What we have learned about prokaryotes from structural genomics

OMICS A Journal of Integrative Biology

Volumn 7, Issue 2, 2003, Pages 211-224

  Frishman, Dmitrij ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

CHEMISTRY; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; NONHUMAN; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; PROKARYOSIS; PROKARYOTE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SHORT SURVEY;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0038298025     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/153623103322246601     Document Type: Short Survey

References (51)

1. ABAGYAN, R.A., TOTROV, M., and KUZNETSOV, M. (1994). ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem. 15, 488-506.
2. ALTSCHUL, S.F., MADDEN, T.L., SCHAFFER, A.A., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
3. BUCHAN, D.W., SHEPHERD, A.J., LEE, D., et al. (2002). Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res 12, 503-514.
4. BURLEY, S.K. (2000). An overview of structural genomics. Nat Struct Biol 7, Suppl, 932-934.
5. CHAKRAVARTY, S., and VARADARAJAN, R. (2002). Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41, 8152-8161.
6. CHRISTENDAT, D., YEE, A., DHARAMSI, A., et al. (2000). Structural proteomics of an archaeon. Nat Struct Biol 7, 903-909.
7. CHRISTENDAT, D., SARIDAKIS, V., KIM, Y., et al. (2002). The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum. Protein Sci 11, 1409-1414.
8. DAS, R., and GERSTEIN, M. (2000). The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct Integr Genomics 1, 76-88.
9. EISENBERG, H. (1995). Life in unusual environments: progress in understanding the structure and function of enzymes from extreme halophilic bacteria. Arch Biochem Biophys 318, 1-5.
10. ERLANDSEN, H., ABOLA, E.E., and STEVENS, R.C. (2000). Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites. Curr Opin Struct Biol 10, 719-730.
11. FISCHER, D., and EISENBERG, D. (1999). Finding families for genomic ORFans. Bioinformatics 15, 759-762.
12. FRISHMAN, D., and MEWES, H.W. (1997). Protein structural classes in five complete genomes. Nat Struct Biol 4, 626-628.
13. FRISHMAN, D., ALBERMANN, K., HANI, J., et al. (2001). Functional and structural genomics using PEDANT. Bioinformatics 17, 44-57.
14. FRISHMAN, D. (2002). Knowledge-based selection of targets for structural genomics. Protein Eng 15, 169-183.
15. FRISHMAN, D., MOKREJS, M., KOSYKH, D., et al. (2003). The PEDANT genome database. Nucleic Acids Res 31, 207-211.
16. GALPERIN, M.Y., and KOONIN, E.V. (2000). Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol 18, 609-613.
17. GERDAY, C., AITTALEB, M., BENTAHIR, M., et al. (2000). Cold-adapted enzymes: from fundamentals to biotechnology. Trends Biotechnol 18, 103-107.
18. GERSTEIN, M. (1998). Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 33, 518-534.
19. GIANESE, G., ARGOS, P., and PASCARELLA, S. (2001). Structural adaptation of enzymes to low temperatures. Protein Eng 14, 141-148.
20. HEGYI, H., and GERSTEIN, M. (1999). The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 288, 147-164.
21. HEINEMANN, U. (2000). Structural genomics in Europe: slow start, strong finish? Nat Struct Biol 7, Suppl, 940-942.
22. JAENICKE, R., and BOHM, G. (1998). The stability of proteins in extreme environments. Curr Opin Struct Biol 8, 738-748.
23. KENNEDY, S.P., NG, W.V., SALZBERG, S.L., (2001). Understanding the adaptation of Halobacterium species NRC1 to its extreme environment through computational analysis of its genome sequence. Genome Res 11, 1641-1650.
24. KIM, S.H. (2000). Structural genomics of microbes: an objective. Curr Opin Struct Biol 10, 380-383.
25. KROGH, A., LARSSON, B., VON HEIJNE, G., et al. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305, 567-580.
26. KUHN, P., LESLEY, S.A., MATHEWS, I.I., et al. (2002). Crystal structure of thyl, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution. Proteins 49, 142-145.
27. LESLEY, S.A., KUHN, P., GODZIK, A., et al. (2002). Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 99, 11664-11669.
28. LIN, J., and GERSTEIN, M. (2000). Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10, 808-818.
29. LINIAL, M., and YONA, G. (2000). Methodologies for target selection in structural genomics. Prog Biophys Mol Biol 73, 297-320.
30. LO CONTE, L., BRENNER, S.E., HUBBARD, T.J., et al. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 30, 264-267.
31. MALLICK, P., GOODWILL, K.E., FITZ-GIBBON, S., et al. (2000). Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing. Proc Natl Acad Sci USA 97, 2450-2455.
32. MARTIN, A.C., ORENGO, C.A., HUTCHINSON, E.G., et al. (1998). Protein folds and functions. Structure 6, 875-84.
33. McGUFFIN, L.J., and JONES, D.T. (2002). Targeting novel folds for structural genomics. Proteins 48, 44-52.
34. MOLLER, S., CRONING, M.D., and APWEILER, R. (2001). Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17, 646-653.
35. MULLER, A., MACCALLUM, R.M., and STERNBERG, M.J. (2002). Structural characterization of the human proteome. Genome Res 12, 1625-1641.
36. MYLLYKALLIO, H., LIPOWSKI, G., LEDUC, D., et al. (2002). An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297, 105-107.
37. ROSATO, V., PUCELLO, N., and GIULIANO, G. (2002). Evidence for cysteine clustering in thermophilic proteomes. Trends Genet 18, 278-281.
38. ROTHSCHILD, L.J., and MANCINELLI, R.L. (2001). Life in extreme environments. Nature 409, 1092-1101.
39. SANCHEZ, R., PIEPER, U., MELO, F., et al. (2000). Protein structure modeling for structural genomics. Nat Struct Biol 7, Suppl, 986-990.
40. SHIN, D.H., YOKOTA, H., KIM, R., et al. (2002). Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc Natl Acad Sci USA 99, 7980-7985.
41. SIPPL, M.J., LACKNER, P., DOMINGUES, F.S., et al. (2001). Assessment of the CASP4 fold recognition category. Proteins 5, Suppl, 55-67.
42. STEVENS, R.C., YOKOYAMA, S., and WILSON, I.A. (2001). Global efforts in structural genomics. Science 294, 89-92.
43. TERWILLIGER, T.C., WALDO, G., PEAT, T.S., et al. (1998). Class-directed structure determination: foundation for a protein structure initiative. Protein Sci 7, 1851-1856.
44. THOMPSON, M.J., and EISENBERG, D. (1999). Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol 290, 595-604.
45. THORNTON, J.M., TODD, A.E., MILBURN, D., et al. (2000). From structure to function: approaches and limitations. Nat Struct Biol 7, Suppl, 991-994.
46. VITKUP, D., MELAMUD, E., MOULT, J., et al. (2001). Completeness in structural genomics. Nat Struct Biol 8, 559-566.
47. WESTBROOK, J., FENG, Z., CHEN, L., et al. (2003). The Protein Data Bank and structural genomics. Nucleic Acids Res 31, 489-491.
48. WOLF, Y.I., BRENNER, S.E., BASH, P.A., et al. (1999). Distribution of protein folds in the three superkingdoms of life. Genome Res 9, 17-26.
49. WOLF, Y.I., GRISHIN, N.V., and KOONIN, E.V. (2000). Estimating the number of protein folds and families from complete genome data. J Mol Biol 299, 897-905.
50. YEE, A., CHANG, X., PINEDA-LUCENA, A., et al. (2002). An NMR approach to structural proteomics. Proc Natl Acad Sci USA 99, 1825-1830.
51. ZAREMBINSKI, T.I., HUNG, L.W., MUELLER-DIECKMANN, H.J., et al. (1998). Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci USA 95, 15189-15193.