sequences by their profiles Protein Sci. 13 2004 1071 1087
30. R. Sanchez, and A. Sali Evaluation of comparative protein structure modeling by MODELLER-3 Proteins: Struct. Funct. Genet. Suppl 1 1997 50 58
31. B. John, and A. Sali Comparative protein structure modeling by iterative alignment, model building and model assessment Nucl. Acids Res. 31 2003 3982 3992
32. F. Melo, R. Sanchez, and A. Sali Statistical potentials for fold assessment Protein Sci. 11 2002 430 448
33. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acids Res. 25 1997 3389 3402
34. K. Karplus, C. Barrett, and R. Hughey Hidden Markov models for detecting remote protein homologies Bioinformatics 14 1998 846 856
35. M. Topf, M.L. Baker, B. John, W. Chiu, and A. Sali Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy J. Struct. Biol. 149 2005 191 203
36. C. Chothia, and A.M. Lesk The relation between the divergence of sequence and structure in proteins EMBO J. 5 1986 823 826
37. R. Sanchez, and A. Sali Large-scale protein structure modeling of the Saccharomyces cerevisiae genome Proc. Natl Acad. Sci. USA 95 1998 13597 13602
38. B. Rost Twilight zone of protein sequence alignments Protein Eng. 12 1999 85 94
39. M.A. Saqi, R.B. Russell, and M.J. Sternberg Misleading local sequence alignments: implications for comparative protein modelling Protein Eng. 11 1998 627 630
40. M. Gribskov, A.D. McLachlan, and D. Eisenberg Profile analysis: detection of distantly related proteins Proc. Natl Acad. Sci. USA 84 1987 4355 4358
41. S.R. Eddy Profile hidden Markov models Bioinformatics 14 1998 755 763
42. J.M. Sauder, J.W. Arthur, and R.L. Dunbrack Jr Large-scale comparison of protein sequence alignment algorithms with structure alignments Proteins: Struct. Funct. Genet. 40 2000 6 22
43. L. Jaroszewski, L. Rychlewski, Z. Li, W. Li, and A. Godzik FFAS03: a server for profile-profile sequence alignments Nucl. Acids Res. 33 2005 W284 W288
44. H. Zhou, and Y. Zhou Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments Proteins: Struct. Funct. Genet. 58 2005 321 328
45. R.C. Edgar, and K. Sjolander A comparison of scoring functions for protein sequence profile alignment Bioinformatics 20 2004 1301 1308
46. T. Ohlson, B. Wallner, and A. Elofsson Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods Proteins: Struct. Funct. Genet. 57 2004 188 197
47. E. Lindahl, and A. Elofsson Identification of related proteins on family, superfamily and fold level J. Mol. Biol. 295 2000 613 625
48. J. Söding Protein homology detection by HMM-HMM comparison Bioinformatics 21 2005 951 960
49. L.J. McGuffin, and D.T. Jones Improvement of the GenTHREADER method for genomic fold recognition Bioinformatics 19 2003 874 881
50. L.A. Kelley, R.M. MacCallum, and M.J. Sternberg Enhanced genome annotation using structural profiles in the program 3D-PSSM J. Mol. Biol. 299 2000 499 520
51. J. Shi, T.L. Blundell, and K. Mizuguchi FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties J. Mol. Biol. 310 2001 243 257
52. R. Karchin, M. Cline, Y. Mandel-Gutfreund, and K. Karplus Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry Proteins: Struct. Funct. Genet. 51 2003 504 514
53. K. Karplus, R. Karchin, J. Draper, J. Casper, Y. Mandel-Gutfreund, M. Diekhans, and R. Hughey Combining local-structure, fold-recognition, and new fold methods for protein structure prediction Proteins: Struct. Funct. Genet. 53 Suppl. 6 2003 491 496
54. A. Godzik Fold recognition methods Methods Biochem. Anal. 44 2003 525 546
55. M.A. Saqi, and M.J. Sternberg A simple method to generate non-trivial alternate alignments of protein sequences J. Mol. Biol. 219 1991 727 732
56. M.A. Saqi, P.A. Bates, and M.J. Sternberg Towards an automatic method of predicting protein structure by homology: an evaluation of suboptimal sequence alignments Protein Eng. 5 1992 305 311
57. B. Contreras-Moreira, P.W. Fitzjohn, and P.A. Bates In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling J. Mol. Biol. 328 2003 593 608
58. M. Levitt, and C. Chothia Structural patterns in globular proteins Nature 261 1976 552 558
59. S.J. Ludtke, P.R. Baldwin, and W. Chiu EMAN: semiautomated software for high-resolution single-particle reconstructions J. Struct. Biol. 128 1999 82 97
60. Z.H. Zhou, M.L. Baker, W. Jiang, M. Dougherty, J. Jakana, and G. Dong Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus Nature Struct. Biol. 8 2001 868 873
61. A. Nakagawa, N. Miyazaki, J. Taka, H. Naitow, A. Ogawa, and Z. Fujimoto The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins Structure (Camb) 11 2003 1227 1238
62. M.S. Madhusudhan, M.A. Marti-Renom, R. Sanchez, and A. Sali Variable gap penalty for protein sequence-structure alignment Protein Eng. Design Select. 2006 In the press
63. I.N. Shindyalov, and P.E. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 11 1998 739 747
64. J. Grimes, A.K. Basak, P. Roy, and D. Stuart The crystal structure of bluetongue virus VP7 Nature 373 1995 167 170
65. M. Topf, and A. Sali Combining electron microscopy and comparative protein structure modeling Curr. Opin. Struct. Biol. 15 2005 578 585
66. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
67. D. Frishman, and P. Argos Knowledge-based protein secondary structure assignment Proteins: Struct. Funct. Genet. 23 1995 566 579