Understanding and predicting protein assemblies with 3D structures

Comparative and Functional Genomics

Volumn 4, Issue 4, 2003, Pages 410-415

  Aloy, Patrick ^a   Russell, Robert B ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

3D structure; Complexes; Interaction discovery; Interaction networks; Prediction; Protein interactions

Indexed keywords

PROTEIN;

ANALYTIC METHOD; BINDING AFFINITY; PREDICTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN INTERACTION; PROTEIN STRUCTURE; PURIFICATION; REVIEW; TWO HYBRID SYSTEM;

EID: 0041384254     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.310     Document Type: Review

References (26)

1. Abbott A. 2002. Proteomics: the society of proteins. Nature 417: 894-896.
2. Aloy P, Ciccarelli FD, Leutwein C, et al. 2002. A complex prediction: three-dimensional model of the yeast exosome. EMBO Rep 3: 628-635.
3. Aloy P, Russell RB. 2002a. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 99: 5896-5901.
4. Aloy P, Russell RB. 2002b. Potential artefacts in protein-interaction networks. FEBS Lett 530: 253-254.
5. Aloy P, Russell RB. 2002c. The third dimension for protein interactions and complexes. Trends Biochem Sci 27: 633-638.
6. Aloy P, Russell RB. 2003. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19: 161-162.
7. Bourne Y, Watson MH, Hickey MJ, et al. 1996. Crystal structure and mutational analysis of the human CDK2 kinase complex with cell cycle-regulatory protein CksHs1. Cell 84: 863-874.
8. Gavin AC, Bosche M, Krause R, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
9. Ho Y, Gruhler A, Heilbut A, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
10. Housni HE, Vandenbroere I, Perez-Morga D, Christophe D, Pirson I. 1998. A rare case of false positive in a yeast two-hybrid screening: the selection of rearranged bait constructs that produce a functional Gal4 activity. Anal Biochem 262: 94-96.
11. Hunte C, Koepke J, Lange C, Rossmanith T, Michel H. 2000. Structure at 2.3 Å resolution of the cytochrome bc(1) complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment. Structure Fold Des 8: 669-684.
12. Ito T, Chiba T, Ozawa R, et al. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98: 4569-4574.
13. Ito T, Tashiro K, Muta S, et al. 2000. Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA 97: 1143-1147.
14. Jeffrey PD, Russo AA, Polyak K, et al. 1995. Mechanism of CDK activation revelated by the structure of a cyclinA-CDK2 complex. Nature 376: 313-320.
15. Jeong H, Mason SP, Barabasi AL, Oltvai ZN. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
16. Kemmeren P, van Berkum NL, Vilo J, et al. 2002. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 9: 1133-1143.
17. Legrain P, Wojcik J, Gauthier JM. 2001. Protein-protein interaction maps: a lead towards cellular functions. Trends Genet 17: 346-352.
18. Ma J, Ptashne M. 1987. A new class of yeast transcriptional activators. Cell 51: 113-119.
19. Paris J, Leplatois P, Nurse P. 1994. Study of the higher eukaryotic gene function CDK2 using fission yeast. J Cell Sci 107: 615-623.
20. Rain JC, Selig L, De Reuse H, et al. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409: 211-215.
21. Roberts DL, Frerman FE, Kim JJ. 1996. Three-dimensional structure of human electron transfer flavoprotein to 2.1 Å resolution. Proc Natl Acad Sci USA 93: 14 355 -14 360.
22. Schutt CE, Myslik JC, Rozycki MD, Goonesekere NC, Lindberg U. 1993. The structure of crystalline profilin-β-actin. Nature 365: 810-816.
23. Schwikowski B, Uetz P, Fields S. 2000. A network of protein-protein interactions in yeast. Nat Biotechnol 18: 1257-1261.
24. Spahn CM, Beckmann R, Eswar N, et al. 2001. Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. Cell 107: 373-386.
25. Uetz P, Giot L, Cagney G, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
26. Von Mering C, Krause R, Snel B, et al. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.