Three-dimensional profiles: A new tool to identify protein surface similarities

Journal of Molecular Biology

Volumn 284, Issue 4, 1998, Pages 1211-1221

  De Rinaldis, Manuel ^b   Ausiello, Gabriele ^b   Cesareni, Gianni ^b   Helmer Citterich, Manuela ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b NONE

Author keywords

Multiple structural alignment; p loop; PDB search; SH2 SH3 domains; Surface 3D profile motifs

Indexed keywords

SUCCINYL COENZYME A SYNTHETASE; SYNTHETASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; DATA BASE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FAMILY; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0032509148     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2248     Document Type: Article

References (61)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
3. Artymiuk P. J., Poirrette A. R., Grindley H. M., Rice D. W., Willett P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol. 243:1994;327-344.
4. Ausiello G., Cesareni G., Helmer Citterich M. ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins: Struct. Funct. Genet. 28:1997;556-567.
5. Bacon D. J., Moult J. Docking by least-squares fitting of molecular surface patterns. J. Mol. Biol. 225:1992;849-858.
6. Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucl. Acids Res. 19:1991;2241-2245.
7. Bairoch A., Bucher P., Hofmann K. The PROSITE database, its status in 1997. Nucl. Acids Res. 25:1997;217-221.
8. Bedford M. T., Chan D. C., Leder P. FBP WW domains and the Abl SH3 domain bind to a specific class of proline-rich ligands. EMBO J. 16:1997;2376-2383.
9. Bjorkegren-Sjogren C., Korenbaum E., Nordberg P., Lindberg U., Karlsson R. Isolation and characterization of two mutants of human profilin I that do not bind poly(L -proline). FEBS Letters. 418:1997;258-264.
10. Blomberg N., Nilges M. Functional diversity of PH domains: an exhaustive modelling study. Folding Des. 6:1997;343-355.
11. Cherfils J., Janin J. Protein docking algorythms: simulating molecular recognition. Curr. Opin. Struct. Biol. 3:1993;265-269.
12. Connolly M. L. Solvent-accessible surface of proteins and nucleic acids. Science. 221:1983a;709-713.
13. Connolly M. L. Analytical molecular surface calculation. J. Appl. Crystallog. 16:1983b;548-558.
14. Eck M. J. A new flavor in phosphotyrosine recognition. Structure. 3:1995;421-424.
15. Fischer D., Norel R., Wolfson H., Nussinov R. Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition. Proteins: Struct. Funct. Genet. 16:1993;278-292.
16. Fischer D., Wolfson H., Lin S. L., Nussinov R. Three-dimensional, sequence-order-independent structural comparison of a serine protease against the crystallografic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Sci. 3:1994;769-778.
17. Fischer D., Lin S. L., Wolfson H. L., Nussinov R. A geometry-based suite of molecular docking processes. J. Mol. Biol. 248:1995;459-477.
18. Gribskov M., Veretnik S. Identification of sequence pattern with profile analysis. Methods Enzymol. 266:1996;198-212.
19. Gribskov M., Mclachlan A. D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA. 84:1987;4355-4358.
20. Helmer-Citterich M., Tramontano A. PUZZLE: a new method for automated protein docking based on surface shape complementarity. J. Mol. Biol. 235:1994;1021-1031.
21. Henikoff S. Scores for sequence searches and alignments. Curr. Opin. Struct. Biol. 6:1996;353-360.
22. Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524.
23. Hobohm U., Scharf, Schneider M. R., Sander C. Selection of representative protein data sets. Protein Sci. 3:1992;409-417.
24. Holm L., Sander C. Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol. 266:1996a;653-662.
25. Holm L., Sander C. Mapping the protein universe. Science. 273:1996b;595-603.
26. Holm L., Sander C. Touring protein fold space with Dali/FSSP. Nucl. Acids Res. 26:1998;316-319.
27. Hubbard S. J., Thornton J. M. NACCESS, Computer Program. 1993;Department of Biochemistry and Molecular BiologyUniversity College London.
28. Hubbard S. J., Campbell, Thornton J. M. Molecular recognition-conformational-analysis of limited proteolytic sites and serine proteinase protein inhibitors. J. Mol. Biol. 220:1991;507-530.
29. Hutchinson E. G., Thornton J. M. PROMOTIF: a program to identify and analyze structural motifs in proteins. Protein Sci. 5:1996;212-220.
30. Kavanaugh W. M., Williams L. T. An alternative to SH2 domains for binding tyrosine-phosphorylated proteins. Science. 266:1994;1862-1865.
31. Kneller G. R. Superposition of molecular structures using quaternions. Mol. Simul. 3:1989;271.
32. Luthy R., Xenarios I., Bucher P. Improving the sensitivity of the sequence profile method. Protein Sci. 3:1994;139-146.
33. Macias M. J., Hyvonen M., Baraldi E., Schultz J., Sudol M., Saraste M., Oschkinat H. Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide. Nature. 382:1996;646-649.
34. Melchionna S. Structural study of monomeric microperoxidases in water and water/methanol solution by molecular dynamics simulations. PhD thesis. 1996;Chemistry Department, University of La Sapienza.
35. Metzler W. J., Bell A. J., Ernst E., Lavoie T. B., Mueller L. Identification of the poly- L -proline-binding site on human profilin. J. Biol. Chem. 269:1994;4620-4625.
36. Mikol V., Baumann G., Keller T. H., Manning U., Zurini M. G. The crystal structures of the SH2 domain of p56lck complexed with two phosphonopeptides suggest a gated peptide binding site. J. Mol. Biol. 246:1995;344-355.
37. Murzin A. G. Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol. 6:1996;386-394.
38. Nam H. J., Haser W. G., Roberts T. M., Frederick C. A. Intramolecular interactions of the regulatory domains of the Bcr-Abl kinase reveal a novel control mechanism. Structure. 4:1996;1105-1114.
39. Orengo C. A., Taylor W. R. SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol. 266:1996;617-635.
40. Pawson T., Gish G. D. SH2 and SH3 domains: from structure to function. Cell. 71:1992;359-362.
41. Pawson T., Schlessinger J. SH2 and SH3 domains. Curr. Biol. 3:1993;434-442.
42. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448.
43. Ranganathan R., Lu K. P., Hunter T., Noel J. P. Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent. Cell. 89:1997;875-886.
44. Russell R. B. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J. Mol. Biol. 279:1998;1211-1227.
45. Sander C., Schneider R. Database of homology-derived protein structures. Proteins. 9:1991;56-68.
46. Saraste M., Sibbald P. R., Wittinghofer A. The P-loop-a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15:1990;430-434.
47. Schwartz R. M., Dayhoff M. O. Matrices for detecting distant relationships. Dayhoff M. O. Atlas of Protein Sequence and Structure. 1979;353-358 National Biomedical Research Foundation, Washington DC.
48. Shoichet B., Kuntz I. D. Protein docking and complementarity. J. Mol. Biol. 221:1991;327-346.
49. Sicheri F., Moarefi I., Kuriyan J. Crystal structure of the Src family tyrosine kinase Hck. Nature. 385:1997;602-609.
50. Smith C. A., Rayment I. Active site comparisons highlight structural similarities between myosin and other p-loop proteins. Biophys. J. 70:1996;1590-1602.
51. Songyang Z., Shoelson S. E., Chaudhuri M., Gish G., Pawson T., Haser W. G., King F., Roberts T., Ratnofsky S., Lechleider R. J., Neel B. G., Birge R. B., Fajardo J. E., Chou M. M., Hanafusa H. et al. SH2 domains recognize specific phosphopeptide sequences. Cell. 72:1993;767-778.
52. Strynadka N. C., Eisenstein M., Katchalski-Katzir E., Shoichet B. K., Kuntz I. D., Abagyan R., Totrov M., Janin J., Cherfils J., Zimmerman F., Olson A., Duncan B., Rao M., Jackson R., Sternberg M. et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Struct. Biol. 3:1996;233-239.
53. Sudol M., Chen H. I., Bougeret C., Einbond A., Bork P. Characterization of a novel protein-binding module-the WW domain. FEBS Letters. 369:1995;67-71.
54. Swindells M. B. Detecting structural similarities: a user's guide. Methods Enzymol. 266:1996;643-653.
55. Taylor W. R., Orengo C. A. Protein structure alignment. J. Mol. Biol. 208:1989;1-22.
56. Thorn K. S., Christensen H. E., Shigeta R., Huddler D., Shalaby L., Lindberg U., Chua N. H., Schutt C. E. The crystal structure of a major allergen from plants. Structure. 5:1997;19-32.
57. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases, and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:1982;945-951.
58. Walls P. H., Sternberg J. E. New algorythm to model protein-protein recognition based on surface complementarity. J. Mol. Biol. 228:1992;277-297.
59. Wolodko W. T., Fraser M. E., James M. N., Bridger W. A. The crystal structure of succinyl-coa synthetase from Escherichia coli at 2.5 Å resolution. J. Biol. Chem. 269:1994;10883-10890.
60. Xu W., Harrison S. C., Eck M. J. Three-dimensional structure of the tyrosine kinase c-Src. Nature. 385:1997;595-602.
61. Zhang Z., Lee C. H., Mandiyan V., Borg J. P., Margolis B., Schlessinger J., Kuriyan J. Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain. EMBO J. 16:1997;6141-6150.