A new strategy for the site-specific modification of proteins in vivo

Biochemistry

Volumn 42, Issue 22, 2003, Pages 6735-6746

  Zhang, Zhiwen ^a   Smith, Brian A C ^b   Wang, Lei ^a   Brock, Ansgar ^c   Cho, Charles ^a   Schultz, Peter G ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b SIDNEY KIMMEL CANCER CENTER   (United States)

^c GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYES; ESCHERICHIA COLI; FLUORESCENCE; GENES;

FLUORESCENT DYES;

PROTEINS;

AMINO ACID; BACTERIAL PROTEIN; CYTOPLASM PROTEIN; FLUORESCENT DYE; HYDRAZIDE DERIVATIVE; LYSINE; OUTER MEMBRANE PROTEIN; PHENYLALANINE DERIVATIVE; PROTEIN LAMB; TRANSFER RNA; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL REACTION; CONTROLLED STUDY; CYTOPLASM; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MODIFICATION; STOP CODON;

AMINO ACYL-TRNA SYNTHETASES; BACTERIAL OUTER MEMBRANE PROTEINS; CELL LINE; DNA PRIMERS; ESCHERICHIA COLI; FLUORESCEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MICROSCOPY, FLUORESCENCE; MUTAGENESIS, SITE-DIRECTED; PHENYLALANINE; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; RNA, TRANSFER; SPECTROMETRY, FLUORESCENCE; STAINING AND LABELING; TYROSINE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; LAMB;

EID: 0038661197     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0300231     Document Type: Article

References (64)

1. Altenbach, C., Marti, T., Khorana, H. G., and Hubbell, W. L. (1990) Transmembrane protein structure: spin labeling of bacteriorhodopsin mutants, Science 248, 1088-1092.
2. Watts, A. (1985) Spin-labels in biochemistry, Biochem. Soc. Trans. 13, 588-593.
3. Braslawsky, G. R., Edson, M. A., Pearce, W., Kaneko, T., and Greenfield, R. S. (1990) Antitumor activity of adriamycin (hydrazone-linked) immunoconjugates compared with free adriamycin and specificity of tumor cell killing, Cancer Res. 50, 6608-6614.
4. Trail, P. A., Willner, D., Lasch, S. J., Henderson, A. J., Hofstead, S., Casazza, A. M., Firestone, R. A., Hellstrom, I., and Hellstrom, K. E. (1993) Cure of xenografted human carcinomas by BR96-doxorubicin immunoconjugates, Science 261, 212-215.
5. Uckun, F. M., Waddick, K. G., Mahajan, S., Jun, X., Takata, M., Bolen, J., and Kurosaki, T. (1996) BTK as a mediator of radiation-induced apoptosis in DT-40 lymphoma B cells, Science 273, 1096-1100.
6. Uckun, F. M., Evans, W. E., Forsyth, C. J., Waddick, K. G., Ahlgren, L. T., Chelstrom, L. M., Burkhardt, A., Bolen, J., and Myers, D. E. (1995) Biotherapy of B-cell precursor leukemia by targeting genistein to CD19-associated tyrosine kinases, Science 267, 886-891.
7. Fancy, D. A. (2000) Elucidation of protein-protein interactions using chemical cross-linking or label transfer techniques, Curr. Opin. Chem. Biol. 4, 28-33.
8. Fancy, D. A., Denison, C., Kim, K., Xie, Y., Holdeman, T., Amini, F., and Kodadek, T. (2000) Scope, limitations and mechanistic aspects of the photoinduced cross-linking of proteins by water-soluble metal complexes, Chem. Biol. 7, 697-708.
9. Carlsson, J., Drevin, H., and Axen, R. (1978) Protein thiolation and reversible protein-protein conjugation. N-Succinimidyl 3-(2-pyridyldithio)propionate, a new heterobifunctional reagent, Biochem. J. 173, 723-737.
10. Yang, T., Horejsh, D. R., Mahan, K. J., Zaluzec, E. J., Watson, T. J., and Gage, D. A. (1996) Mapping cross-linking sites in modified proteins with mass spectrometry: an application to cross-linked hemoglobins, Anal. Biochem. 242, 55-63.
11. El-Gewely, M. R. (1991) Site-directed mutagenesis and protein engineering, Elsevier, Amsterdam.
12. Arpicco, S., Dosio, F., Brusa, P., Crosasso, P., and Cattel, L. (1997) New coupling reagents for the preparation of disulfide cross-linked conjugates with increased stability, Bioconjugate Chem. 8, 327-337.
13. Green, L. S., Bell, C., and Janjic, N. (2001) Aptamers as reagents for high-throughput screening, BioTechniques 30, 1094-1096, 1098, 1100.
14. Goodson, R. J., and Katre, N. V. (1990) Site-directed pegylation of recombinant interleukin-2 at its glycosylation site, Biotechnology 8, 343-346.
15. Chilkoti, A., Chen, G., Stayton, P. S., and Hoffman, A. S. (1994) Site-specific conjugation of a temperature-sensitive polymer to a genetically-engineered protein, Bioconjugate Chem. 5, 504-507.
16. Geoghegan, K. F., and Stroh, J. G. (1992) Site-directed conjugation of nonpeptide groups to peptides and proteins via periodate oxidation of a 2-amino alcohol. Application to modification at N-terminal serine, Bioconjugate Chem. 3, 138-146.
17. Dawson, P. E., and Kent, S. B. (2000) Synthesis of native proteins by chemical ligation, Annu. Rev. Biochem. 69, 923-960.
18. Schnolzer, M., and Kent, S. B. (1992) Constructing proteins by dovetailing unprotected synthetic peptides: backbone-engineered HIV protease, Science 256, 221-225.
19. Dawson, P. E., Muir, T. W., Clark-Lewis, I., and Kent, S. B. (1994) Synthesis of proteins by native chemical ligation, Science 266, 776-779.
20. Xu, M. Q., and Perler, F. B. (1996) The mechanism of protein splicing and its modulation by mutation, EMBO J. 15, 5146-5153.
21. Chong, S., Mersha, F. B., Comb, D. G., Scott, M. E., Landry, D., Vence, L. M., Perler, F. B., Benner, J., Kucera, R. B., Hirvonen, C. A., Pelletier, J. J., Paulus, H., and Xu, M. Q. (1997) Single-column purification of free recombinant proteins using a self-cleavable affinity tag derived from a protein splicing element, Gene 192, 271-281.
22. Southworth, M. W., Amaya, K., Evans, T. C., Xu, M. Q., and Perler, F. B. (1999) Purification of proteins fused to either the amino or carboxy terminus of the Mycobacterium xenopi gyrase A intein, BioTechniques 27, 110-114, 116, 118-120.
23. Witte, K., Sears, P., and Wong, C.-H. (1997) J. Am. Chem. Soc. 119, 2114-2118.
24. Chang, T. K., Jackson, D. Y., Burnier, J. P., and Wells, J. A. (1994) Subtiligase: a tool for semisynthesis of proteins, Proc. Natl. Acad. Sci. U.S.A. 91, 12544-12548.
25. Kent, S. B. (1988) Chemical synthesis of peptides and proteins, Annu. Rev. Biochem. 57, 957-989.
26. Severinov, K., and Muir, T. W. (1998) Expressed protein ligation, a novel method for studying protein-protein interactions in transcription, J. Biol. Chem. 273, 16205-16209.
27. Muir, T. W., Sondhi, D., and Cole, P. A. (1998) Expressed protein ligation: a general method for protein engineering, Proc. Natl. Acad. Sci. U.S.A. 95, 6705-6710.
28. Ellman, J. A., Mendel, D., and Schultz, P. G. (1992) Methods Enzymol. 202, 301-306.
29. Bain, J. D., Glabe, C. G., Dix, T. A., and Chamberlain, A. R. (1989) J. Am. Chem. Soc. 111, 8013-8014.
30. Cornish, V. W., Hahn, K. M., and Schultz, P. G. (1996) Site-specific protein modification using a ketone handle. J. Am. Chem. Soc. 118, 8150-8151.
31. Shao, J., and Tam, J. (1995) J. Am. Chem. Soc. 117, 3893-3899.
32. Wang, L., Brock, A., Herberich, B., and Schultz, P. G. (2001) Expanding the genetic code of Escherichia coli, Science 292, 498-500.
33. Wang, L., Brock, A., and Schultz, P. G. (2002) Adding L-3-(2-Naphthyl)alanine to the genetic code of Escherichia coli, J. Am. Chem. Soc. 124, 1836-1837.
34. Zhang, Z., Wang, L., Brock, A., and Schultz, P. G. (2002) The selective incorporation of alkenes into proteins in E. coli, Angew. Chem., Int. Ed. 41, 2840-2842.
35. Chin, J. W., Santoro, S. W., Martin, A. B., King, D. S., Wang, L., and Schultz, P. G. (2002) Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli, J. Am. Chem. Soc. 124, 9026-9027.
36. Chin, J. W., Martin, A. B., King, D. S., Wang, L., and Schultz, P. G. (2002) Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 99, 11020-11024.
37. Santoro, S. W., Wang, L., Herberich, B., King, D. S., and Schultz, P. G. (2002) An efficient system for the evolution of aminoacyl-tRNA synthetase specificity, Nat. Biotechnol. 20, 1044-1048.
38. Wang, L., Zhang, Z., Ansgar, B., and Schultz, P. G. (2003) Addition of the keto functional group to the genetic code of E. coli, Proc. Natl. Acad. Sci. U.S.A. 100, 56-61.
39. Liu, H., Wang, L., Brock, A., Wong, C.-H., and Schultz, P. G. (2003) J. Am. Chem. Soc. 125, 1702-1703.
40. Hang, H. C., and Bertozzi, C. R. (2001) Chemoselective approaches to glycoprotein assembly, Acc. Chem. Res. 34, 727-736.
41. Lee, J. H., Baker, T. J., Mahal, L. K., Zabner, J., Bertozzi, C. R., Wiemer, D. F., and Welsh, M. J. (1999) Engineering novel cell surface receptors for virus-mediated gene transfer, J. Biol. Chem. 274, 21878-21884.
42. Mahal, L. K., Yarema, K. J., and Bertozzi, C. R. (1997) Engineering chemical reactivity on cell surfaces through oligosac-charide biosynthesis, Science 276, 1125-1128.
43. Stemmer, W. P. (1994) Rapid evolution of a protein in vitro by DNA shuffling, Nature 370, 389-391.
44. Stemmer, W. P. (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution, Proc. Natl. Acad. Sci. U.S.A. 91, 10747-10751.
45. Cadwell, R. C., and Joyce, G. F. (1994) Mutagenic PCR, PCR Methods Appl. 3, S136-S140.
46. Wang, L., Magliery, T. J., Liu, D. R., and Schultz, P. G. (2000) A new functional suppressor tRNA/aminoacyl-tRNA synthetase pair for the in vivo incorporation of unnatural amino acids into proteins, J. Am. Chem. Soc. 122, 5010-5011.
47. Brick, P., Bhat, T. N., and Blow, D. M. (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate, J. Mol. Biol. 208, 83-98.
48. Axe, D. D., Foster, N. W., and Fersht, A. R. (1996) Active barnase variants with completely random hydrophobic cores, Proc. Natl. Acad. Sci. U.S.A. 93, 5590-5594.
49. Yazynin, S. A., Deyev, S. M., Jucovic, M., and Hartley, R. W. (1996) A plasmid vector with positive selection and directional cloning based on a conditionally lethal gene, Gene 169, 131-132.
50. Wang, L., and Schultz, P. G. (2001) A general approach for the generation of orthogonal tRNAs, Chem. Biol. 8, 883-890.
51. Cadwell, R. C., and Joyce, G. F. (1992) Randomization of genes by PCR mutagenesis, PCR Methods Appl. 2, 28-33.
52. Diaz, E., Ferrandez, A., Prieto, M. A., and Garcia, J. L. (2001) Biodegradation of aromatic compounds by Escherichia coli, Microbiol. Mol. Biol. Rev. 65, 523-569.
53. Kenworthy, A. K. (2001) Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy, Methods 24, 289-296.
54. Majoul, I., Straub, M., Duden, R., Hell, S. W., and Soling, H. D. (2002) Fluorescence resonance energy transfer analysis of protein-protein interactions in single living cells by multifocal multiphoton microscopy, J. Biotechnol. 82, 267-277.
55. Periasamy, A. (2001) Fluorescence resonance energy transfer microscopy: a mini review, J. Biomed. Opt. 6, 287-291.
56. Schirmer, T. (1998) General and specific porins from bacterial outer membranes, J. Struct. Biol. 121, 101-109.
57. Jap, B. K., and Walian, P. J. (1996) Structure and functional mechanism of porins, Physiol. Rev. 76, 1073-1088.
58. Newton, S. M., Klebba, P. E., Michel, V., Hofnung, M., and Charbit, A. (1996) Topology of the membrane protein LamB by epitope tagging and a comparison with the X-ray model, J. Bacteriol. 178, 3447-3456.
59. Klebba, P. E., Hofnung, M., and Charbit, A. (1994) A model of maltodextrin transport through the sugar-specific porin, LamB, based on deletion analysis, EMBO J. 13, 4670-4675.
60. Wang, J., Hofnung, M., and Charbit, A. (2000) The C-terminal portion of the tail fiber protein of bacteriophage lambda is responsible for binding to LamB, its receptor at the surface of Escherichia coli K-12, J. Bacteriol. 182, 508-512.
61. Charbit, A., Werts, C., Michel, V., Klebba, P. E., Quillardet, P., and Hofnung, M. (1994) A role for residue 151 of LamB in bacteriophage lambda adsorption: possible steric effect of amino acid substitutions, J. Bacteriol. 176, 3204-3209.
62. Hofnung, M. (1995) An intelligent Channel (and More), Science 267, 473-474.
63. Charbit, A., Ronco, J., Michel, V., Werts, C., and Hofnung, M. (1991) Permissive sites and topology of an outer membrane protein with a reporter epitope, J. Bacteriol. 173, 262-275.
64. Charbit, A., Gehring, K., Nikaido, H., Ferenci, T., and Hofnung, M. (1988) Maltose transport and starch binding in phage-resistant point mutants of maltoporin. Functional and topological implications, J. Mol. Biol. 201, 487-496.