Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling

Structure

Volumn 21, Issue 7, 2013, Pages 1097-1106

  Degiacomi, Matteo T ^a,b   Dal Peraro, Matteo ^a  

^a EPFL   (Switzerland)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; MACROMOLECULE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ASSEMBLY; PROTEIN INTERACTION; REACTION ANALYSIS;

ALGORITHMS; HUMANS; MOLECULAR DYNAMICS SIMULATION; MULTIPROTEIN COMPLEXES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS;

EID: 84879843809     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.05.014     Document Type: Article

References (42)

1. A. Abraham, and H. Liu Turbulent particle swarm optimization using fuzzy parameter tuning Foundations of Computational Intelligence 3 2009 291 312
2. F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, and B.T. Chait Determining the architectures of macromolecular assemblies Nature 450 2007 683 694
3. 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
4. D. Alemani, F. Collu, M. Cascella, and M. Dal Peraro A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements J. Chem. Theory Comput. 6 2010 315 324
5. I. Andre, P. Bradley, C. Wang, and D. Baker Prediction of the structure of symmetrical protein assemblies Proc. Natl. Acad. Sci. 104 2007 17656 17661
6. P. Angeline Evolutionary optimization versus particle swarm optimization: Philosophy and performance differences Evolutionary Programming VII, Lecture Notes in Computer Science 1447 1998 601 610
7. R.P. Bahadur, and M. Zacharias The interface of protein-protein complexes: analysis of contacts and prediction of interactions Cell. Mol. Life Sci. 65 2008 1059 1072
8. A. Berchanski, D. Segal, and M. Eisenstein Modeling oligomers with Cn or Dn symmetry: application to CAPRI target 10. Proteins Structure, Function, and Bioinformatics 60 2005 202 206
9. D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini, and L. Vanneschi A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Lecture Notes in Computer Science 5483 2009 116 127
10. D.D. Boehr, R. Nussinov, and P.E. Wright The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 2009 789 796
11. S. Chaudhury, and J.J. Gray Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles J. Mol. Biol. 381 2008 1068 1087
12. H.M. Chen, B.F. Liu, H.L. Huang, S.F. Hwang, and S.Y. Ho SODOCK: swarm optimization for highly flexible protein-ligand docking J. Comput. Chem. 28 2007 612 623
13. 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
14. R.O. Dror, R.M. Dirks, J.P. Grossman, H. Xu, and D.E. Shaw Biomolecular simulation: a computational microscope for molecular biology Annu. Rev. Biophys. 41 2012 429 452
15. E. Elbeltagi, T. Hegazy, and D. Grierson Comparison among five evolutionary-based optimization algorithms Adv. Eng. Inform. 19 2005 43 53
16. A.C. Gavin, M. Bösche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, and C.M. Cruciat Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147
17. S.D. Goldberg, C.S. Soto, C.D. Waldburger, and W.F. Degrado Determination of the physiological dimer interface of the PhoQ sensor domain J. Mol. Biol. 379 2008 656 665
18. D.S. Goodsell, and A.J. Olson Structural symmetry and protein function Annu. Rev. Biophys. Biomol. Struct. 29 2000 105 153
19. R. Grünberg, J. Leckner, and M. Nilges Complementarity of structure ensembles in protein-protein binding Structure 12 2004 2125 2136
20. T. Hofmeyer, S. Schmelz, M.T. Degiacomi, M. Dal Peraro, M. Daneschdar, A. Scrima, J. van den Heuvel, D.W. Heinz, and H. Kolmar Arranged sevenfold: structural insights into the C-terminal oligomerization domain of human C4b-binding protein J. Mol. Biol. 425 2013 1302 1317
21. I. Iacovache, M.T. Degiacomi, L. Pernot, S. Ho, M. Schiltz, M. Dal Peraro, and F.G. van der Goot Dual chaperone role of the C-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin PLoS Pathog. 7 2011 e1002135
22. J. Kennedy, and R. Eberhart Particle swarm optimization Proceedings of the IEEE International Conference 4 1995 1942 1948
23. O.F. Lange, N.A. Lakomek, C. Farès, G.F. Schröder, K.F. Walter, S. Becker, J. Meiler, H. Grubmüller, C. Griesinger, and B.L. de Groot Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Science 320 2008 1471 1475
24. K. Lasker, F. Förster, S. Bohn, T. Walzthoeni, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, and W. Baumeister Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach Proc. Natl. Acad. Sci. USA 109 2012 1380 1387
25. T. Lemmin, C.S. Soto, G. Clinthorne, W.F. DeGrado, and M. Dal Peraro Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations PLoS Comput. Biol. 9 2013 e1002878
26. M.F. Lensink, and S.J. Wodak Docking and scoring protein interactions: CAPRI 2009 Proteins 78 2010 3073 3084
27. E. Mashiach-Farkash, R. Nussinov, and H.J. Wolfson SymmRef: a flexible refinement method for symmetric multimers Proteins 79 2011 2607 2623
28. R. Meier, M. Pippel, F. Brandt, W. Sippl, and C. Baldauf ParaDockS: a framework for molecular docking with population-based metaheuristics J. Chem. Inf. Model. 50 2010 879 889
29. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 19 1999 1639 1662
30. D. Mustard, and D.W. Ritchie Docking essential dynamics eigenstructures Proteins 60 2005 269 274
31. V. Namasivayam, and R. Günther pso@autodock: a fast flexible molecular docking program based on Swarm intelligence Chem. Biol. Drug Des. 70 2007 475 484
32. M.W. Parker, J.T. Buckley, J.P.M. Postma, A.D. Tucker, K. Leonard, F. Pattus, and D. Tsernoglou Structure of the Aeromonas toxin proaerolysin in its water-soluble and membrane-channel states Nature 367 1994 292 295
33. J.H. Peters, and B.L. de Groot Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection PLoS Comput. Biol. 8 2012 e1002704
34. B. Pierce, W. Tong, and Z. Weng M-ZDOCK: a grid-based approach for Cn symmetric multimer docking Bioinformatics 21 2005 1472 1478
35. K.W. Plaxco, and M. Gross Protein complexes: the evolution of symmetry Curr. Biol. 19 2009 R25 R26
36. D. Russel, K. Lasker, B. Webb, J. Velázquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, and A. Sali Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies PLoS Biol. 10 2012 e1001244
37. D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, and H.J. Wolfson PatchDock and SymmDock: servers for rigid and symmetric docking Nucleic Acids Res. 33 Web Server issue 2005 W363 W367
38. E.S. Shih, and M.J. Hwang On the use of distance constraints in protein-protein docking computations Proteins 80 2012 194 205
39. G.R. Smith, M.J.E. Sternberg, and P.A. Bates The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking J. Mol. Biol. 347 2005 1077 1101
40. L.G. Trabuco, E. Villa, K. Mitra, J. Frank, and K. Schulten Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics Structure 16 2008 673 683
41. Y. Tsitrin, C.J. Morton, C. el-Bez, P. Paumard, M.C. Velluz, M. Adrian, J. Dubochet, M.W. Parker, S. Lanzavecchia, and F.G. van der Goot Conversion of a transmembrane to a water-soluble protein complex by a single point mutation Nat. Struct. Biol. 9 2002 729 733
42. W. Wriggers Using Situs for the integration of multi-resolution structures Biophys. Rev. 2 2010 21 27