BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics

Molecular and Cellular Proteomics

Volumn 8, Issue 2, 2009, Pages 273-286

  Petrotchenko, Evgeniy V ^a   Xiao, Kunhong ^b   Cable, Jennifer ^a   Chen, Yiwen ^a   Dokholyan, Nikolay V ^a   Borchers, Christoph H ^a,c  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF VICTORIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ARRESTIN 2; BIMANE BISTHIOPROPIONIC ACID N SUCCINIMIDYL ESTER; CROSS LINKING REAGENT; G PROTEIN COUPLED RECEPTOR; PEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; CONTROLLED STUDY; FLUORESCENCE; GEL ELECTROPHORESIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR MODEL; MONITORING; NONHUMAN; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RAT; STRUCTURAL PROTEOMICS; SYNTHESIS;

EID: 61649117943     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800265-MCP200     Document Type: Article

References (27)

1. Sinz, A. (2003) Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes. J. Mass Spectrom. 38, 1225-1237
2. Sinz, A. (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682
3. Back, J. W., De Jong, L., Muijsers, A. O., and De Koster, C. G. (2003) Chemical cross-linking and mass spectrometry for protein structural modeling. J. Mol. Biol. 331, 303-313
4. Sinz, A., and Wang, K. (2001) Mapping protein interfaces with a fluorogenic cross-linker and mass spectrometry: application to nebulin-calmodulin complexes. Biochemistry 40, 7903-7913
5. Young, M. M., Tang, N., Hempel, J. C., Oshiro, C. M., Taylor, E. W., Kuntz, 1. D., Gibson, B. W., and Dollinger, G. (2000) High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 97, 5802-5806
6. Kruppa, G. H., Schoeniger, J., and Young, M. M. (2003) A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry. Rapid Commun. Mass Spectrom. 17, 155-162
7. Muller, D. R., Schindler, P., Wirth, U., Voshol, H., Hoving, S., and Steinmetz, M. 0. (2001) Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal. Chem. 73, 1927-1934
8. 18O labeling. Anal. Chem. 74, 4417-4422
9. Petrotchenko, E. V., Olkhovik, V. K., and Borchers, C. H. (2005) Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes. Mol. Cell. Proteomics 4, 1167-1179
10. Petrotchenko, E. V., Pasek, D., Elms, P., Dokholyan, N. V., Meissner, G., and Borchers, C. H. (2006) Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins. Anal. Chem. 78, 7959-7966
11. Lefkowitz, R. J., Rajagopal, K., and Whalen, E. J. (2006) New roles for β-arrestins in cell signaling: not just for seven-transmembrane receptors. Mol. Cell 24, 643-652
12. Baker, B. R., Querry, M. V., Bernstein, S., Safir, S. R., and Subbarow, Y. (1947) A second synthesis of 2-(δ-carboxybutyl)-thiophane-3,4-dicarboxylic acid. J. Org. Chem. 12, 167-173
13. Kast, J., Parker, C. E., van der Drift, K., Dial, J. M., Milgram, S. L., Wilm, M., Howell, M., and Borchers, C. H. (2003) Matrix-assisted laser desorption/ionization directed nano-electrospray ionization tandem mass spectrometric analysis for protein identification. Rapid Commun. Mass Spectrom. 17, 1825-1834
14. Borchers, C., Peter, J. F., Hall, M. C., Kunkel, T. A., and Tomer, K. B. (2000) Identification of in-gel digested proteins by complementary peptide-mass fingerprinting and tandem mass spectrometry data obtained on an electrospray ionization quadrupole time-of-flight mass spectrometer. Anal. Chem. 72, 1163-1168
15. Parker, C. E., Warren, M. R., Loiselle, D., Dicheva, N. N., Scarlett, C. O., and Borchers, C. H. (eds) (2005) Identification of Components of Protein Complexes, in Methods in Molecular Biology (Patterson, W. C., ed) Vol. 301, pp. 117-151, Humana Press, New Jersey
16. Xiao, K., Shenoy, S. K., Nobles, K., and Lefkowitz, R. J. (2004) Activation-dependent Conformational Changes in β-arrestin 2. J. Biol. Chem. 279, 55744-55753
17. Nobles, K. N., Guan, Z., Xiao, K., Oas, T. G., and Lefkowitz, R. J. (2007) The active conformation of β-arrestin1. Direct evidence for the phosphate sensor in the N-domain and conformational differences in the active states of β-arrestinsl and -2. J. Biol. Chem. 282, 21370-21381
18. Borchers, C., and Tomer, K. B. (1999) Characterization of the noncovalent complex of human immunodeficiency virus glycoprotein 120 with its cellular receptor CD4 by matrix-assisted laser desorption/ ionization mass spectrometry. Biochemistry 38, 11734-11740
19. Ding, F., Dokholyan, N. V., and Shakhnovich, E. (2006) Emergence of protein fold families through rational design. PLoS Comput. Biol. 2, e85
20. Yin, S., Ding, F., and Dokholyan, N. V. (2007) Modeling backbone flexibility improves protein stability estimation. Structure (Lond.) 15, 1567-1576
21. Yin, S., Ding, F., and Dokholyan, N. V. (2007) Eris: an automated estimator of protein stability. Nat. Methods 4, 466-467
22. Rost, B., Sander, C., and Schneider, R. (1994) PHD - an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10, 53-60
23. Sugita, Y., and Okamoto, Y. (1999) Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141-151
24. Chen, R., Li, L., and Weng, Z. (2003) RDOCK: refinement of rigid-body protein docking predictions. Proteins 52, 80-87
25. Wiehe, K., Pierce, B., Mintseris, J., Tong, W. W., Anderson, R., Chen, R., and Weng, Z. (2005) ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins 60, 207-213
26. Kim, E. E., Varadarajan, R., Wyckoff, H. W., and Richards, F. M. (1992) Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures. Biochemistry 31, 12304-12314
27. Gurevich, V. V., and Gurevich, E. V. (2006) The structural basis of arrestin-mediated regulation of G-protein-coupled receptors. Pharmacol. Ther. 110, 465-502