Recognition of functional sites in protein structures

Journal of Molecular Biology

Volumn 339, Issue 3, 2004, Pages 607-633

  Shulman Peleg, Alexandra ^a   Nussinov, Ruth ^a,b   Wolfson, Haim J ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

3D database searches; ALBP, adipocyte lipid binding protein; binding sites similarity; computer aided drug design; HFABP, heart muscle fatty acid binding protein; pharmacophore; protein function prediction; RMSD, root mean square deviation

Indexed keywords

ESTRADIOL; FATTY ACID BINDING PROTEIN;

ANALYTIC METHOD; ARTICLE; BINDING SITE; COMPUTER AIDED DESIGN; DATA BASE; DRUG DESIGN; EVALUATION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 2442614144     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.012     Document Type: Article

References (72)

1. Nagano N., Orengo C.A., Thornton J.M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321:2002;741-765
2. Dror O., Shulman-Peleg A., Nussinov R., Wolfson H.J. Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications for drug design. Curr. Med. Chem. 11:2004;71-90
3. Lemmen C., Lengauer T. Computational methods for the structural alignment of molecules. J. Comput. Aided Mol. Des. 14:2000;215-232
4. Schneidman-Duhovny D., Nussinov R., Wolfson H. Predicting molecular interactions in silico II: protein-protein and protein-drug docking. Curr. Med. Chem. 11:2004;91-107
5. Halperin I., Ma B., Wolfson H.J., Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins: Struct. Funct. Genet. 47:2002;409-443
6. Taylor R.D., Jewsbury P.J., Essex J.W. A review of protein-small molecule docking methods. J. Comput. Aided Mol. Des. 16:2002;151-166
7. Abagyan R., Totrov M. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5:2001;375-382
8. Langer T., Hoffmann R.D. Virtual screening: an effective tool for lead structure dicovery. Curr. Pharm. Des. 7:2001;509-527
9. Shatsky M., Dror O., Schneidman-Duhovny D., Nussinov R., Wolfson H.J. BioInfo3D: a suite of tools for structural bioinformatics. Nucl. Acids Res. 2004;. In the press
10. Phillips C.L., Ullman B., Brennan R.G., Hill C.P. Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani. EMBO J. 18:1999;3533-3545
11. Ma B., Shatsky M., Wolfson H.J., Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11:2002;184-197
12. Milne G.M.A. Pharmacophore and drug discovery. Schleyer P.v R., Allinger N.L., Clark T., Gasteiger J., Kollman P.A., Schaefer H.F. III, Schreiner P.R. Encyclopedia of Computational Chemistry. 1998;2046-2056 Wiley, Chichester
13. Eidhammer I., Jonassen I., Taylor W.R. Structure comparison and structure patterns. J. Comput. Biol. 7:2001;685-716
14. 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
15. Ullmann J.R. An algorithm for subgraph isomorphism. J. Assoc. Comput. Mach. 23:1976;31-42
16. Spriggs R.V., Artymiuk P.J., Willett P. Searching for patterns of amino acids in 3d protein structures. J. Chem. Inf. Comput. Sci. 43:2003;412-421
17. Wallace A.C., Borkakoti N., Thornton J.M. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6:1997;2308-2323
18. Wallace A.C., Laskowski R.A., Thornton J.M. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5:1996;1001-1013
19. Lamdan, Y. & Wolfson, H. J. (1988). Geometric hashing: a general and efficient model-based recognition scheme. Proc. IEEE Int. Conf. Computer Vision, pp. 238-249, IEEE Computer Society Press.
20. Nussinov R., Wolfson H.J. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl Acad. Sci. USA. 88:1991;10495-10499
21. Bachar O., Fischer D., Nussinov R., Wolfson H.J. A computer vision based technique for 3-D sequence independent structural comparison. Protein Eng. 6:1993;279-288
22. Barker J.A., Thornton J.M. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics. 19:2003;1644-1649
23. Binkowski T., Adamian L., Liang J. Inferring functional relationship of proteins from local sequence and spatial surface patterns. J. Mol. Biol. 232:2003;505-526
24. Binkowski T., Naghibzadeh S., Liang J. CASTp: computed atlas of surface topography of proteins. Nucl. Acids Res. 31:2003;3352-3355
25. Jones S., Thornton J.M. Searching for functional sites in protein structures. Curr. Opin. Chem. Biol. 8:2004;3-7
26. Moodie S.L., Mitchell J.B.O., Thornton J.M. Protein recognition of adenylate: an example of a fuzzy recognition template. J. Mol. Biol. 263:1996;486-500
27. Denessiouk K.A., Rantanen V., Johnson M. Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins: Struct. Funct. Genet. 44:2001;282-291
28. Rosen M., Lin S., Wolfson H.J., Nussinov R. Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng. 11:1998;263-277
29. Lin S., Nussinov R., Fischer D., Wolfson H.J. Molecular surface representation by sparse critical points. Proteins: Struct. Funct. Genet. 18:1994;94-101
30. Lin S., Nussinov R. Molecular recognition via face center representation of a molecular surface. J. Mol. Graph. 14:1996;78-90
31. Kinoshita K., Furui J., Nakamura H. Identification of proteins functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics. 2:2001;9-22
32. Kinoshita K., Nakamura H. Identification of protein biochemical functions by similarity search using the molecular surface database ef-site. Protein Sci. 12:2003;1589-1595
33. Bron C., Kerbosch J. Finding all cliques of an undirected graph. Commun. ACM. 16:1973;575-577
34. Connolly M. Analytical molecular surface calculation. J. Appl. Crystallog. 16:1983;548-558
35. Schmitt S., Kuhn D., Klebe G. A new method to detect related function among proteins independent of sequence or fold homology. J. Mol. Biol. 323:2002;387-406
36. Hendlich M., Bergner A., Gunther J., Klebe G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J. Mol. Biol. 326:2003;607-620
37. Garey M.R., Johnson D.S. Computers and Intractability: A Guide to the Theory of NP-Completeness. 1979;Freeman and Co, New York
38. Cormen T.H., Leiserson C.E., Rivest R.L. Introduction to Algorithms. 1990;MIT Press, McGraw-Hill, New York
39. Connolly M. Solvent-accessible surfaces of proteins and nucleic acids. Science. 221:1983;709-713
40. Duhovny D., Nussinov R., Wolfson H.J. Efficient unbound docking of rigid molecules. Guigo R., Gusfield D. Proc. ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science. Proc. ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science. vol. 2452:2002;185-200 LNCS, Springer
41. Connolly M.L. Measurement of protein surfaces shape by solid angles. J. Mol. Graph. 4:1986;3-6
42. Duhovny, D. (2003). Active sites detection and docking. Master's thesis School of Computer Science, Tel-Aviv University.
43. Wolfson H.J., Rigoutsos I. Geometric hashing: an overview. IEEE Comput. Sci. Eng. 11:1997;263-278
44. Stockman G. Object recognition and localization via pose clustering. J. Comput. Vis. Graphics Image Processing. 40:1987;361-387
45. Kaindl K., Steipe B. Metric properties of the root-mean-square deviation of vector sets. Acta Crystallog. sect. A. 53:1997;809
46. Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A. 34:1978;827-828
47. Mehlhorn K., Näher S. The LEDA Platform of Combinatorial and Geometric Computing. 1999;Cambridge University Press, Cambridge
48. Kuttner Y.Y., Sobolev V., Raskind A., Edelman M. A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes. Proteins: Struct. Funct. Genet. 52:2003;400-411
49. Zarembinski T.I., Hung L.W., Mueller-Dieckmann H.J., Kim K.K., Yokota H., Kim R., Kim S.H. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc. Natl Acad. Sci. USA. 95:1998;15189-15193
50. Yang H., Yang M., Ding Y., Liu Y., Lou Z., Zhou Z., et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl Acad. Sci. USA. 100:2003;13190-13195
51. Anand K., Ziebuhr J., Wadhwani P., Mesters J., Hilgenfeld R. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 300:2003;1763-1767
52. Gunasekaran K., Hagler A.T., Gierasch L.M. Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions. Proteins: Struct. Funct. Genet. 2004;. In the press
53. Banaszak L., Winter N., Xu Z., Bernlohr D., Cowan S., Jones T. Lipid-binding proteins: a family of fatty acid and retinoid transport proteins. Advan. Protein Chem. 230:1994;89-151
54. Murzin A., Brenner S., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540
55. Shatsky M., Nussinov R., Wolfson H.J. MultiProt - a multiple protein structural alignment algorithm. Guigo R., Gusfield D. Proc. ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science. Proc. ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science. vol. 2452:2002;235-250 LNCS, Springer
56. Shatsky M., Nussinov R., Wolfson H.J. A method for simultaneous alignment of multiple protein structures. Proteins: Struct. Funct. Genet. 2004;. In the press
57. Balendiran G.K., Schnutgen F., Scapin G., Borchers T., Xhong N., Lim K., et al. Crystal structure and thermodynamic analysis of human brain fatty acid-binding protein. J. Biol. Chem. 275:2000;27045-27054
58. Thompson J., Winter N., Terwey D., Bratt J., Banaszak L. The crystal structure of the liver fatty acid-binding protein. a complex with two bound oleates. J. Biol. Chem. 272:1997;7140-7150
59. Kuntz L., Blaney J., Oatley S., Langridge R., Ferrin T. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161:1982;269-288
60. Brady G., Stouten P. Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. 14:2000;383-401
61. Laskowski R.A. SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph. Model. 13:1995;323-330
62. Liang J., Edelsbrunner H., Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7:1998;1884-1897
63. Masuya M., Doi J. Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphology operations. J. Mol. Graph. Model. 13:1995;331-336
64. Meier R., Ackermann F., Hermann G., Posch S., Sagerer G. Segmentation of molecular surfaces based on their convex hull. Proc. Int. Conf. Image Processing. 1995;552-555
65. Berman H., Westbrook J., Feng Z., Gilliland G., Bhat T., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242
66. Brenner S., Koehl P., Levitt M. The astral compendium for sequence and structure analysis. Nucl. Acids Res. 28:2000;254-256
67. Chandonia J.M., Walker N.S., Lo Conte L., Koehl P., Levitt M., Brenner S. Astral compendium enhancements. Nucl. Acids Res. 30:2002;260-263
68. Chandonia J.M., Hon G., Walker N.S., Lo Conte L., Koehl P., Levitt M., Brenner S. The astral compendium in 2004. Nucl. Acids Res. 32:2004;189-192
69. Cavarelli J., Prevost G., Bourguet W., Moulinier L., Chevrier B., Delagoutte B., et al. The structure of Staphylococcus aureus epidermolytic toxin a, an atypic serine protease, at 1.7 Å resolution. Structure. 5:1997;813-824
70. Wlodawer A., Li M., Dauter Z., Gustchina A., Uchida K., Oyama H., et al. Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes. Nature Struct. Biol. 8:2001;442-446
71. Hwang K.Y., Chung J.H., Kim S.H., Han Y.S., Cho Y. Structure-based identification of a novel ntpase from Methanococcus jannaschii. Nature Struct. Biol. 6:1999;691-696
72. Abele U., Schulz G.E. High-resolution structures of adenylate kinase from yeast ligated with inhibitor ap5a, showing the pathway of phosphoryl transfer. Protein Sci. 4:1995;1262-1271