Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the saccharomyces cerevisiae proteome

Genome Research

Volumn 13, Issue 6 A, 2003, Pages 1146-1154

  Lu, Long ^a,b   Arakaki, Adrian K ^a   Lu, Hui ^c   Skolnick, Jeffrey ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c University of Illinois at Chicago   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; MESSENGER RNA; POLYMER;

ALGORITHM; ANALYTIC METHOD; ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; GENETIC CODE; GENOMICS; INTERMETHOD COMPARISON; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS;

DNA, FUNGAL; DNA-BINDING PROTEINS; FUNGAL PROTEINS; GENOME, FUNGAL; GUANINE NUCLEOTIDE EXCHANGE FACTORS; MACROMOLECULAR SUBSTANCES; NUCLEAR PROTEINS; PHOSPHOPROTEINS; PREDICTIVE VALUE OF TESTS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN KINASES; PROTEIN STRUCTURE, TERTIARY; PROTEOME; RAS PROTEINS; RECOMBINATION, GENETIC; RIBONUCLEOPROTEINS; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE PROTEINS; TELOMERE-BINDING PROTEINS; TRANSCRIPTION FACTORS;

SACCHAROMYCES CEREVISIAE;

EID: 0038817799     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1145203     Document Type: Article

References (46)

1. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J.D. 1994. Molecular biology of the cell, chapter 3. Garland Publishing Inc., New York, London.
2. Aloy, P. and Russell, R.B. 2002. Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. 99: 5896-5901.
3. Boulton, SJ. and Jackson, S.P. 1996. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 15: 5093-5103.
4. Crechet, J.B., Poullet, P., Mistou, M.Y., Parmeggiani, A., Camonis, J., Boy-Marcotte, E., Damak, F., and Jacquet, M. 1990. Enhancement of the GDP-GTP exchange of RAS proteins by the carboxyl-terminal domain of SCD25. Science 248: 866-868.
5. Dunbar, D.A., Wormsley, S., Agentis, T.M., and Baserga, S.J. 1997. Mpp10p, a U3 small nucleolar ribonucleoprotein component required for pre-18S rRNA processing in yeast. Mol. Cell. Biol. 17: 5803-5812.
6. Frieden, C. 1971. Protein-protein interaction and enzymatic activity. Annu. Rev. Biochem. 40: 653-696.
7. Gabb, H.A., Jackson, R.M., and Sternberg, M.J. 1997. Modeling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272: 106-120.
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., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
9. Ge, H., Liu, Z., Church, G.M., and Vidal, M. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29: 482-486.
10. Gilson, M.K. and Honig, B. 1988. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins 4: 7-18.
11. Gygi, S.P., Rochon, Y., Franza, B.R., and Aebersold, R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19: 1720-1730.
12. Helmer-Citterich, M. and Tramontano, A. 1994. PUZZLE: A new method for automated protein docking based on surface shape complementarity. J. Mol. Biol. 235: 1021-1031.
13. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
14. Hollingsworth, N.M., Ponte, L., and Halsey, C. 1995. MSHS, a novel MutS homolog, facilitates meiotic reciprocal recombination between homologs in Saccharomyces cerevisiae but not mismatch repair. Genes & Dev. 9: 1728-1739.
15. Hunter, T. and Plowman, G.D. 1997. The protein kinases of budding yeast: Six score and more. Trends Biochem. Sci. 22: 18-22.
16. Huynen, M., Snel, B., Lathe III, W. and Bork, P. 2000. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res. 10: 1204-1210.
17. 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. 98: 4569-4574.
18. Janin, J. 1995. Protein-protein recognition. Prog. Biophys. Mol. Biol. 64: 145-166.
19. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30: 42-46.
20. Lacoste, N., Utley, R,T., Hunter, J.M., Poirier, G.G., and Cote, J. 2002. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J. Biol. Chem. 277: 30421-30424.
21. Laroche, T., Martin, S.G., Gotta, M., Gorham, H.C., Pryde, F.E., Louis, E.J., and Gasser, S.M. 1998. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curr. Biol. 8: 653-656.
22. Legrain, P., Wojcik, J., and Gauthier, J.M. 2001. Protein-protein interaction maps: A lead towards cellular functions. Trends Genet. 17: 346-352.
23. Lu, H, Lu, L., and Skolnick, J. 2003. Development of united statistical potentials describing protein-protein interactions. Biophys. J. 84: 1895-1901.
24. Lu, L., Lu, H., and Skolnick, J. 2002. MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364.
25. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
26. Mimori, T. and Hardin, J.A. 1986. Mechanism of interaction between Ku protein and DNA. J. Biol. Chem. 261: 10375-10379.
27. Mishra, K. and Shore, D. 1999. Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins. Curr. Biol. 9: 1123-1126.
28. Ng, H.H., Feng, Q., Wang, H., Erdjument-Bromage, H., Tempst, P., Zhang, Y., and Struhl, K. 2002. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes & Dev. 16: 1518-1527.
29. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., and Maltsev, N. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. 96: 2896-2901.
30. Pazos, F. and Valencia, A. 2002. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219-227.
31. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., and Yeates, T.O. 1999. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. 96: 4285-4288.
32. San-Segundo, P.A. and Roeder, G.S. 2000. Role for the silencing protein Dot1 in meiotic checkpoint control. Mol. Biol. Cell 11: 3601-3615.
33. Singer, M.S., Kahana, A., Wolf, A.J., Meisinger, L.L., Peterson, S.E., Goggin, C., Mahowald, M., and Gottschling, D.E. 1998. Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150: 613-632.
34. Skolnick, J. and Kihara, D. 2001. Defrosting the frozen approximation: PROSPECTOR-A new approach to threading. Proteins 42: 319-331.
35. Sussman, J.L., Lin, D., Jiang, J., Manning, N.O., Prilusky, J., Ritter, O., and Abola, E.E. 1998. Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D Biol. Crystallogr. 54: 1078-1084.
36. Terns, M.P. and Terns, R.M. 2002. Small nucleolar RNAs: Versatile trans-acting molecules of ancient evolutionary origin. Gene Expr. 10: 17-39.
37. Tong, A.H., Evangelista, M., Parsons, A.B., Xu, H., Bader, G.D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C.W., Bussey, H., et al. 2001. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
38. Tornow, J., Zeng, X., Gao, W., and Santangelo, G.M. 1993. GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain. EMBO J. 12: 2431-2437.
39. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
40. Vakser, I.A. and Aflalo, C. 1994. Hydrophobic docking: A proposed enhancement to molecular recognition techniques. Proteins 20: 320-329.
41. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., and Bork, P. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
42. Wiederkehr, T., Pretot, R.F., and Minvielle-Sebastia, L. 1998. Synthetic lethal interactions with conditional poly(A) polymerase alleles identify LCP5, a gene involved in 18S rRNA maturation. RNA 4: 1357-1372.
43. Wigge, P.A. and Kilmartin, J.V. 2001. The Ndc80p complex from Saccharomyces cerevisiae contains conserved centromere components and has a function in chromosome segregation. J. Cell Biol. 152: 349-360.
44. Wormsley, S., Samarsky, D.A., Fournier, M.J., and Baserga, S.J. 2001. An unexpected, conserved element of the U3 snoRNA is required for Mpp10p association. RNA 7: 904-919.
45. Wuchty, S. 2002. Interaction and domain networks of yeast. Proteomics 2: 1715-1723.
46. Zhu, H, Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., et al. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101-2105.