Protein modules and protein-Protein interaction: Introduction

Advances in Protein Chemistry

Volumn 61, Issue , 2002, Pages 1-8

  Janin, Joël ^a   Wodak, Shoshana J ^b  

^a LABORATOIRE D ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES   (France)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENE PRODUCT; PROTEIN; RNA;

ALTERNATIVE RNA SPLICING; ANTIGEN ANTIBODY COMPLEX; CELL STRUCTURE; DNA SEQUENCE; EDITORIAL; GENE FUNCTION; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEOMICS; QUANTITATIVE DIAGNOSIS; STRUCTURE ACTIVITY RELATION;

EID: 0036421126     PISSN: 00653233     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0065-3233(02)61000-9     Document Type: Review

References (33)

1. Bader, G. D., Donaldson, I., Wolting, C., Ouellette, B. F., Pawson, T., and Hogue, C. W. (2001). BIND-The biomolecular interaction network database. Nucleic Acids Res. 29(1), 242-245.
2. Brenner, S. E., Chothia, C., and Hubbard, T. J. (1997). Population statistics of protein structures: Lessons from structural classifications. Curr. Opin. Struct. Biol. 7(3), 369-376.
3. C. elegans Sequencing Consortium (1988). Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282(5396), 2012-2018.
4. Chothia, C. (1992). Proteins: One thousand families for the molecular biologist. Nature 357(6379), 543-544.
5. Enright, A. J., Iliopoulos, I., Kyrpides, N. C., and Ouzounis, C. A. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature 402(6757), 86-90.
6. Fields, S. (2001). Proteomics. Proteomics in genomeland. Science 291(5507), 1221-1224.
7. Fields, S., and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340(6230), 245-624b.
8. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T, Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., Superti-Furga, and G. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
9. Hazbun, T. R., and Fields, S. (2001). Networking proteins in yeast. Proc. Natl. Acad. Sci. USA 98(8), 4277-4278.
10. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A. R., Sassi, H., Nielsen, P. A., Rasmussen, K. J., Andersen, J. R., Johansen, L. E., Hansen, L. H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B. D., Matthiesen, J., Hendrickson, R. C., Gleeson, E, Pawson, T., Moran, M. F., Durocher, D., Mann, M., Hogue, C. W., Figeys, D., and Tyers, M. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
11. International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409(6822), 860-921.
12. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98(8), 4569-4574.
13. Janin, J., and Wodak, S. J. (1983). Structural domains in proteins and their role in the dynamics of protein function. Prog. Biophys. Mol. Biol. 42(1), 21-78.
14. Jeong, H., Mason, S. P., Barabasi, A. L., and Oltvai, Z. N. (2001). Lethality and centrality in protein networks. Nature 411(6833), 41-42.
15. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R. (1999). Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17(7), 676-682.
16. Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999a). Detecting protein function and protein-protein interactions from genome sequences. Science 285(5428), 751-753.
17. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O., and Eisenberg, D. (1999b). A combined algorithm for genome-wide prediction of protein function. Nature 402(6757), 83-86.
18. Neubauer, G., King, A., Rappsilber, J., Calvio, C., Watson, M., Ajuh, P., Sleeman, J., Lamond, A., and Mann, M. (1998). Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat. Genet. 20(1), 46-50.
19. Orengo, C. A., Jones, D. T., and Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature 372(6507), 631-634.
20. Park, J., Lappe, M., and Teichmann, S. A. (2001). Mapping protein family Interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 307(3), 929-938.
21. Peltier, J. B., Friso, G., Kalume, D. E., Roepstorff, P., Nilsson, F., Adamska, I., and van Wijk, K. J. (2000). Proteomics of the chloroplast: Systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12(3), 319-341.
22. Rain, J. C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, C., Petel, F., Wojcik, J., and Schachter, V. (2001). The protein-protein interaction map of Helicobacter pylori. Nature 409(6817), 211-215.
23. Rose, G. D. (1979). Hierarchic organization of domains in globular proteins. J. Mol. Biol. 134(3), 447-470.
24. Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000). The yeast nuclear pore complex: Composition, architecture, and transport mechanism. J. Cell Biol. 148(4), 635-651.
25. Schwikowski, B., Uetz, P., and Fields, S. (2000). A network of protein-protein interactions in yeast. Nat. Biotechnol. 18(12), 1257-1261.
26. Stagljar, I., Korostensky, C., Johnsson, N., and te Heesen, S. (1998). A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl. Acad. Sci. USA 95(9), 5187-5192.
27. Tsoka, S., and Ouzounis, C. A. (2000). Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion. Nat. Genet. 26(2), 141-142.
28. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., and Pochart, P. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403(6770), 623-627.
29. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., and Holt, R. A. (2001). The sequence of the human genome. Science 291(5507), 1304-1351.
30. Walhout, A. J., Sordella, R., Lu, X., Hartley, J. L., Temple, G. F., Brasch, M. A., Thierry-Mieg, N., and Vidal, M. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287(5450), 116-122.
31. Washburn, M. P., Wolters, D., and Yates, J. R. (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19(3), 242-247.
32. Wetlaufer, D. B. (1973). "Nucleation, rapid folding, and globular intrachain regions in proteins." Proc. Natl. Acad. Sci. USA 70(3), 697-701.
33. Xenarios, I., Rice, D. W., Salwinski, L., Baron, M. K., Marcotte, E. M., and Eisenberg, D. (2000). DIP: The database of interacting proteins. Nucleic Acids Res. 28(1), 289-591.