Protein fold recognition using sequence profiles and its application in structural genomics

Advances in Protein Chemistry

Volumn 54, Issue , 2000, Pages 245-275

  Koonin, Eugene V ^a   Wolf, Yuri I ^a   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; BACTERIUM; DATA BASE; EUKARYOTE; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; REVIEW;

EID: 0033941641     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0065-3233(00)54008-x     Document Type: Review

References (106)

1. Adams, M. D., Kerlavage, A. R., Fleischmann, R. D., Fuldner, R. A., Bult, C. J., Lee, N. H., Kirkness, E. F., Weinstock, K. G., Gocayne, J. D., White, O., et al. (1995). Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377, 3S-174S.
2. Allison, T. J., Wood, T. C., Briercheck, D. M., Rastinejad, F., Richardson, J. P., and Rule, G. S. (1998). Crystal structure of the RNA-binding domain from transcription termination factor rho. Nat. Struct. Biol. 5, 352-356.
3. Altschul, S. F., Boguski, M. S., Gish, W., and Wootton, J. C. (1994). Issues in searching molecular sequence databases. Nat. Genet. 6, 119-129.
4. Altschul, S. F., and Gish, W. (1996). Local alignment statistics. Methods Enzymol. 266, 460-480.
5. Altschul, S. F., and Koonin, E. V. (1998). PSI-BLAST - a tool for making discoveries in sequence databases. Trends Biochem. Sci. 23, 444-447.
6. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
7. Aravind, L., Galperin, M. Y., and Koonin, E. V. (1998a). The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem. Sci. 23, 127-129.
8. Aravind, L., and Koonin, E. V. (1999). Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol. 287, 1023-1040.
9. Aravind, L., and Koonin, E. V. (1998a). The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23, 469-472.
10. Aravind, L., and Koonin, E. V. (1998b). Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 26, 3746-3752.
11. Aravind, L., Leipe, D. D., and Koonin, E. V. (1998b). Toprim-a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26, 4205-4213.
12. Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R., and Koonin, E. V. (1998c). Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14, 442-444.
13. Baldi, P. (1995). Substitution matrices and hidden Markov models. J. Comput. Biol. 2, 487-491.
14. Baldi, P., Chauvin, Y., Hunkapiller, T., and McClure, M. A. (1994). Hidden Markov models of biological primary sequence information. Proc. Natl. Acad. Sci. U.S.A. 91, 1059-1063.
15. Ban, C., Junop, M., and Yang, W. (1999). Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair. Cell 97, 85-97.
16. Ban, C., and Yang, W. (1998). Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis. Cell 95, 541-552.
17. Berger, J. M., Fass, D., Wang, J. C., and Harrison, S. C. (1998). Structural similarities between topoisomerases that cleave one or both DNA strands. Proc. Natl. Acad. Sci. U.S.A. 95, 7876-7881.
18. Bergerat, A., de Massy, B., Gadelle, D., Varoutas, P. C., Nicolas, A., and Forterre, P. (1997). An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386, 414-417.
19. Bilwes, A. M., Alex, L. A., Crane, B. R., and Simon, M. I. (1999). Structure of CheA, a signal-transducing histidine kinase. Cell 96, 131-141.
20. Bochkarev, A., Pfuetzner, R. A., Edwards, A. M., and Frappier, L. (1997). Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385, 176-181.
21. Bork, P., and Koonin, E. V. (1998). Predicting functions from protein sequences - where are the bottlenecks? Nat. Genet. 18, 313-318.
22. Bork, P., Sander, C., and Valencia, A. (1992). An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. U.S.A. 89, 7290-7294.
23. Brenner, S. E., Chothia, C., and Hubbard, T. J. (1998). Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. U.S.A. 95, 6073-6078.
24. Brown, M., Hughey, R., Krogh, A., Mian, I. S., Sjolander, K., and Haussler, D. (1993). Using Dirichlet mixture priors to derive hidden Markov models for protein families. Ismb 1, 47-55.
25. Bryant, S. H., and Altschul, S. F. (1995). Statistics of sequence-structure threading. Curr. Opin. Struct. Biol. 5, 236-244.
26. Bycroft, M., Hubbard, T. J., Proctor, M., Freund, S. M., and Murzin, A. G. (1997). The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88, 235-242.
27. Callebaut, I., and Mornon, J. P. (1998). The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD fingerlike domain, as revealed by sequence analysis. Cell Mol. Life Sci. 54, 880-891.
28. Cusack, S., Yaremchuk, A., and Tukalo, M. (1996). The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA (Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 15, 6321-6334.
29. Doolittle, W. F. (1999). Phylogenetic classification and the universal tree. Science 284, 2124-2129.
30. Doolittle, W. F. (1998). You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14, 307-311.
31. Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics 14, 755-763.
32. Eddy, S. R., Mitchison, G., and Durbin, R. (1995). Maximum discrimination hidden Markov models of sequence consensus J. Comput. Biol. 2, 9-23.
33. Fischer, D., and Eisenberg, D. (1997). Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc. Natl. Acad. Sci. U.S.A. 94, 11929-11934.
34. Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R., and Steitz, T. A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl. Acad. Sci. U.S.A. 85, 8924-8928.
35. Frishman, D., and Mewes, H. W. (1997). Protein structural classes in five complete genomes. Nat. Struct. Biol. 4, 626-628.
36. Gaasterland, T. (1998a). Structural genomics taking shape. Trends Genet. 14, 135.
37. Gaasterland, T. (1998b). Structural genomics: bioinformatics in the driver's seat. Nat. Biotechnol. 16, 625-627.
38. Gerloff, D. L., Joachimiak, M., Cohen, F. E., Cannarozzi, G. M., Chamberlin, S. G., and Benner, S. A. (1998). Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family. Biochem. Biophys. Res. Commun. 251, 173-181.
39. Gerstein, M. (1997). A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J. Mol. Biol. 274, 562-576.
40. Gerstein, M., and Hegyi, H. (1998). Comparing genomes in terms of protein structure: surveys of a finite parts list. FEMS Microbiol. Rev. 22, 277-304.
41. Gerstein, M., and Levitt, M. (1997). A structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. U.S.A. 94, 11911-11916.
42. Godzik, A., and Skolnick, J. (1992). Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc. Natl. Acad. Sci. U.S.A. 89, 12098-12102.
43. Goldberg, J., Huang, H. B., Kwon, Y. G., Greengard, P., Nairn, A. C., and Kuriyan, J. (1995). Three-dimensional structure of the catalytic subunit of protein serine/ threonine phosphatase-1. Nature 376, 745-753.
44. Govindarajan, S., Recabarren, R., and Goldstein, R. A. (1999). Estimating the total number of protein folds. Proteins 35, 408-414.
45. Gribskov, M. (1992). Translational initiation factors IF-1 and eIF-2 alpha share an RNA-binding motif with prokaryotic ribosomal protein S1 and polynucleotide phosphorylase. Gene 119, 107-111.
46. Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987). Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. U.S.A. 84, 4355-4358.
47. Gribskov, M., and Veretnik, S. (1996). Identification of sequence pattern with profile analysis. Methods Enzymol. 266, 198-212.
48. Hall, D. R., Gourley, D. G., Duke, E. M., Leonard, G. A., Anderson, L. A., Pau, R. N., Boxer, D. H., and Hunter, W. N. (1999). Two crystal forms of ModE, the molybdate-dependent transcriptional regulator from Escherichia coli. Acta Crystallogr. D. Biol. Crystallogr. 55, 542-543.
49. Henikoff, S. (1996). Scores for sequence searches and alignments. Curr. Opin. Struct. Biol. 6, 353-360.
50. Hisano, T., Hata, Y., Fujii, T., Liu, J. Q., Kurihara, T., Esaki, N., and Soda, K. (1996). Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/ beta hydrolase structure that is different from the alpha/beta hydrolase fold. J. Biol. Chem. 271, 20322-20330.
51. Holm, L., and Sander, C. (1996). Mapping the protein universe. Science 273, 595-603.
52. Holm, L., and Sander, C. (1997). New structure - novel fold? Structure 5, 165-171.
53. Huang, S., Li, B., Gray, M. D., Oshima, J., Mian, I. S., and Campisi, J. (1998). The premature ageing syndrome protein, WRN, is a 3′→5′ exonuclease. Nat. Genet. 20, 114-116.
54. Hubbard, T. J., Ailey, B., Brenner, S. E., Murzin, A. G., and Chothia, C. (1999). SCOP: a Structural Classification of Proteins database. Nucleic Acids Res. 27, 254-256.
55. Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y., and Bork, P. (1998). Homology-based fold predictions for Mycoplasma genitalium proteins. J. Mol. Biol. 280, 323-326.
56. Ito, N., Phillips, S. E., Yadav, K. D., and Knowles, P. F. (1994). Crystal structure of a free radical enzyme, galactose oxidase. J. Mol. Biol. 238, 794-814.
57. Jones, D. T. (1999). GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
58. Karlin, S., and Altschul, S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268.
59. Karlin, S., Bucher, P., Brendel, V., and Altschul, S. F. (1991). Statistical methods and insights for protein and DNA sequences. Annu. Rev. Biophys. Biophys. Chem. 20, 175-203.
60. Kim, S. H. (1998). Shining a light on structural genomics. Nat. Struct. Biol. 5 Suppl, 643-645.
61. Kim, Y., Eom, S. H., Wang, J., Lee, D. S., Suh, S. W., and Steitz, T. A. (1995). Crystal structure of Thermus aquations DNA polymerase. Nature 376, 612-616.
62. Koonin, E. V., Mushegian, A. R., Galperin, M. Y., and Walker, D. R. (1997). Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25, 619-637.
63. Kraulis, P. (1991). A program to produce both detailed and schematic plots of proteins. J. Appl. Crystallography 24, 946-950.
64. Krogh, A., Mian, I. S., and Haussler, D. (1994). A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res. 22, 4768-4778.
65. Lathrop, R. H. (1994). The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068.
66. Lawson, D. M., Williams, C. E., Mitchenall, L. A., and Pau, R. N. (1998). Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA. Structure 6, 1529-1539.
67. Lesk, A. M. (1997). CASP2: report on ab initia predictions. Proteins Suppl. 1, 151-166.
68. Madej, T., Boguski, M. S., and Bryant, S. H. (1995). Threading analysis suggests that the obese gene product may be a helical cytokine. FEBS Lett. 373, 13-18.
69. Moser, M. J., Holley, W. R., Chatterjee, A., and Mian, I. S. (1997). The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res. 25, 5110-5118.
70. Moult, J. (1996). The current state of the art in protein structure prediction. Curr. Opin. Biotechnol. 7, 422-427.
71. Moult, J., Hubbard, T., Bryant, S. H., Fidelis, K., and Pedersen, J. T. (1997). Critical assessment of methods of protein structure prediction (CASP) : round II. Proteins Suppl. 1, 2-6.
72. Murzin, A. G. (1998). How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8, 380-387.
73. Murzin, A. G. (1993). OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12, 861-867.
74. Murzin, A. G. (1996). Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol. 6, 386-394.
75. Murzin, A. G., and Bateman, A. (1997). Distant homology recognition using structural classification of proteins. Proteins Suppl. 1, 105-112.
76. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
77. Mushegian, A. R., Bassett, D. E., Jr., Boguski, M. S., Bork, P., and Koonin, E. V. (1997). Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc. Natl. Acad. Sci. U.S.A. 94, 5831-5836.
78. Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., McDonald, L., Utterback, T. R., Malek, J. A., Linher, K. D., Garrett, M. M., Stewart, A. M., Cotton, M. D., Pratt, M. S., Phillips, C. A., Richardson, D., Heidelberg, J., Sutton, G. G., Fleischmann, R. D., Eisen, J. A., Salzberg, S. L., Smith, H. O., Venter, J. C., and Fraser, C. M. (1999). Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329.
79. Orengo, C. A., Todd, A. E., and Thornton, J. M. (1999). From protein structure to function. Curr. Opin. Struct. Biol. 9, 374-382.
80. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T., and Chothia, C. (1998). Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284, 1201-1210.
81. Pawlowski, K., Zhang, B., Rychlewski, L., and Godzik, A. (1999). The Helicobacter pylori genome: from sequence analysis to structural and functional predictions. Proteins 36, 20-30.
82. Rychlewski, L., Zhang, B., and Godzik, A. (1998). Fold and function predictions for Mycoplasma genitalium proteins. Fold. Des. 3, 229-238.
83. Rychlewski, L., Zhang, B., and Godzik, A. (1999). Functional insights from structural predictions: analysis of the Escherichia coli genome. Protein Sci. 8, 614-624.
84. Sali, A. (1998). 100,000 protein structures for the biologist [see comments]. Nat. Struct. Biol. 5, 1029-1032.
85. Sanchez, R., and Sali, A. (1997). Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7, 206-214.
86. Sanchez, R., and Sali, A. (1998). Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. U.S.A. 95, 13597-13602.
87. Schaffer, A. A., Wolf, Y. I., Ponting, C. P., Koonin, E. V., Aravind, L., and Altschul, S. F. (2000). IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific scoring matrices. Bioinformatics, in press.
88. Schuller, D. J., Grant, G. A., and Banaszak, L. J. (1995). The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2, 69-76.
89. Self, W. T., Grunden, A. M., Hasona, A., and Shanmugam, K. T. (1999). Transcriptional regulation of molybdoenzyme synthesis in Escherichia coli in response to molybdenum: ModE-molybdate, a repressor of the modABCD (molybdate transport) operon is a secondary transcriptional activator for the hyc and nar operons. Microbiology 145, 41-55.
90. Shapiro, L., and Lima, C. D. (1998). The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. Structure 6, 265-267.
91. Shortle, D. (1999). Structure prediction: The state of the art. Curr. Biol. 9, R205-209.
92. Singleton, M. R., Hakansson, K., Timson, D. J., and Wigley, D. B. (1999). Structure of the adenylation domain of an NAD+ - dependent DNA ligase. Structure Fold. Des. 7, 35-42.
93. Sjolander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I. S., and Haussler, D. (1996). Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12, 327-345.
94. Smith, T. F., Lo Conte, L., Bienkowska, J., Gaitatzes, C., Rogers, R. G., Jr., and Lathrop, R. (1997). Current limitations to protein threading approaches. J. Comput. Biol. 4, 217-225.
95. Stebbins, C. E., Russo, A. A., Schneider, C., Rosen, N., Hard, F. U., and Pavletich, N. P. (1997). Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent. Cell 89, 239-250.
96. Subramanya, H. S., Doherty, A. J., Ashford, S. R., and Wigley, D. B. (1996). Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607-615.
97. Tanaka, H., Ishikawa, M., Asai, K., and Konagaya, A. (1993). Hidden Markov models and iterative aligners: study of their equivalence and possibilities. Ismb 1, 395-401.
98. Tanaka, T., Saha, S. K., Tomomori, C., Ishima, R., Liu, D., Tong, K. I., Park, H., Dutta, R., Qin, L., Swindells, M. B., Yamazaki, T., Ono, A. M., Kainosho, M., Inouye, M., and Ikura, M. (1998). NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ. Nature 396, 88-92.
99. Tatusov, R. L., Altschul, S. F., and Koonin, E. V. (1994). Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. U.S.A. 91, 12091-12095.
100. Teichmann, S. A., Chothia, C., and Gerstein, M. (1999). Advances in structural genomics. Curr. Opin. Struct. Biol. 9, 390-399.
101. Teichmann, S. A., Park, J., and Chothia, C. (1998). Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. U.S.A. 95, 14658-14663.
102. Thioulouse, J., Chessel, D., Dolidec, S., and Olivier, J. M. (1997) ADE-4: a multivariate analysis and graphical display software. Statistics and Computing 7, 75-83.
103. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
104. Wallin, E., and von Heijne, G. (1998). Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7, 1029-1038.
105. Wigley, D. B., Davies, G. J., Dodson, E. J., Maxwell, A., and Dodson, G. (1991). Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351, 624-629.
106. Wolf, Y. I., Brenner, S. E., Bash, P. A., and Koonin, E. V. (1999). Distribution of protein folds in the three superkingdoms of life. Genome Res. 9, 17-26.