Biological function made crystal clear - Annotation of hypothetical proteins via structural genomics

Current Opinion in Biotechnology

Volumn 11, Issue 1, 2000, Pages 25-30

  Eisenstein, Edward ^a   Gilliland, Gary L ^a   Herzberg, Osnat ^a   Moult, John ^a   Orban, John ^a   Poljak, Roberto J ^a   Banerjei, Linda ^b   Richardson, Delwood ^b   Howard, Andrew J ^c  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c Center for Synchrotron Radiation Research and Instrumentation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; GENE PRODUCT;

CRYSTALLIZATION; GENE SEQUENCE; GENE STRUCTURE; HAEMOPHILUS INFLUENZAE; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW;

BACTERIA (MICROORGANISMS); HAEMOPHILUS INFLUENZAE; NEGIBACTERIA;

EID: 0033976524     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(99)00063-4     Document Type: Review

References (64)

1. TIGR Microbial Database on World Wide Web URL: http://www.tigr.org/tdb/mdb/mdb.html This website at TIGR gives the status of the latest developments in microbial genome sequencing, including links to sequence and annotation information.
2. Professor Sung-Hou Kim's Homepage on World Wide Web URL: http://www.cchem.berkeley.edu/~shkgrp/index.html The website for the laboratory of Sung-Ho Kim includes information about the structural genomics project using proteins from the hyperthermophilc archaebacteria Methanococcus jannaschii.
3. Los Alamos National Laboratory Life Sciences Division Research Projects on World Wide Web URL: http://Isdiv.lanl.gov/research.htm A website describing the approach and results of the US Department of Energy/University of California Los Angeles collaboration on the structural genomics of the hyperthermophilic archaebacteria Pyrobaculum aerophilum.
4. Structural Genomics Pilot Project on World Wide Web URL: http://genome5.bio.bnl.gov/Proteome The website for the structural genomics collaboration between Brookhaven National Laboratory, Rockefeller University, and Albert Einstein College of Medicine focused on proteins from the yeast Saccharomyces cerevisiae.
5. Structural Proteomics: Structural Biology on Genome-wide Scale on World Wide Web URL: http://diana.oci.utoronto.ca/arrowsmith/proteomics/index.html A website summarizing the approach and results of the Ontario Cancer Institute's structural genomics project on 500 proteins from Methanobacterium thermoautotrophicum.
6. From Gene Structure to Function Project on World Wide Web URL: \ http://s2f.carb.nist.gov The website for the CARB-TIGR collaborative project on the structure and function of hypothetical proteins from Haemophilus influenzae.
7. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J-F., Doughertry B.A., Merrick J.M.et al. Whole-genome random sequencing and assmembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
8. Claros M.G., von Heijn G. TopPredII: an improved software for membrane protein structure predictions. Comput Appl Biosci. 10:1994;685-686.
9. Worley K.C., Wiese B.A., Smith R.F. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res. 5:1995;173-184.
10. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA. 85:1988;2444-2448.
11. Baitroch A., Bucher P., Hafmann K. The PROSITE database, its status in 1995. Nucleic Acids Res. 24:1995;189-196.
12. Bairoch A., Apweiler R. The SWISS-PROT protein sequence databank and its new supplement TrEMBL. Nucleic Acids Res. 24:1996;21-25.
13. Scharf M., Schneider R., Casari G., Bork P., Valencia A., Ouzounis C., Sander C. GeneQuiz: a workbench for sequence analysis. Ismb. 2:1994;348-353.
14. Genomic Threading Database on World Wide Web URL: http://globin.bio.warwick.ac.uk/genome/hi/.
15. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
16. Salamov A.A., Suwa M., Orengo C.A., Swindells M.B. Genome analysis: assigning protein coding regions to three-dimensional structures. Protein Sci. 8:1999;771-777.
17. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. A combined algorithm for genome wide prediction of protein function. Nature. 402:1999;83-86.
18. Amann E., Brosius J. 'ATG vectors' for regulated high-level expression of cloned genes in Escherichia coli. Gene. 40:1985;183-190.
19. Studier F.W., Rosenberg A.H., Dunn J.J., Dubendorff J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185:1990;60-89.
20. Hensley P. Defining the structure and stability of macromolecular assemblies in solution: the re-emergence of analytical ultracentrifugation as a practical tool. Structure. 4:1996;367-373.
21. Schuster T.M., Toedt J.M. New revolutions in the evolution of analytical ultracentrifugation. Curr Opin Struct Biol. 6:1996;650-658.
22. Frerre-D'Amare A.R., Burley S.K. Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure. 2:1994;357-359.
23. Jancarik J., Kim S-H. Sparse matrix sampling: a screening method for crystallization of proteins. J Appl Crystallog. 24:1991;409-411.
24. Gilliland G.L., Tung M., Ladner J. The biological macromolecule crystallization database and NASA protein crystal growth archive. J Res Natl Inst Stand Technol. 101:1996;309-320.
25. McPherson A. Crystallization of Biological Macromolecules. 1999;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. Shaw Stewart P.D., Baldock P.F.M. Practical experimental design techniques for automatic and manual protein crystallization. J Crystal Growth. 196:1999;665-673.
27. Garman E.F., Schneider T.R. Macromolecular cryocrystallography. J Appl Crystallogr. 30:1997;211-237.
28. Garman E., Mitchell E. Glycerol concentrations required for cryoprotection of 50 typical protein crystallization solutions. J Appl Crystallogr. 29:1996;584-587.
29. Karle J. Some developments in anomalous dispersion for the structural investigation of macromolecular systems in biology. Int J Quantum Chem: Quantum Biol Symp. 7:1980;357-367.
30. Hendrickson W.A. Analysis of protein structure from diffraction measurement at multiple wavelengths. Trans Am Crystallogr Assoc. 25:1985;11-21.
31. Terwilliger T.C., Berendzen J. Automated structure solution for MIR and MAD. Acta Crystallogr. 55:1999;849-861.
32. Sheldrick G.M. SHELEX: applications to macromolecules. Forteir S. Direct Methods for Solving Macromolecular Structures. 1998;401-411 Kluwer Academic Publishers, Dordrecht.
33. Otwinowski Z. Maximum likelihood refinement of heavy atom parameters. Wolf W., Evans P.R., Leslie A.G.W. Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend 25-26 January, 1991. 1991;80-86 Daresbury Laboratory, Warrington, England.
34. Wang B-C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115:1985;90-112.
35. Bricogne G. Geometric sources of redundancy in intensity data and their use for phase determination. Acta Crystallogr. 30:1974;395-405.
36. Cowtan K. An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography. 31:1994;34-38.
37. Perrakis A., Morris R., Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nat Struct Biol. 6:1999;458-463.
38. Jones T.A., Zou J-Y., Cowan S.W., Kjelgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. 47:1991;110-119.
39. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunsleve W., Jiang J-S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. 54:1998;905-921.
40. Moseley H.N.B., Montelione G.T. Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol. 9:1999;635-642.
41. Zimmerman D.E., Kulikowski C.A., Huang Y., Feng W., Tashiro M., Shimotakahara S., Chien C-Y., Powers R., Montelione G.T. Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol. 269:1997;592-610.
42. 13C chemical shift data. J Biomol NMR. 4:1994;171-180.
43. Cornilescu G., Delaglio F., Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR. 13:1999;289-302.
44. 13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol. 4:1997;732-738.
45. Nilges M., Macias M.J., O'Donoghue S.I., Oschkinat H. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J Mol Biol. 269:1997;408-422.
46. Mumenthaler C., Guntert P., Braun W., Wuthrich K. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J Biomol NMR. 10:1997;351-362.
47. Xu Y., Wu J., Gorenstein D., Braun W. Automated 2D NOESY assignment and structure calculation of crambin (S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs. J Magnet Resonance. 136:1999;76-85.
48. Murzin A., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classfication of proteins database for investigation of sequences and structures. J Mol Biol. 247:1995;536-540.
49. Wallace A.C., Laskowski R.A., Thornton J.M. Derivation of 3D co-ordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5:1996;1001-1013.
50. Laskowski R.A., Luscombe N.M., Swindells M.B., Thornton J.M. Protein clefts in molecular recognition and function. Protein Sci. 5:1996;2438-2452.
51. Kuntz I.D. Structure-based strategies for drug design and discovery. Science. 257:1992;1078-1082.
52. Shoichet B.K., Kuntz I.D. Matching chemistry and shape in molecular docking. Protein Eng. 6:1993;723-732.
53. Eisen M.B., Karplus M. HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecular binding site. Proteins. 19:1994;199-221.
54. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 268:1995;1144-1149.
55. Jones D., Thornton J.M. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol. 63:1995;31-65.
56. Lichtarge O., Bourne H.R., Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 257:1996;342-358.
57. Strynadka N.C., Eisenstein M., Katchalski-Katzir E., Shoichet B.K., Kuntz I.D., Abagyan R., Totrov M., Janin J., Cherfils J., Zimmerman F.et al. Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nat Struct Biol. 3:1996;233-239.
58. Pazos F., Helmer-Citterich M., Ausiello G., Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol. 271:1997;511-523.
59. Arigoni F., Talabot F.P.M., Edgerton M.D., Meldrum E., Allet E., Fish R., Jamotte T., Curchod M.L., Loferer H. A genome-based approach for the identification of essential bacterial genes. Nat Biotechnol. 16:1998;851-856.
60. Akerley B.J., Rubin E.J., Camilli A., Lampe D.J., Robertson H.M., Mekalanos J.J. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc Natl Acad Sci USA. 95:1998;8927-8932.
61. Reich K.A., Chovan L., Hessler P. Genome scanning in Haemophilus influenzae for identification of essential genes. J Bacteriol. 181:1999;4961-4968. Transposon insertional mutagenesis is combined with analyses of growth rates of mutant strains to rapidly identify essential genes.
62. Barcak G.J., Chandler M.S., Redfield R.J., Tomb J. Genetic systems in Haemophilus influenzae. Methods Enzymol. 204:1991;321-342.
63. 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. This is the first example of an hypothetical protein structure that has been determined as part of a structural genomics project. The biochemical studies that complimented the structural work followed the identification of bound ATP.
64. Hwang K.Y., Chung J.H., Kim S-H., Han Y.S., Cho Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat Struct Biol. 6:1999;691-696. In this case, fold recognition suggested testing for nucleotide hydrolysis, and it was confirmed that the protein could hydrolyze some nonstandard nucleotides.