In VIVO application of photocleavable protein interaction reporter technology

Journal of Proteome Research

Volumn 11, Issue 2, 2012, Pages 1027-1041

  Yang, Li ^a   Zheng, Chunxiang ^b   Weisbrod, Chad R ^b   Tang, Xiaoting ^b   Munske, Gerhard R ^a   Hoopmann, Michael R ^b   Eng, Jimmy K ^b   Bruce, James E ^b  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

cross linking; E. coli; in vivo protein interactions; multimeric protein complex; photocleavable protein interaction reporter; protein topologies

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL CELL; CONTROLLED STUDY; CRYSTALLOGRAPHY; ESCHERICHIA COLI; IN VIVO STUDY; NONHUMAN; PHOTOCLEAVABLE PROTEIN INTERACTION REPORTER TECHNOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; ULTRAVIOLET RADIATION;

AMINO ACID SEQUENCE; BINDING SITES; CROSS-LINKING REAGENTS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIPROTEIN COMPLEXES; PEPTIDE FRAGMENTS; PHOTOCHEMISTRY; PHOTOLYSIS; PROTEIN INTERACTION MAPPING; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; ULTRAVIOLET RAYS;

ESCHERICHIA COLI;

EID: 84863011763     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200775j     Document Type: Article

References (28)

1. Fields, S.; Song, O. A novel genetic system to detect protein-protein interactions Nature 1989, 340 (6230) 245-6
2. Anderson, N. G. Co-immunoprecipitation. Identification of interacting proteins Methods Mol. Biol. 1998, 88, 35-45
3. Gould, K. L.; Ren, L.; Feoktistova, A. S.; Jennings, J. L.; Link, A. J. Tandem affinity purification and identification of protein complex components Methods 2004, 33 (3) 239-44
4. Back, J. W.; de Jong, L.; Muijsers, A. O.; de Koster, C. G. Chemical cross-linking and mass spectrometry for protein structural modeling J. Mol. Biol. 2003, 331 (2) 303-13
5. Leitner, A.; Walzthoeni, T.; Kahraman, A.; Herzog, F.; Rinner, O.; Beck, M.; Aebersold, R. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics Mol. Cell. Proteomics 2010, 9 (8) 1634-49
6. Sinz, A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions Mass Spectrom. Rev. 2006, 25 (4) 663-82
7. Jin Lee, Y. Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes Mol. Biosyst. 2008, 4 (8) 816-23
8. Ho, Y.; Gruhler, A.; Heilbut, A.; Bader, G. D.; Moore, L.; Adams, S. L.; Millar, A.; Taylor, P.; Bennett, K.; Boutilier, K.; Yang, L.; Wolting, C.; Donaldson, I.; Schandorff, S.; Shewnarane, J.; Vo, M.; Taggart, J.; Goudreault, M.; Muskat, B.; Alfarano, C.; Dewar, D.; Lin, Z.; Michalickova, K.; Willems, A. R.; Sassi, H.; Nielsen, P. A.; Rasmussen, K. J.; Andersen, J. R.; Johansen, L. E.; Hansen, L. H.; Jespersen, H.; Podtelejnikov, A.; Nielsen, E.; Crawford, J.; Poulsen, V.; Sorensen, B. D.; Matthiesen, J.; Hendrickson, R. C.; Gleeson, F.; Pawson, T.; Moran, M. F.; Durocher, D.; Mann, M.; Hogue, C. W.; Figeys, D.; Tyers, M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415 (6868) 180-3
9. Rigaut, G.; Shevchenko, A.; Rutz, B.; Wilm, M.; Mann, M.; Seraphin, B. A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 1999, 17 (10) 1030-2
10. Walhout, A. J.; Vidal, M. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping Methods 2001, 24 (3) 297-306
11. Rinner, O.; Seebacher, J.; Walzthoeni, T.; Mueller, L. N.; Beck, M.; Schmidt, A.; Mueller, M.; Aebersold, R. Identification of cross-linked peptides from large sequence databases Nat. Methods 2008, 5 (4) 315-8
12. Zhang, H.; Tang, X.; Munske, G. R.; Tolic, N.; Anderson, G. A.; Bruce, J. E. Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry Mol. Cell. Proteomics 2009, 8 (3) 409-20
13. Zheng, C.; Yang, L.; Hoopmann, M. R.; Eng, J. K.; Tang, X.; Weisbrod, C. R.; Bruce, J. E. Cross-linking measurements of in vivo protein complex topologies Mol Cell Proteomics 2011, 10 (10) M110 006841
14. Tang, X.; Bruce, J. E. A new cross-linking strategy: protein interaction reporter (PIR) technology for protein-protein interaction studies Mol. Biosyst. 2010, 6 (6) 939-47
15. Tang, X.; Munske, G. R.; Siems, W. F.; Bruce, J. E. Mass spectrometry identifiable cross-linking strategy for studying protein-protein interactions Anal. Chem. 2005, 77 (1) 311-8
16. Yang, L.; Tang, X.; Weisbrod, C. R.; Munske, G. R.; Eng, J. K.; von Haller, P. D.; Kaiser, N. K.; Bruce, J. E. A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies Anal. Chem. 2010, 82 (9) 3556-66
17. Weisbrod, C.R.; Hoopmann, M. R.; Senko, M.W.; Bruce, J.E. personal communication.
18. Anderson, G. A.; Tolic, N.; Tang, X.; Zheng, C.; Bruce, J. E. Informatics strategies for large-scale novel cross-linking analysis J. Proteome Res. 2007, 6 (9) 3412-21
19. Hoopmann, M. R.; Weisbrod, C. R.; Bruce, J. E. Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology J. Proteome Res. 2010, 9 (12) 6323-33
20. Schneidman-Duhovny, D.; Inbar, Y.; Nussinov, R.; Wolfson, H. J. PatchDock and SymmDock: servers for rigid and symmetric docking Nucleic Acids Res. 2005, 33 (Web Server issue) W363-7
21. Gardy, J. L.; Spencer, C.; Wang, K.; Ester, M.; Tusnady, G. E.; Simon, I.; Hua, S.; deFays, K.; Lambert, C.; Nakai, K.; Brinkman, F. S. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria Nucleic Acids Res. 2003, 31 (13) 3613-7
22. Guillier, F.; Orain, D.; Bradley, M. Linkers and cleavage strategies in solid-phase organic synthesis and combinatorial chemistry Chem. Rev. 2000, 100 (6) 2091-158
23. Karp, P. D.; Keseler, I. M.; Shearer, A.; Latendresse, M.; Krummenacker, M.; Paley, S. M.; Paulsen, I.; Collado-Vides, J.; Gama-Castro, S.; Peralta-Gil, M.; Santos-Zavaleta, A.; Penaloza-Spinola, M. I.; Bonavides-Martinez, C.; Ingraham, J. Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Res. 2007, 35 (22) 7577-90
24. Adachi, O.; Shinagawa, E.; Matsushita, K.; Ameyama, M. Crystallization and properties of 5-keto-D-gluconate reductase from Gluconobacter suboxydans Agric. Biol. Chem. 1979, 43, 75-83
25. Sweeney, N. J.; Laux, D. C.; Cohen, P. S. Escherichia coli F-18 and E. coli K-12 eda mutants do not colonize the streptomycin-treated mouse large intestine Infect. Immun. 1996, 64, 3504-3511
26. Zhang, Q.; Peng, H.; Gao, F.; Liu, Y.; Cheng, H.; Thompson, J.; Gao, G. F. Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes Protein Sci. 2009, 18 (2) 294-303
27. Yun, M.; Park, C. G.; Kim, J. Y.; Park, H. W. Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes Biochemistry 2000, 39 (35) 10702-10
28. Kuriyan, J.; Eisenberg, D. The origin of protein interactions and allostery in colocalization Nature 2007, 450 (7172) 983-90