Modeling of protein binary complexes using structural mass spectrometry data

Protein Science

Volumn 17, Issue 1, 2008, Pages 79-94

  Kamal, J K Amisha ^a   Chance, Mark R ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Actin cofilin; Actin gelsolin segment 1; ClusPro; Docking; Footprinting constraints; Hydroxyl radical mediated oxidation; Mass spectrometry; Protein protein complex; Radiolytic footprinting; Three dimensional structure

Indexed keywords

ACTIN; COFILIN; DEOXYRIBONUCLEASE I; GELSOLIN; GELSOLIN SEGMENT 1; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL MODEL; COMPLEX FORMATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ELECTRICITY; ENERGY TRANSFER; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLVATION; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

ACTINS; AMINO ACIDS; BINDING SITES; ENZYMES; MASS SPECTROMETRY; MODELS, MOLECULAR; PROFILINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STRESS, MECHANICAL; SURFACE PROPERTIES;

EID: 37549046752     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.073071808     Document Type: Article

References (55)

1. Agbulut, O., Huet, A., Niederlander, N., Puceat, M., Menasche, P., and Coirault, C. 2007. Green fluorescent protein impairs actin-myosin interactions by binding to the actin-binding site of myosin. J. Biol. Chem. 282: 10465-10471.
2. Amann, K.J. and Pollard, T.D. 2000. Cellular regulation of actin network assembly. Curr. Biol. 10: R728-R730.
3. Baker, D. and Sali, A. 2001. Protein structure prediction and structural genomics. Science 294: 93-96.
4. Blanchoin, L. and Pollard, T.D. 1998. Interaction of actin monomers with Acanthamoeba actophorin (ADF/cofilin) and profilin. J. Biol. Chem. 273: 25106-25111.
5. Bonanno, J.B., Almo, S.C., Bresnick, A., Chance, M.R., Fiser, A., Swaminathan, S., Jiang, J., Studier, F.W., Shapiro, L., Lima, C.D., et al. 2005. New York-Structural GenomiX Research Consortium (NYSGXRC): A large scale center for the protein structure initiative. J. Struct. Funct. Genomics 6: 225-232.
6. Chance, M.R., Fiser, A., Sali, A., Pieper, U., Eswar, N., Xu, G., Fajardo, J.E., Radhakannan, T., and Marinkovic, N. 2004. High-throughput computational and experimental techniques in structural genomics. Genome Res. 14: 2145-2154.
7. Chandonia, J.M. and Brenner, S.E. 2005. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 58: 166-179.
8. Chiu, W., Baker, M.L., and Almo, S.C. 2006. Structural biology of cellular machines. Trends Cell Biol. 16: 144-150.
9. Comeau, S.R. 2007. "Development of high-throughput tools for the automated generation of protein-protein complexes." Ph.D. thesis, Boston University, Boston, MA.
10. Comeau, S.R., Gatchell, D.W., Vajda, S., and Camacho, C.J. 2004a. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. 32: W96-W99.
11. Comeau, S.R., Gatchell, D.W., Vajda, S., and Camacho, C.J. 2004b. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20: 45-50.
12. Comeau, S.R., Vajda, S., and Camacho, C.J. 2005. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins 60: 239-244.
13. Davies, M.J. and Dean, R.T. 1997. Radical-mediated protein oxidation: From chemistry to medicine. Oxford University Press, Oxford, UK.
14. DesMarais, V., Ghosh, M., Eddy, R., and Condeelis, J.S. 2005. Cofilin takes the lead. J. Cell Sci. 118: 19-26.
15. Dominguez, R. 2004. Actin-binding proteins: A unifying hypothesis. Trends Biochem. Sci. 29: 572-578.
16. Ewing, R.M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom-Cerajewski, L., Robinson, M.D., O'Connor, L., Li, M., et al. 2007. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3: 89. doi: 10.1038/msb4100134.
17. Fedorov, A.A., Lappalainen, P., Fedorov, E.V., Drubin, D.G., and Almo, S.C. 1997. Structure determination of yeast cofilin. Nat. Struct. Biol. 4: 366-369.
18. Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B., et al. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
19. Ghosh, M., Song, X., Mouneimne, G., Sidani, M., Lawrence, D.S., and Condeelis, J.S. 2004. Cofilin promotes actin polymerization and defines the direction of cell motility. Science 304: 743-746.
20. Goldsmith, S.C., Guan, J.Q., Almo, S., and Chance, M. 2001. Synchrotron protein footprinting: A technique to investigate protein-protein interactions. J. Biomol. Struct. Dyn. 19: 405-418.
21. Gruschus, J.M., Greene, L.E., Eisenberg, E., and Ferretti, J.A. 2004. Experimentally biased model structure of the Hsc70/auxilin complex: Substrate transfer and interdomain structural change. Protein Sci. 13: 2029-2044.
22. Guan, J.Q. and Chance, M.R. 2005. Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem. Sci. 30: 583-592.
23. Guan, J.Q., Vorobiev, S., Almo, S.C., and Chance, M.R. 2002. Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting. Biochemistry 41: 5765-5775.
24. Guan, J.Q., Almo, S.C., Reisler, E., and Chance, M.R. 2003. Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent. Biochemistry 42: 11992-12000.
25. Guan, J.Q., Almo, S.C., and Chance, M.R. 2004. Synchrotron radiolysis and mass spectrometry: A new approach to research on the actin cytoskeleton. Acc. Chem. Res. 37: 221-229.
26. Guan, J.Q., Takamoto, K., Almo, S.C., Reisler, E., and Chance, M.R. 2005. Structure and dynamics of the actin filament. Biochemistry 44: 3166-3175.
27. Halperin, I., Ma, B., Wolfson, H., and Nussinov, R. 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47: 409-443.
28. Janin, J., Henrick, K., Moult, J., Eyck, L.T., Sternberg, M.J., Vajda, S., Vakser, I., and Wodak, S.J. 2003. Critical assessment of predicted interactions. Proteins 52: 2-9.
29. Jones, S. and Thornton, J.M. 1996. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. 93: 13-20.
30. Kamal, J.K.A., Benchaar, S.A., Takamoto, K., Reisler, E., and Chance, M.R. 2007. Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data. Proc. Natl. Acad. Sci. 104: 7910-7915.
31. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., and Vakser, I.A. 1992. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. 89: 2195-2199.
32. Kontoyianni, M., McClellan, L.M., and Sokol, G.S. 2004. Evaluation of docking performance: Comparative data on docking algorithms. J. Med. Chem. 47: 558-565.
33. Lappalainen, P., Fedorov, E.V., Fedorov, A.A., Almo, S.C., and Drubin, D.G. 1997. Essential functions and actin-binding surfaces of yeast cofilin revealed by systematic mutagenesis. EMBO J. 16: 5520-5530.
34. Mannherz, H.G., Ballweber, E., Galla, M., Villard, S., Granier, C., Steegborn, C., Schmidtmann, A., Jaquet, K., Pope, B., and Weeds, A.G. 2007. Mapping the ADF/cofilin binding site on monomeric actin by competitive cross-linking and peptide array: Evidence for a second binding site on monomeric actin. J. Mol. Biol. 366: 745-755.
35. McLaughlin, P.J., Gooch, J.T., Mannherz, H.G., and Weeds, A.G. 1993. Structure of gelsolin segment 1-actin complex and the mechanism of filament severing. Nature 364: 685-692.
36. Mendez, R., Leplae, R., De Maria, L., and Wodak, S.J. 2003. Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins 52: 51-67.
37. Orlova, A., Galkin, V.E., VanLoock, M.S., Kim, E., Shvetsov, A., Reisler, E., and Egelman, E.H. 2001. Probing the structure of F-actin: Cross-links constrain atomic models and modify actin dynamics. J. Mol. Biol. 312: 95-106.
38. Paavilainen, V.O., Bertling, E., Falck, S., and Lappalainen, P. 2004. Regulation of cytoskeletal dynamics by actin-monomer-binding proteins. Trends Cell Biol. 14: 386-394.
39. Pavlov, D., Muhlrad, A., Cooper, J., Wear, M., and Reisler, E. 2006. Severing of F-actin by yeast cofilin is pH independent. Cell Motil. Cytoskeleton 63: 533-542.
40. Perola, E., Walters, W.P., and Charifson, P.S. 2004. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56: 235-249.
41. Pollard, T.D., Blanchoin, L., and Mullins, R.D. 2000. Molecular mechanisms controlling actin filament dynamics in nonmuscle cells. Annu. Rev. Biophys. Biomol. Struct. 29: 545-576.
42. Pons, T., Gonzalez, B., Ceciliani, F., and Galizzi, A. 2006. FlgM anti-σ factors: Identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure- function relationships. J. Mol. Model. 12: 973-983.
43. Pope, B.J., Zierler-Gould, K.M., Kuhne, R., Weeds, A.G., and Ball, L.J. 2004. Solution structure of human cofilin: Actin binding, pH sensitivity, and relationship to actin-depolymerizing factor. J. Biol. Chem. 279: 4840-4848.
44. Reboul, J., Vaglio, P., Rual, J.F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R., et al. 2003. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34: 35-41.
45. Sali, A., Glaeser, R., Earnest, T., and Baumeister, W. 2003. From words to literature in structural proteomics. Nature 422: 216-225.
46. Schwede, T., Kopp, J., Guex, N., and Peitsch, M.C. 2003. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31: 3381-3385.
47. Shortle, D., Simons, K.T., and Baker, D. 1998. Clustering of low energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. 95: 11158-11162.
48. Takamoto, K. and Chance, M.R. 2006. Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biophys. Biomol. Struct. 35: 251-276.
49. Ten Eyck, L.F., Mandell, J., Roberts, V.A., and Pique, M.E. 1995. Surveying molecular interactions with DOT. In ACM/IEEE Supercomputing Conference, p. 22. IEEE Computer Society Press, Los Alamitos, CA.
50. Tovchigrechko, A. and Vakser, I.A. 2006. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 34: W310-W314. doi: 10.1093/nar/gkl206.
51. Truhlar, S.M., Croy, C.H., Torpey, J.W., Koeppe, J.R., and Komives, E.A. 2006. Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry. J. Am. Soc. Mass Spectrom. 17: 1490-1497.
52. Tyers, M. and Mann, M. 2003. From genomics to proteomics. Nature 422: 193-197.
53. Vitkup, D., Melamud, E., Moult, J., and Sander, C. 2001. Completeness in structure genomics. Nat. Struct. Biol. 8: 559-566.
54. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., and Bork, P. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
55. Wriggers, W., Tang, J.X., Azuma, T., Marks, P.W., and Janmey, P.A. 1998. Cofilin and gelsolin segment-1: Molecular dynamics simulation and biochemical analysis predict a similar actin binding mode. J. Mol. Biol. 282: 921-932.