Efficient site-specific labeling of proteins via cysteines

Bioconjugate Chemistry

Volumn 19, Issue 3, 2008, Pages 786-791

  Kim, Younggyu ^a   Ho, Sam O ^a   Gassman, Natalie R ^a   Korlann, You ^a   Landorf, Elizabeth V ^c   Collart, Frank R ^c   Weiss, Shimon ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL MODIFICATION; FLUORESCENCE; MOLECULAR BIOLOGY; PROTEINS; SULFUR COMPOUNDS;

AMINO ACID CHAINS; CHEMICAL MODIFICATION OF PROTEINS; COVALENT LABELING; LABELINGS; PROTEOME ANALYSIS; RAPID PROCEDURES; REACTIVE DYES; SITE-SPECIFIC; SPECIFIC CONJUGATIONS; SPECIFIC SITES;

AMINO ACIDS;

CYSTEINE; RNA POLYMERASE;

ARTICLE; CHEMICAL MODIFICATION; CONTROLLED STUDY; DIALYSIS; ESCHERICHIA COLI; FLUORESCENCE; GEL PERMEATION CHROMATOGRAPHY; NONHUMAN; PROTEOMICS; SHEWANELLA ONEIDENSIS; SITE DIRECTED MUTAGENESIS; SOLID STATE; ULTRAVIOLET SPECTROSCOPY;

EID: 41149141793     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc7002499     Document Type: Article

References (34)

1. Hermanson, G. T. (1996) Bioconjugate techniques, Academic Press, San Diego.
2. Aslam, M., and Dent, A. (1998) Bioconjugation: Protein coupling techniques for biomedical sciences., MacMillan Reference Ltd., London.
3. Kapanidis, A. N., and Weiss, S. (2002) Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J. Chem. Phys. 117, 10953-10964.
4. Schuler, B. (2005) Single-molecule fluorescence spectroscopy of protein folding. ChemPhysChem 6, 1206-1220.
5. Michalet, X., Weiss, S., and Jager, M. (2006) Single-molecule fluorescence studies of protein folding and conformational dynamics. Chem. Rev. 106, 1785-1813.
6. Holmes, K. L., and Lantz, L. M. (2001) Protein labeling with fluorescent probes. Methods Cell Biol. 63, 185-204.
7. Gentle, I. E., De Souza, D. P., and Baca, M. (2004) Direct production of proteins with N-terminal cysteine for site-specific conjugation. Bioconjugate Chem. 15, 658-63.
8. Scheck, R. A., and Francis, M. B. (2007) Regioselective labeling of antibodies through N-terminal transamination. ACS Chem. Biol. 2, 247-51.
9. Lin, C. W., and Ting, A. Y. (2006) Transglutaminase-catalyzed site-specific conjugation of small-molecule probes to proteins in vitro and on the surface of living cells. J. Am. Chem. Soc. 128, 4542-3.
10. Jager, M., Nir, E., and Weiss, S. (2006) Site-specific labeling of proteins for single-molecule FRET by combining chemical and enzymatic modification. Protein Sci. 15, 640-646.
11. Keppler, A., Gendreizig, S., Gronemeyer, T., Pick, H., Vogel, H., and Johnsson, K. (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat. Biotechnol. 21, 86-9.
12. Duckworth, B. P., Zhang, Z., Hosokawa, A., and Distefano, M. D. (2007) Selective labeling of proteins by using protein farnesyltransferase. ChemBioChem 8, 98-105.
13. Chin, J. W., Cropp, T. A., Anderson, J. C., Mukherji, M., Zhang, Z., and Schultz, P. G. (2003) An expanded eukaryotic genetic code. Science 301, 964-7.
14. Lin, F. L., Hoyt, H. M., van Halbeek, H., Bergman, R. G., and Bertozzi, C. R. (2005) Mechanistic investigation of the staudinger ligation. J. Am. Chem. Soc. 127, 2686-95.
15. Adams, S. R., Campbell, R. E., Gross, L. A., Martin, B. R., Walkup, G. K., Yao, Y., Llopis, J., and Tsien, R. Y. (2002) New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc. 124, 6063-76.
16. Kapanidis, A. N., Ebright, Y. W., and Ebright, R. H. (2001) Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling with (Ni(2+): nitrilotriacetic Acid (n)-fluorochrome conjugates. J. Am. Chem. Soc. 123, 12123-5.
17. Mukhopadhyay, J., Kapanidis, A. N., Mekler, V., Kortkhonjia, E., Ebright, Y. W., and Ebright, R. H. (2001) Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106, 453-63.
18. Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A. N., Niu, W., Ebright, Y. W., Levy, R., and Ebright, R. H. (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108, 599-614.
19. Kapanidis, A. N., Margeat, E., Laurence, T. A., Doose, S., Ho, S. O., Mukhopadhyay, J., Kortkhonjia, E., Mekler, V., Ebright, R. H., and Weiss, S. (2005) Retention of transcription initiation factor s 70 in transcription elongation: single-molecule analysis. Mol. Cell 20, 347-356.
20. Margeat, E., Kapanidis, A. N., Tinnefeld, P., Wang, Y., Mukhopadhyay, J., Ebright, R. H., and Weiss, S. (2006) Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophys. J. 90, 1419-1431.
21. Lee, N. K., Kapanidis, A. N., Koh, H. R., Korlann, Y., Ho, S. O., Kim, Y., Gassman, N., Kim, S. K., and Weiss, S. (2007) Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances. Biophys. J. 92, 303-12.
22. Kapanidis, A. N., Margeat, E., Ho, S. O., Kortkhonjia, E., Weiss, S., and Ebright, R. H. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1144-7.
23. Kapanidis, A. N., Lee, N. K., Laurence, T. A., Doose, S., Margeat, E., and Weiss, S. (2004) Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc. Natl. Acad. Sci. U.S.A. 101, 8936-41.
24. Gralnick, J. A., and Hau, H. H. (2006) Ecology and biotechnology of the genus Shewanella. Annu. Rev. Microbiol.
25. Venkateswaran, K., Moser, D. P., Dollhopf, M. E., Lies, D. P., Saffarini, D. A., MacGregor, B. J., Ringelberg, D. B., White, D. C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K. H. (1999) Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int. J. Syst. Bacteriol. 49, 705-24.
26. Tiedje, J. M. (2002) Shewanella - the environmentally versatile genome. Nat. Biotechnol. 20, 1118-23.
27. Dieckman, L. J., Hanly, W. C., and Collart, E. R. (2006) Strategies for high-throughput gene cloning and expression. Genet. Eng. (NY) 27, 179-90.
28. Lin, C. T., Moore, P. A., Auberry, D. L., Landorf, E. V., Peppler, T., Victry, K. D., Collart, F. R., and Kery, V. (2006) Automated purification of recombinant proteins: combining high-throughput with high yield. Protein Expr. Purif. 47, 16-24.
29. Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. H. (2000) Structural organization of the RNA polymerase-promoter open complex. Cell 101, 601-11.
30. Levison, M. E., Josephson, A. S., and Kirschenbaum, D. M. (1969) Reduction of biological substances by water-soluble phosphines: gamma-globulin (IgG). Experientia 25, 126-7.
31. Getz, E. B., Xiao, M., Chakrabarty, T., Cooke, R., and Selvin, P. R. (1999) A comparison between the sulfhydryl reductants tris(2-carboxyethyl) phosphine and dithiothreitol for use in protein biochemistry. Anal. Biochem. 273, 73-80.
32. Tyagarajan, K., Pretzer, E., and Wiktorowicz, J. E. (2003) Thiol-reactive dyes for fluorescence labeling of proteomic samples. Electrophoresis 24, 2348-58.
33. Englard, S., and Seifter, S. (1990) Precipitation techniques. Methods Enzymol. 182, 285-300.
34. Cech, C. L., and McClure, W. R. (1980) Characterization of ribonucleic acid polymerase-T7 romoter binary complexes. Biochemistry 19, 2440-2447.