Structure-based functional discovery of proteins: Structural proteomics

Journal of Biochemistry and Molecular Biology

Volumn 37, Issue 1, 2004, Pages 28-34

  Jung, Jin Won ^a   Lee, Weontae ^a  

^a Yonsei University   (South Korea)

Author keywords

High throughput structure determination; NMR; Protein folding space; Structural proteomics; X ray crystallography

Indexed keywords

PROTEIN;

ELECTRON MICROSCOPY; GENOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 1642446970     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: 10.5483/bmbrep.2004.37.1.028     Document Type: Review

References (46)

1. Abola, E., Kuhn, P., Earnest, T. and Stevens, R. C. (2000) Automation of X-ray crystallography. Nat. Struct. Biol. 7, Suppl, 973-977.
2. Boggon, T. J., Shan, W. S., Santagata, S., Myers, S. C. and Shapiro, L. (1999) Implication of tubby proteins as transcription factors by structure-based functional analysis. Science 286, 2119-2125.
3. Christendat, D., Yee, A., Dharamsi, A., Kluger, Y., Savchenkol, A., Cort, J. R., Booth, V., Mackereth, C. D., Saridakis, V., Ekiel, I. et al. (2000) Structural proteomics of an archaeon. Nat. Struc. Biol. 7, 903-909.
4. Fernandez, C., Adeishvili, K. and Wüthrich, K. (2001) Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles Proc. Natl. Acad. Sci. USA 98, 2358-2363.
5. Fowler, C. A., Tian, E, Al-Hashimi, H. M. and Prestegard, J. H. (2000) Rapid determination of protein folds using residual dipolar couplings. J. Mol. Biol 304, 447-460.
6. Garrett, D. S., Seok, Y. J., Peterkofsky, A., Gronenborn, A. M. and Clore, G. M. (1999) Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nat. Struct. Biol. 6, 166-173.
7. Goldsmith-Fischman, S. and Honig, B. (2003) Structural genomics: computational methods for structure analysis. Protein Sci. 12, 1813-1821.
8. Goto, N. K. and Kay, L. E. (2000) New development in isotope labeling strategies for protein solution NMR spectroscopy. Curr. Opin. Struct. Biol. 10, 585-592.
9. Greenfield, N. J., Huang, Y. J., Palm, T., Swapna, G. V., Monleon, D., Montelione, G. T. and Hitchcock-DeGregori, S. E. (2001) Solution NMR structure and folding dynamics of the N terminus of a rat non-muscle alpha-tropomyosin in an engineered chimeric protein. J. Mol. Biol. 312, 833-847.
10. Güntert, P., Salzmann, M., Braun, D. and Wüthrich, K. (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J. Biomol. NMR 18, 129-137.
11. Henderson, R. (1995) The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unconstrained biological molecules. Q. Rev. Biophys. 28, 171-193.
12. Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E. and Downing, K. H. (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213, 899-929.
13. Herrmann, T., Güntert, P. and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209-227.
14. Huang, L., Hung, L., Odell, M., Yokota, H., Kim, R. and Kim, S-. H. (2002) Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii. J. Struct. Funct. Genomics 2, 121-127.
15. Hui, R. and Edwards, A. (2003) High-throughput protein crystallization J. Struct. Biol 142, 154-161.
16. Hwang, K. Y., Chung, J. H., Kim, S. H., Han, Y. S. and Cho, Y. (1999) Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat. Struct. Biol. 6, 691-696.
17. Jung, J. -W., An, J. -H., Na, K. -B., Kim, Y. S. and Lee, W. (2000) Active site and substrate binding mode of malonyl-coa synthetase determined by trandsfered nuclear overhauser effect spectroscopy, site directed mutagenesis and comparative modeling studies. Protein Sci. 9, 1294-1303.
18. Karain, W. I., Bourenkov, G. P., Blume, H. and Bartunik, H. D. (2002) Automated mounting, centering and screening of crystals for high-throughput protein crystallography. Acta Crystallogr. D. Biol. Crystallogr. 58, 1519-1522.
19. Kigawa, T., Muto, Y. and Yokoyama, S. (1995) Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis. J. Biomol. NMR 6, 129-134.
20. Kigawa, T., Yabuki, T., Yoshida, Y., Tsutsui, M., Ito, Y., Shibata, T. and Yokoyama, S. (1999) Cell-free production and stable-isotope labeling of milligram-quantities of proteins. FEBS Lett. 442, 15-19.
21. Kim, S.-H. (1998) Shining light on structural genomics. Nat. Struc. Biol. 5, 643-645.
22. Lee, C. -H., Jung, J. -W., Yee, A., Arrowsmith, C. H. and Lee, W. (2004) Solution Structure of a novel calcium binding protein, mth1880 from methanobacterium thermoautotrophicum. Protein Sci. in press.
23. Medek, A., Olejniczak, E. T., Meadows, R. P. and Fesik, S. W. (2000) An approach for high-throughput structure determination of proteins by NMR spectroscopy. J. Biomol. NMR 8, 229-238.
24. Montelione, G. T., Zheng, D., Huang, Y. J., Gunsalus, K. C. and Szyperski, T. (2000) Protein NMR spectroscopy in structural genomics. Nat. Struct. Biol. 7 Supl, 982-985.
25. Moseley, H. N. B. and Montelione, G. T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. biol. 9, 635-642.
26. Mumenthaler, C., Güntert, P., Braun, W. and Wüthrich, K. (1997) Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR 10, 351-362.
27. Nilges, M., Macias, M. C., ODonoghue, S. I. and Oschkinat, H. (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from alpha-spectrin. J. Mol. Biol. 269, 408-422.
28. Nogales, E., Wolf, S. G. and Downing, K. H. (1998) Structure of the α,β tubulin dimer by electron crystallography. Nature 391, 199-203.
29. O'Connell, J. F., Pryor, K. D., Grant, S. K. and Leiting, B. (1999) A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: application of an automated assignment strategy using GARANT. J. Biomol. NMR 13, 311-324.
30. Pervushin, K., Riek, R., Wider., G. and Wüthrich, K. (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an venue to NMR structures of very large biological macromolecules in solution Proc. Natl. Acad. Sci. USA 94, 12366-12371.
31. Rockel, B., Peters, J., Kuhlmorgen, B., Glaeser, R. M. and Baumeister, W. (2002) A giant protease with a twist: the TPP II complex from Drosophila studied by electron microscopy. EMBO J. 21, 5979-5984.
32. Rosen, M. K., Gardner, K. H., Willis, R. C., Parris, W. E., Pawson, T. and Kay, L. E. (1996) Selective methyl group protonation of perdeuterated proteins. J. Mol. Biol. 263, 627-636.
33. Rupp, B. (2003) High-throughput crystallography at an affordable cost: The TB structural genomics consortium crystallization facility, Acc. Chem. Res. 36, 173-181
34. Sali, A., Glaeser, R., Earnest, T. and Baumeister, W. (2003) From words to literature in structural proteomics Nature 422, 216-225.
35. Sanchez, R., Pieper, U., Melo, F., Eswar, N., Marti-Renom, M. A., Madhusudhan, M. S., Mirkovic, N. and Sali, A. (2000) Protein structure modeling for structural genomics. Nat. Struct. Biol. 7 Suppl, 986-990.
36. Schmid, M. B. (2002) Structural proteomics: the potential of high-throughput structure determination. Trends Microbiol. 10, S27-31.
37. Service, R. F. (1998) NMR researchers look to the next generation of machines. Science 279, 1127-1128.
38. Staunton, D., Owen, J. and Campbell, I. D. (2003) NMR and structural genomics. Acc. Chem. Res. 36, 207-214.
39. Terwilliger, T. C. (2003) Automated structure solution, density modification and model building. Acta Crystallogr. D. Biol. Crystallogr. 58, 1937-1940.
40. Tjandra, N., Omichinski, J. G., Gronenborn, A. M., Clore, G. M. and Bax, A. (1997) Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat. Struct. Biol. 4, 732-738.
41. Wagner, G. (1993) Prospects for NMR of large proteins. J. Biomol. NMR 3, 375-385.
42. Yamazaki, T., Otomo, T., Oda, N., Kyogoku, Y., Uegaki, K., Ito, N., Ishino, Y. and Nakamura, H. (1998) Segmental isotope labeling for protein NMR using peptide splicing. J. Am. Chem. Soc. 120, 5591-5592.
43. Yee, A., Chang, X., Pineda-Lucena, A., Wu, B., Semesi, A., Le B, Ramelot, T., Lee, G. M., Bhattacharyya, S., Gutierrez, P. et al. (2002) An NMR approach to structural proteomics Proc. Natl. Acad. Sci. USA 99, 1825-1830.
44. Yee, A., Pardee, K., Christendat, D., Savchenko, A., Edwards, A. M. and Arrowsmith, C. H. (2003) Structural proteomics: toward high-throughput structural biology as a tool in functional genomics. Acc. Chem. Res. 36, 183-189.
45. Zarembinski, T. I., Hung, L. W., Mueller-Dieckmann, H. J., Kim, K. K., Yokota, H., Kim, R. and Kim, S. H. (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.
46. Zhang, P., Beatty, A., Milne, J. L. and Subramaniam, S. (2001) Automated data collection with a Tecnai 12 electron microscope: applications for molecular imaging by cryomicroscopy. J. Struct. Biol. 135, 251-261.