Protein subcomplexes - Molecular machines with highly specialized functions

IEEE Transactions on Nanobioscience

Volumn 6, Issue 1, 2007, Pages 86-93

  Hollunder, Jens ^a   Beyer, Andreas ^b   Wilhelm, Thomas ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Gene annotation; Molecular machines; Protein complex; Protein protein interaction

Indexed keywords

BACTERIA; CELLS; COMPLEXATION; ESCHERICHIA COLI; MOLECULAR BIOLOGY; STATISTICAL METHODS;

GENE ANNOTATION; MOLECULAR MACHINES; PROTEIN COMPLEX; PROTEIN-PROTEIN INTERACTION;

PROTEINS;

PROTEIN;

ARTICLE; ESCHERICHIA COLI; GENETIC CONSERVATION; PROTEIN ASSEMBLY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; COMPUTERS, MOLECULAR; NANOTECHNOLOGY; PROTEIN INTERACTION MAPPING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 33947100885     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2007.891884     Document Type: Article

References (21)

1. A.-C. Gavin and G. Superti-Furga, "Protein complexes and proteome organization from yeast to man," Curr. Opin. Chem. Biol., vol. 7, pp. 21-27, 2003.
2. T. Wilhelm, H.-P. Nasheuer, and S. Huang, "Physical and functional modularity of the protein network in yeast," Mol. Cell. Prot., vol. 2, pp. 292-298, 2003.
3. U. de Lichtenberg, L. J. Jensen, S. Brunak, and P. Bork, "Dynamic complex formation during the yeast cell cycle," Science, vol. 307, pp. 724-727, 2005.
4. C. von Mering, R. Krause, B. Snel, M. Cornell, S. G. Oliver, S. Fields, and P. Bork, "Comparative assessment of large-scale data sets of protein-protein interactions," Nature, vol. 4, pp. 17 399-17 403, 2002.
5. Z. Dezso, Z. N. Oltvai, and A. L. Barabasi, "Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae," Genome Res., vol. 13, pp. 2450-2454, 2003.
6. A.-C. Gavin, M. Boesche, R. Krause, P. Grandi, M. Marzioch, and A. Bauer et al., "Functional organization of the yeast proteome by systematic analysis of protein complexes," Nature, vol. 415, pp. 141-147, 2002.
7. Y. Ho, A. Gruhler, A. Heilbut, G. D. Bader, L. Moore, and S. L. Adams et al., "Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry," Nature, vol. 415, pp. 180-183, 2002.
8. N. J. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo, and A. Ignatchenko et al., "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae," Nature, vol. 440, pp. 637-643, 2006.
9. A. C. Gavin, P. Aloy, P. Grandi, R. Krause, M. Boesche, and M. Marzioch et al., "Proteome survey reveals modularity of the yeast cell machinery," Nature, vol. 440, pp. 631-636.
10. G. Butland, J. M. Peregrin-Alvarez, J. Li, W. Yang, X. Yang, and V. Canadien et al., "Interaction network containing conserved and essential protein complexes in Escherichia coli," Nature, vol. 433, pp. 531-537, 2005.
11. C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, and K. Bantoft et al., "The biomolecular interaction network database and related tools 2005 update," Nucl. Acids Res., vol. 33, pp. D418-D424, 2005.
12. J. Hollunder, A. Beyer, and T. Wilhelm, "Identification and characterization of protein subcomplexes in yeast," Proteomics, no. 5, pp. 2082-2089, 2005.
13. J. Hollunder, M. Friedel, A. Beyer, C. T. Workman, and T. Wilhelm, "DASS: Efficient discovery and p-value calculation of substructures in unordered data," Bioinformatics, vol. 23, pp. 77-83, 2007, submitted for publication.
14. M. Sharon, T. Taverner, X. I. Ambroggio, R. J. Deshaies, and C. V. Robinson, "Structural organization of the 19S proteasome Lid: Insights from MS of intact complexes," PLoS Biol., vol. 4, p. e267, 2006.
15. U. Güldener, M. Munsterkotter, G. Kastenmuller, N. Strack, J. van Helden, and C. Lemer et al., "CYGD: the comprehensive yeast genome database," Nucl. Acids Res., vol. 33, pp. D356-D268, 2005.
16. F. R. Blattner, G. Plunkett, 3rd, C. A. Bloch, N. T. Perna, V. Burland, and M. Riley et al., "The complete genome sequence of Escherichia coli K-12," Science, vol. 277, pp. 1453-1474, 1997.
17. S. Y. Gerdes, M. D. Scholle, J. W. Campbell, G. Balazsi, E. Ravasz, and M. D. Daugherty et al., "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655," J. Bacteriol., vol. 185, pp. 5673-5684, 2003.
18. S. A. Chervitz, L. Aravind, G. Sherlock, C. A. Ball, E. V. Koonin, and S. S. Dwight et al., "Comparison of the complete protein sets of worm and yeast: orthology and divergence," Science, vol. 282, pp. 2022-2028, 1998.
19. N. Higgs and T. D. Pollard, "Regulation of actin filament network formation through Arp2/3 complex: activation by a diverse array of proteins," Annu. Rev. Biochem., vol. 70, pp. 649-676, 2001.
20. B. Przybyla-Zawislak, D. M. Gadde, K. Ducharme, and M. T. McCammon, "Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes," Genetics, vol. 152, pp. 153-166, 1999.
21. G. M. Rubin, M. D. Yandell, J. R. Wortman, G. L. Gabor Miklos, C. R. Nelson, and I. K. Hariharan et al., "Comparative genomics of the eukaryotes," Science, vol. 4, pp. 2204-2215, 2000.