Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-electron microscopy data

Structure

Volumn 23, Issue 5, 2015, Pages 949-960

  Van Zundert, Gydo C P ^a   Melquiond, Adrien S J ^a,b   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; CRYOELECTRON MICROSCOPY; METABOLISM; MOLECULAR DOCKING; PROCEDURES; PROTEIN DATABASE;

COMPUTATIONAL BIOLOGY; CRYOELECTRON MICROSCOPY; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MULTIPROTEIN COMPLEXES; USER-COMPUTER INTERFACE;

EID: 84930188630     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.03.014     Document Type: Article

References (49)

1. F. Alber, F. Förster, D. Korkin, M. Topf, and A. Sali Integrating diverse data for structure determination of macromolecular assemblies Annu. Rev. Biochem. 77 2008 443 477
2. 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
3. S. Birmanns, and W. Wriggers Multi-resolution anchor-point registration of biomolecular assemblies and their components J. Struct. Biol. 157 2007 271 280
4. D. Boehringer, H.C. O'Farrell, J.P. Rife, and N. Ban Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis J. Biol. Chem. 287 2012 10453 10459
5. A.T. Brunger Version 1.2 of the Crystallography and NMR system Nat. Protoc. 2 2007 2728 2733
6. M.I. Daudén, J. Martín-Benito, J.C. Sánchez-Ferrero, C. Pulido-Cid, J.M. Valpuesta, and J.L. Carrascosa Large terminase conformational change induced by connector binding in bacteriophage T7 J. Biol. Chem. 288 2013 16998 17007
7. S.J. De Vries, and M. Zacharias ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps PLoS One 7 2012 e49733
8. S.J. De Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar, and A.M.J.J. Bonvin HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets Proteins 69 2007 726 733
9. S.J. De Vries, M. van Dijk, and A.M.J.J. Bonvin The HADDOCK web server for data-driven biomolecular docking Nat. Protoc. 5 2010 883 897
10. S.J. De Vries, A.S.J. Melquiond, P.L. Kastritis, E. Karaca, A. Bordogna, M. van Dijk, J.P.G.L.M. Rodrigues, and A.M.J.J. Bonvin Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions Proteins 78 2010 3242 3249
11. C. Dominguez, R. Boelens, and A.M.J.J. Bonvin HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
12. J. Esquivel-Rodríguez, and D. Kihara Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors J. Phys. Chem. B 116 2012 6854 6861
13. J. Esquivel-Rodríguez, and D. Kihara Computational methods for constructing protein structure models from 3D electron microscopy maps J. Struct. Biol. 184 2013 93 102
14. J. Fernández-Recio, M. Totrov, and R. Abagyan Identification of protein-protein interaction sites from docking energy landscapes J. Mol. Biol. 335 2004 843 865
15. T.D. Goddard, C.C. Huang, and T.E. Ferrin Visualizing density maps with UCSF Chimera J. Struct. Biol. 157 2007 281 287
16. Q. Guo, Y. Yuan, Y. Xu, B. Feng, L. Liu, K. Chen, M. Sun, Z. Yang, J. Lei, and N. Gao Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy Proc. Natl. Acad. Sci. USA 108 2011 13100 13105
17. T.V. Hoang, X. Cavin, and D.W. Ritchi gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration J. Struct. Biol. 184 2013 348 354
18. S.-Y. Huang Search strategies and evaluation in protein-protein docking: principles, advances and challenges Drug Discov. Today 19 2014 1081 1096
19. H. Hwang, T. Vreven, J. Janin, and Z. Weng Protein-protein docking benchmark version 4.0 Proteins 78 2010 3111 3114
20. J. Janin, K. Henrick, J. Moult, L.T. Eyck, M.J.E. Sternberg, S. Vajda, I. Vakser, and S.J. Wodak CAPRI: a Critical Assessment of PRedicted Interactions Proteins 52 2003 2 9
21. A.C. Joerger, and A.R. Fersht Structure-function-rescue: the diverse nature of common p53 cancer mutants Oncogene 26 2007 2226 2242
22. W.L. Jorgensen, and J. Tirado-Rives The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 110 1988 1657 1666
23. E. Karaca, and A.M.J.J. Bonvin A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes Structure 19 2011 555 565
24. E. Karaca, and A.M.J.J. Bonvin Advances in integrative modeling of biomolecular complexes Methods 59 2013 372 381
25. E. Karaca, and A.M.J.J. Bonvin On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys Acta Crystallogr. D Biol. Crystallogr. 69 2013 683 694
26. E. Karaca, A.S.J. Melquiond, S.J. de Vries, P.L. Kastritis, and A.M.J.J. Bonvin Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server Mol. Cell. Proteomics 9 2010 1784 1794
27. T. Kawabata Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model Biophys. J. 95 2008 4643 4658
28. K. Lage Protein-protein interactions and genetic diseases: the interactome Biochim. Biophys. Acta 1842 2014 1971 1980
29. K. Lasker, A. Sali, and H.J. Wolfson Determining macromolecular assembly structures by molecular docking and fitting into an electron density map Proteins 78 2010 3205 3211
30. D.M. McCraw, J.K. O'Donnel, K.A. Taylor, S.M. Stagg, and M.S. Chapman Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 Virology 431 2012 40 49
31. I.S. Moreira, P.A. Fernandes, and M.J. Ramos Protein-protein docking dealing with the unknown J. Comput. Chem. 31 2010 317 342
32. R. Mosca, A. Céol, and P. Aloy Interactome3D: adding structural details to protein networks Nat. Methods 10 2013 47 53
33. K. Murakami, H. Elmlund, N. Kalisman, D.A. Bushnell, C.M. Adams, M. Azubel, D. Elmlund, Y. Levi-Kalisman, X. Liu, and B.J. Gibbons Architecture of an RNA polymerase II transcription pre-initiation complex Science 342 2013 1238724
34. J. Navaza, J. Lepault, F.A. Rey, C. Alvarez-Rúa, 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
35. T.L. Nero, C.J. Morton, J.K. Holien, J. Wielens, and M.W. Parker Oncogenic protein interfaces: small molecules, bit challenges Nat. Rev. Cancer 14 2014 248 262
36. E.V. Orlova, and H.R. Saibil Structural analysis of macromolecular assemblies by electron microscopy Chem. Rev. 111 2011 7710 7748
37. D. Petrey, and B. Honig Structural bioinformatics of the interactome Annu. Rev. Biophys. 43 2014 193 210
38. J.P.G.L.M. Rodrigues, and A.M.J.J. Bonvin Integrative computational modeling of protein interactions FEBS J. 281 2014 1988 2003
39. D. Schneidman-Duhovny, A. Rossi, A. Avila-Sakar, S.J. Kim, J. Velázquez-Muriel, P. Strop, H. Liang, K.A. Kurkenberg, M. Liao, and H.M. Kim A method for integrative structure determination of protein-protein complexes Bioinformatics 28 2012 3282 3289
40. E. Shacham, B. Sheehan, and N. Volkmann Density-based score for selecting near-native atomic models of unknown structures J. Struct. Biol. 158 2007 188 195
41. M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, and A. Sali Protein structure fitting and refinement guided by cryo-EM density Structure 16 2008 295 307
42. M. Trellet, A.S.J. Melquiond, and A.M.J.J. Bonvin A unified conformational selection and induced fit approach to protein-peptide docking PLoS One 8 2013 e58769
43. M. Van Dijk, A.D.J. van Dijk, V. Hsu, R. Boelens, and A.M.J.J. Bonvin Information-driven protein-DNA docking HADDOCK: it is a matter of flexibility Nucleic Acids Res. 34 2006 3317 3325
44. J. Velázquez-Muriel, K. Lasker, D. Russel, J. Phillips, B.M. Webb, D. Schneidman-Duhovny, and A. Sali Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images Proc. Natl. Acad. Sci. USA 109 2012 18821 18826
45. Z. Wang, L. Li, J.G. Pennington, J. Sheng, M.L. Yap, P. Plevka, G. Meng, L. Sun, W. Jiang, and M.G. Rossmann Obstruction of dengue virus maturation by Fab fragments of the 2H2 antibody J. Virol. 87 2013 8909 8915
46. R. Wells, and C.L. McClendon Reaching for high-hanging fruit in drug discovery at protein-protein interfaces Nature 450 2007 1001 1009
47. W. Wriggers, R.A. Milligan, K. Schulten, and J.A. McCammon Self-organizing neural networks bridge the biomolecular resolution gap J. Mol. Biol. 284 1998 1247 1254
48. Z. Xu, H.C. O'Farrell, J.P. Rife, and G.M. Culver A conserved rRNA methyltransferase regulates ribosome biogenesis Nat. Struct. Mol. Biol. 15 2008 534 536
49. S. Zhang, D. Vasishtan, M. Xu, M. Topf, and F. Alber A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps Bioinformatics 26 2010 i261 i268