Академический Документы
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A combination of matricial and screening approaches for protein interactions
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17. Young K, Lin S, Sun L, Lee E, Modi M, Hellings S, Husbands M, characterization and proteome exploration. Nat Biotechnol 1999,
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18. Dove SL, Joung JK, Hochschild A: Activation of prokaryotic sion, which is not possible for complexes of unknown composition and which
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37. Celis JE, Gromov P: 2D protein electrophoresis: can it be
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domain-directed reassembly of active dihydrofolate reductase
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20. Karimova G, Pidoux J, Ullmann A, Ladant D: A bacterial two-hybrid extracted from normal or Plasmodium falciparum-infected
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Proc Natl Acad Sci USA 1998, 95:5752-5756.
39. Cordwell SJ, Nouwens AS, Verrills NM, McPherson JC, Hains PG,
21. Pelletier JN, Arndt KM, Pluckthun A, Michnick SW: An in vivo library- Van Dyk DD, Walsh BJ: The microbial proteome database — an
versus-library selection of optimized protein–protein interactions. automated laboratory catalogue for monitoring protein
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transduction pathways by phage display. Nat Biotechnol 1999, MALDI-TOF post source peptide fragmentation used with an appropriate
17:1193-1198. software tool is shown to be sufficient for the identification of
post-translational modifications and might be automated for
24. Jespers LS, Messens JH, De Keyser A, Eeckhout D, Van den Brande I, proteome-wide studies.
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25. Santini C, Brennan D, Mennuni C, Hoess RH, Nicosia A, Cortese R,
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26. Palzkill T, Huang W, Weinstock GM: Mapping protein–ligand 43. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R:
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A method for quantitative differential analysis of protein expression on a pro-
27. Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M,
teome-wide scale is described. It makes use of differentially labelled protein
Vorm O, Mortensen P, Boucherie H, Mann M: Linking genome and
extracts analysed by liquid chromatography and ESI mass spectrometry and
proteome by mass spectrometry: large-scale identification of
yeast proteins from two dimensional gels. Proc Natl Acad Sci USA does not require 2D gel electrophoresis.
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28. Wigge PA, Jensen ON, Holmes S, Soues S, Mann M, Kilmartin JV: Functional proteomics of signal transduction by membrane
Analysis of the Saccharomyces spindle pole by matrix-assisted receptors. Electrophoresis 1999, 20:952-961.
laser desorption/ionization (MALDI) mass spectrometry. J Cell 45. Witzmann FA, Fultz CD, Grant RA, Wright LS, Kornguth SE, Siegel FL:
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Differential expression of cytosolic proteins in the rat kidney cortex
29. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, and medulla: preliminary proteomics. Electrophoresis 1998,
Garvik BM, Yates JR III: Direct analysis of protein complexes using 19:2491-2497.
mass spectrometry. Nat Biotechnol 1999, 17:676-682.
46. Page MJ, Amess B, Townsend RR, Parekh R, Herath A, Brusten L,
30. Grant PA, Schieltz D, Pray-Grant MG, Steger DJ, Reese JC, Yates JR III, Zvelebil MJ, Stein RC, Waterfield MD, Davies SC et al.: Proteomic
Workman JL: A subset of TAF(II)s are integral components of the definition of normal human luminal and myoepithelial breast cells
SAGA complex required for nucleosome acetylation and purified from reduction mammoplasties. Proc Natl Acad Sci USA
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31. Neubauer G, Gottschalk A, Fabrizio P, Seraphin B, Luhrmann R, 47. Jungblut PR, Schaible UE, Mollenkopf HJ, Zimny-Arndt U,
Mann M: Identification of the proteins of the yeast U1 small Raupach B, Mattow J, Halada P, Lamer S, Hagens K,
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Natl Acad Sci USA 1997, 94:385-390. Mycobacterium tuberculosis and Mycobacterium bovis BCG
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32. Gygi SP, Han DK, Gingras AC, Sonenberg N, Aebersold R: Protein
analysis by mass spectrometry and sequence database Mol Microbiol 1999, 33:1103-1117.
searching: tools for cancer research in the post-genomic era. 48. Jungblut PR, Zimny-Arndt U, Zeindl-Eberhart E, Stulik J, Koupilova K,
Electrophoresis 1999, 20:310-319. •• Pleissner KP, Otto A, Muller EC, Sokolowska-Kohler W, Grabher G
33. Houry WA, Frishman D, Eckerskorn C, Lottspeich F, Hartl FU: et al.: Proteomics in human disease: cancer, heart and infectious
• Identification of in vivo substrates of the chaperonin GroEL. diseases. Electrophoresis 1999, 20:2100-2110.
Nature 1999, 402:147-154. In this review, the substractive analysis of 2D gels is shown to be a power-
About 300 proteins of E. coli were defined as GroEL-binding proteins and ful method to identify proteins specifically associated to various diseases.
observed on 2D gels. 52 of them were further identified by MALDI-TOF mass Applications to diagnostic tests are described.
spectrometry, thereby suggesting a definition for the typical GroEL substrate.
49. Witzmann FA, Bauer MD, Fieno AM, Grant RA, Keough TW,
34. Ogryzko VV, Kotani T, Zhang X, Schlitz RL, Howard T, Yang XJ, Kornguth SE, Lacey MP, Siegel FL, Sun Y, Wright LS et al.:
Howard BH, Qin J, Nakatani Y: Histone-like TAFs within the PCAF Proteomic analysis of simulated occupational jet fuel exposure
histone acetylase complex. Cell 1998, 94:35-44. in the lung. Electrophoresis 1999, 20:3659-3669.
From the analysis of protein complexes to proteome-wide linkage maps Legrain, Jestin and Schächter 407
50. Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, 55. Dandekar T, Snel B, Huynen M, Bork P: Conservation of gene order:
• Smith HO, Venter JC: Global transposon mutagenesis and a a fingerprint of proteins that physically interact. Trends Biochem
minimal Mycoplasma genome. Science 1999, 286:2165-2169. Sci 1998, 23:324-328.
Global transposon mutagenesis was used to identify nonessential genes in
Mycoplasma genitalium. 56. Overbeek R, Fonstein M, D’Souza M, Pusch GD, Maltsev N: The use
of gene clusters to infer functional coupling. Proc Natl Acad Sci
51. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, USA 1999, 96:2896-2901.
• Andre B, Bangham R, Benito R, Boeke JD, Bussey H et al.:
Functional characterization of the S. cerevisiae genome by gene 57. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA: Protein
deletion and parallel analysis. Science 1999, 285:901-906. • interaction maps for complete genomes based on gene fusion
An extensive analysis of yeast deletion mutant strains. events [see comments]. Nature 1999, 402:86-90.
A careful study of the results of the ‘gene-fusion based’ prediction method
52. Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A,
•• Jansen R, Cheung KH, Sheehan A, Symoniatis D, Umansky L et al.: for protein–protein interactions applied to three bacterial genomes. An inter-
Large-scale analysis of the yeast genome by transposon tagging esting discussion on method scope and results interpretation.
and gene disruption. Nature 1999, 402:413-418. 58. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D:
A transposon-tagging strategy for the genome-wide analysis in yeast of dis- Detecting protein function and protein–protein interactions from
ruption phenotypes, gene expression and protein localization.
genome sequences. Science 1999, 285:751-753.
53. Zambrowicz BP, Friedrich GA, Buxton EC, Lilleberg SL, Person C,
Sands AT: Disruption and sequence identification of 2,000 genes 59. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D:
in mouse embryonic stem cells. Nature 1998, 392:608-611. •• A combined algorithm for genome-wide prediction of protein
function. Nature 1999, 402:83-86.
54. Blaschke C, Andrade M, Ouzounis C, Valencia A: Automatic A first study on the combination of different computational techniques to pre-
• extraction of biological information from scientific text: protein- dict functional links on a genome-wide basis.
protein interactions. Seventh International Conference on Intelligent
Systems for Molecular Biology: 1999; Heidelberg. La Jolla, CA: 60. Eilbeck K, Brass A, Paton N, Hodgman C: INTERACT: an object-
ISMB; 1999:60-67. oriented protein–protein interaction database. Seventh
A fairly simple yet seemingly efficient approach to information extraction from International Conference of Intelligent Systems for Molecular
Medline abstracts. Biology: 1999; Heidelberg. La Jolla, CA: ISMB; 1999:87-94.