Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain-Domain Interactions Mediating Protein-Protein Interactions

Journal of Molecular Biology

Volumn 362, Issue 4, 2006, Pages 861-875

  Jothi, Raja ^a   Cherukuri, Praveen F ^a,b   Tasneem, Asba ^c   Przytycka, Teresa M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b BOSTON UNIVERSITY   (United States)

^c BOOZ ALLEN HAMILTON   (United States)

Author keywords

co evolution; domain domain interaction; protein protein interaction

Indexed keywords

DNA DIRECTED RNA POLYMERASE; PROTEIN SEC23P; PROTEIN SEC24P; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; COMPLEX FORMATION; COMPUTER PREDICTION; CRYSTAL STRUCTURE; FUNCTIONAL GENOMICS; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEAR PORE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS; VALIDATION PROCESS;

EID: 33748333117     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.07.072     Document Type: Article

References (74)

1. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403 (2000) 623-627
2. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., and Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98 (2001) 4569-4574
3. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 141-147
4. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 (2002) 180-183
5. Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., et al. A protein interaction map of Drosophila melanogaster. Science 302 (2003) 1727-1736
6. Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., et al. A map of the interactome network of the metazoan C. elegans. Science 303 (2004) 540-543
7. Butland G., Peregrin-Alvarez J.M., Li J., Yang W., Yang X., Canadien V., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 (2005) 531-537
8. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 (2006) 637-643
9. Dandekar T., Snel B., Huynen M., and Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23 (1998) 324-328
10. Enright A.J., Iliopoulos I., Kyrpides N.C., and Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402 (1999) 86-90
11. Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., and Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 285 (1999) 751-753
12. Overbeek R., Fonstein M., D'Souza M., Pusch G.D., and Maltsev N. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1 (1999) 93-108
13. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., and Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96 (1999) 4285-4288
14. Goh C.S., Bogan A.A., Joachimiak M., Walther D., and Cohen F.E. Co-evolution of proteins with their interaction partners. J. Mol. Biol. 299 (2000) 283-293
15. Wojcik J., and Schachter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 17 Suppl. 1 (2001) S296-S305
16. Pazos F., and Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14 (2001) 609-614
17. Pazos F., and Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins: Struct. Funct. Genet. 47 (2002) 219-227
18. Date S.V., and Marcotte E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnol. 21 (2003) 1055-1062
19. Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N.J., Chung S., Emili A., et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302 (2003) 449-453
20. Lappe M., and Holm L. Unraveling protein interaction networks with near-optimal efficiency. Nature Biotechnol. 22 (2004) 98-103
21. Pagel P., Wong P., and Frishman D. A domain interaction map based on phylogenetic profiling. J. Mol. Biol. 344 (2004) 1331-1346
22. Kim Y., and Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins: Struct. Funct. Genet. 62 (2006) 1115-1124
23. Sharan R., Suthram S., Kelley R.M., Kuhn T., McCuine S., Uetz P., et al. Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA 102 (2005) 1974-1979
24. Apic G., Gough J., and Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310 (2001) 311-325
25. Chothia C., Gough J., Vogel C., and Teichmann S.A. Evolution of the protein repertoire. Science 300 (2003) 1701-1703
26. Sprinzak E., and Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol. 311 (2001) 681-692
27. Kim W.K., Park J., and Suh J.K. Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Genome Inform. Ser. Workshop Genome Inform. 13 (2002) 42-50
28. Ng S.K., Zhang Z., and Tan S.H. Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19 (2003) 923-929
29. Albrecht M., Huthmacher C., Tosatto S.C., and Lengauer T. Decomposing protein networks into domain-domain interactions. Bioinformatics 21 Suppl. 2 (2005) ii220-ii221
30. Deng M., Mehta S., Sun F., and Chen T. Inferring domain-domain interactions from protein-protein interactions. Genome Res. 12 (2002) 1540-1548
31. Nye T.M., Berzuini C., Gilks W.R., Babu M.M., and Teichmann S.A. Statistical analysis of domains in interacting protein pairs. Bioinformatics 21 (2005) 993-1001
32. Chen X.W., and Liu M. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 21 (2005) 4394-4400
33. Riley R., Lee C., Sabatti C., and Eisenberg D. Inferring protein domain interactions from databases of interacting proteins. Genome Biol. 6 (2005) R89
34. Littler S.J., and Hubbard S.J. Conservation of orientation and sequence in protein domain-domain interactions. J. Mol. Biol. 345 (2005) 1265-1279
35. Gong S., Park C., Choi H., Ko J., Jang I., Lee J., et al. A protein domain interaction interface database: InterPare. BMC Bioinformatics 6 (2005) 207
36. Shoemaker B.A., Panchenko A.R., and Bryant S.H. Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci. 15 (2006) 352-361
37. Neduva V., Linding R., Su-Angrand I., Stark A., de Masi F., Gibson T.J., et al. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol. 3 (2005) e405
38. Aloy P., and Russell R.B. Structural systems biology: modelling protein interactions. Nature Rev. Mol. Cell Biol. 7 (2006) 188-197
39. Goh C.S., and Cohen F.E. Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324 (2002) 177-192
40. Ramani A.K., and Marcotte E.M. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327 (2003) 273-284
41. Gertz J., Elfond G., Shustrova A., Weisinger M., Pellegrini M., Cokus S., and Rothschild B. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics 19 (2003) 2039-2045
42. Jothi R., Kann M.G., and Przytycka T.M. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 21 Suppl. 1 (2005) i241-i250
43. Pazos F., Ranea J.A., Juan D., and Sternberg M.J. Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J. Mol. Biol. 352 (2005) 1002-1015
44. Sato T., Yamanishi Y., Kanehisa M., and Toh H. The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21 (2005) 3482-3489
45. Fraser H.B., Hirsh A.E., Wall D.P., and Eisen M.B. Coevolution of gene expression among interacting proteins. Proc. Natl Acad. Sci. USA 101 (2004) 9033-9038
46. Tirosh I., and Barkai N. Computational verification of protein-protein interactions by orthologous co-expression. BMC Bioinformatics 6 (2005) 40
47. Moyle W.R., Campbell R.K., Myers R.V., Bernard M.P., Han Y., and Wang X. Co-evolution of ligand-receptor pairs. Nature 368 (1994) 251-255
48. Pazos F., Helmer-Citterich M., Ausiello G., and Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271 (1997) 511-523
49. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242
50. Finn R.D., Marshall M., and Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21 (2005) 410-412
51. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., et al. The Pfam protein families database. Nucl. Acids Res. 32 (2004) D138-D141
52. Boyer P.D., and Kohlbrenner W.E. In: Selman B., and Selman-Reiner S. (Eds). Energy Coupling in Photosynthesis (1981), Elsevier Science Publishing Co, New York 231-240
53. Cox G.B., Jans D.A., Fimmel A.L., Gibson F., and Hatch L. Hypothesis. The mechanism of ATP synthase. Conformational change by rotation of the beta-subunit. Biochim. Biophys. Acta 768 (1984) 201-208
54. Mitchell P. Molecular mechanics of protonmotive F0F1 ATPases. Rolling well and turnstile hypothesis. FEBS Letters 182 (1985) 1-7
55. Oosawa F., and Hayashi S. The loose coupling mechanism in molecular machines of living cells. Advan. Biophys. 22 (1986) 151-183
56. Abrahams J.P., Leslie A.G., Lutter R., and Walker J.E. Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Nature 370 (1994) 621-628
57. Lederkremer G.Z., Cheng Y., Petre B.M., Vogan E., Springer S., Schekman R., Walz T., and Kirchhausen T. Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. Proc. Natl Acad. Sci. USA 98 (2001) 10704-10709
58. Kim W.K., and Ison J.C. Survey of the geometric association of domain-domain interfaces. Proteins: Struct. Funct. Genet. 61 (2005) 1075-1088
59. Caffrey D.R., Somaroo S., Hughes J.D., Mintseris J., and Huang E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?. Protein Sci. 13 (2004) 190-202
60. Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res. 14 (2004) 1310-1314
61. Wuchty S., Oltvai Z.N., and Barabasi A.L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nature Genet. 35 (2003) 176-179
62. Fraser H.B., Wall D.P., and Hirsh A.E. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3 (2003) 11
63. Hood J.K., and Silver P.A. Cse1p is required for export of Srp1p/importin-alpha from the nucleus in Saccharomyces cerevisiae. J. Biol. Chem. 273 (1998) 35142-35146
64. Schroeder A.J., Chen X.H., Xiao Z., and Fitzgerald-Hayes M. Genetic evidence for interactions between yeast importin alpha (Srp1p) and its nuclear export receptor. Cse1p. Mol. Gen. Genet. 261 (1999) 788-795
65. Mrowka R., Patzak A., and Herzel H. Is there a bias in proteome research?. Genome Res. 11 (2001) 1971-1973
66. Deane C.M., Salwinski L., Xenarios I., and Eisenberg D. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell. Proteomics 1 (2002) 349-356
67. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., and Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417 (2002) 399-403
68. Sprinzak E., Sattath S., and Margalit H. How reliable are experimental protein-protein interaction data?. J. Mol. Biol. 327 (2003) 919-923
69. Pawson T., and Scott J.D. Signaling through scaffold, anchoring, and adaptor proteins. Science 278 (1997) 2075-2080
70. Sudol M. From Src homology domains to other signaling modules: proposal of the 'protein recognition code'. Oncogene 17 (1998) 1469-1474
71. Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5 (2004) 113
72. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
73. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucl. Acids Res. 31 (2003) 3497-3500
74. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., and Eisenberg D. The database of interacting proteins: 2004 update. Nucl. Acids Res. 32 (2004) D449-D451