Unnatural amino acid mutagenesis: A precise tool for probing protein structure and function

Biochemistry

Volumn 43, Issue 37, 2004, Pages 11623-11629

  England, Pamela M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MEMBRANES; CELLS; MUTAGENESIS; PROTEINS;

CELL-EXTRACTS; LIGAND-BINDING SITES; TRANSMEMBRANE PROTEINS;

AMINO ACIDS;

AMINO ACID; DNA; MEMBRANE PROTEIN; PROTEIN; TRANSFER RNA;

BINDING SITE; ESCHERICHIA COLI; LIGAND BINDING; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SACCHAROMYCES CEREVISIAE;

AMINO ACIDS; ANIMALS; CODON, NONSENSE; DNA; MOLECULAR STRUCTURE; MUTAGENESIS; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; PROTEINS; RNA, TRANSFER;

ESCHERICHIA COLI; NEGIBACTERIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 4644252142     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048862q     Document Type: Review

References (76)

1. Heckler, T. G., Chang, L.-H., Zama, Y., Naka, T., Chorghade, M. S., and Hecht, S. M. (1984) T4 RNA ligase mediated preparation of novel 'chemically misacylated' tRNAPhes, Biochemistry 23, 1468-1473.
2. Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C., and Schultz, P. G. (1989) A general method for site-specific incorporation of unnatural amino acids into proteins, Science 244, 182-188.
3. Bain, J. D., Glabe, C. G., Dix, T. A., and Chamberlin, A. R. (1989) Biosynthetic site-specific incorporation of a nonnatural amino acid into a polypeptide, J. Am. Chem. Soc. 111, 8013-8014.
4. Ellman, J., Mendel, D., Anthony-Cahill, S. J., Noren, C. J., and Schultz, P. G. (1991) Biosynthetic method for introducing unnatural amino acids site-specifically into proteins, Methods Enzymol. 202, 301-336.
5. Cornish, V. W., and Schultz, P. G. (1994) A new tool for studying protein structure and function, Curr. Opin. Struct. Biol. 4, 601-607.
6. Nowak, M. W., Gallivan, J. P., Silverman, S. K., Labarca, C. G., Dougherty, D. A., and Lester, H. A. (1998) In vivo incorporation of unnatural amino acids into ion channels in a Xenopus oocyte expression system, Methods Enzymol. 293, 504-529.
7. Gillmore, M. A., Steward, L. E., and Chamberlin, A. R. (1999) Incorporation of noncoded amino acids by in vitro protein biosynthesis, Top. Curr. Chem. 202, 77-99.
8. Dougherty, D. A. (2000) Unnatural amino acids as probes of protein structure and function, Curr. Opin. Chem. Biol. 4, 645-652.
9. Hohsaka, T., and Sisido, M. (2002) Incorporation of nonnatural amino acids into proteins, Curr. Opin. Chem. Biol. 6, 809-815.
10. Beene, D. L., Dougherty, D. A., and Lester, H. A. (2003) Unnatural amino acid mutagenesis in mapping ion channel function, Curr. Opin. Neurobiol. 13, 264-270.
11. Petersson, E. J., Brandt, G. S., Zacharias, N. M., Dougherty, D. A., and Lester, H. A. (2003) Caging proteins through unnatural amino acid mutagenesis, Methods Enzymol. 360, 258-273.
12. Brunner, J. (1993) Biosynthetic incorporation of nonnatural amino acids into proteins, Chem. Soc. Rev. 183-189.
13. Link, A. J., Mock, M. L., and Tirrell, D. A. (2003) Non-canonical amino acids in protein engineering, Curr. Opin. Biotech. 14, 603-609.
14. Dedkova, L. M., Fahmi, N. E., Golovine, S. Y., and Hecht, S. M. (2003) Enhanced D-amino acid incorporation into protein by modified ribosomes, J. Am. Chem. Soc. 125, 6616-6617.
15. Bain, J. D., Wacker, D. A., Kuo, E. E., and Chamberlin, A. R. (1991) Site-specfic incorporation of nonnatural residues into peptides: Effect of residue structure on suppression and translation efficiencies, Tetrahedron 47, 2389-2400.
16. Koh, J. T., Cornish, V. W., and Schultz, P. G. (1997) An experimental approach to evaluating the role of backbone interactions in proteins using unnatural amino acid mutagenesis, Biochemistry 36, 11314-11322.
17. England, P. M., Lester, H. A., and Dougherty, D. A. (1999) Mapping disulfide connectivity using backbone ester hydrolysis, Biochemistry 38, 14409-14415.
18. England, P. M., Lester, H. A., and Dougherty, D. A. (1999) Incorporation of esters into proteins: improved synthesis of the hydroxyacyl tRNAs, Tetrahedron Lett. 40, 6189-6193.
19. England, P. M., Zhang, Y., Dougherty, D. A., and Lester, H. A. (1999) Backbone mutations in transmembrane domains of a ligand-gated ion channel: implications for the mechanism of gating, Cell 96, 89-98.
20. Hentzen, D., Mandel, P., and Garel, J.-P. (1972) Relation between aminoacyl-tRNA stability and the fixed amino acid, Biochim. Biophys. Acta 281, 228-232.
21. Schuber, F., and Pinck, M. (1974) On the chemical reactivity of aminoacyl-tRNA ester bond. I. Influence of pH and nature of the acyl group on the rate of hydrolysis, Biochimie 56, 383-390.
22. Schuber, F., and Pinck, M. (1974) On the chemical reactivity of aminoacyl-tRNA ester bond. II. Aminolysis by tris and diethanolamine, Biochemie 56, 391-395.
23. Schuber, F., and Pinck, M. (1974) On the chemical reactivity of aminoacyl-tRNA ester bond. III. Influence of ionic strength, spermidine and methanol on the rate of hydrolysis, Biochimie 56, 397-403.
24. Cornish, V. W., Mendel, D., and Schultz, P. G. (1995) Probing protein-structure and function with an expanded genetic-code, Angew. Chem. 34, 621-633.
25. Cload, S. T., Liu, D. R., Froland, W. A., and Schultz, P. G. (1996) Development of improved tRNAs for in vitro biosynthesis of proteins containing unnatural amino acids, Chem. Biol. 3, 1033-1038.
26. Cornish, V. W., Benson, D. R., Altenbach, C. A., Hideg, K., Hubbel, W. L., and Schultz, P. G. (1994) Site-specific incorporation of biophysical probes into proteins, Proc. Natl. Acad. Sci. U. S.A. 91, 2910-2914.
27. Robertson, S. A., Ellman, J. A., and Schultz, P. G. (1991) A general and efficient route for chemical aminoacylation of transfer RNAs, J. Am. Chem. Soc. 113, 2722-2729.
28. Lodder, M., Golovine, S. Y., and Hecht, S. M. (1997) Chemical deprotection strategy for the elaboration of misacylated transfer RNA's, J. Org. Chem. 62, 778-779.
29. Bruce, A. G., Atkins, J. F., Wills, N., Uhlenbeck, O., and Gesteland, R. F. (1982) Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe, Proc. Natl. Acad. Sci. U.S.A. 79, 7127-7131.
30. Saks, M. E., Sampson, J. R., Nowak, M. W., Kearney, P. C., Du, F., Abelson, J. N., Lester, H. A., and Dougherty, D. A. (1996) An engineered Tetrahymena tRNAGln for in vivo incorporation of unnatural amino acids in proteins by nonsense suppression, J. Biol. Chem. 271, 23169-23175.
31. Wang, L., and Schultz, P. G. (2001) A general approach for the generation of orthogonal tRNAs, Chem. Biol. 8, 883-890.
32. Normanly, J., Masson, J. M., Kleina, L. G., Abelson, J., and Miller, J. H. (1986) Construction of two Escherichia coli amber suppressor tRNA genes: tRNAPheCUA and tRNACysCUA, Proc. Natl. Acad. Sci. U.S.A. 83, 705-717.
33. Kleina, L. G., Masson, J. M., Normanly, J., Abelson, J., and Miller, J. H. (1990) Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency, J. Mol. Biol. 213, 705-717.
34. Normanly, J., Kleina, L. G., Masson, J. M., Abelson, J., and Miller, J. H. (1990) Construction of Escherichia coli amber suppressor tRNA genes. III. Determination of tRNA specificity, J. Mol. Biol. 213, 719-726.
35. Hohsaka, T., Ashizuka, Y., Murakami, H., and Sisido, M. (1996) Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression, J. Am. Chem. Soc. 118, 9778-9779.
36. Murakami, H., Hohsaka, T., Ashizuka, Y., and Sisido, M. (1998) Site-directed incorporation of p-nitrophenylalanine into streptavidin and site-to-site photoinduced electron transfer from a pyrenyl group to a nitrophenyl group on the protein framework, J. Am. Chem. Soc. 120, 7520-7529.
37. Hohsaka, T., Ashizuka, Y., Murakami, H., and Sisido, M. (2001) Five-base codons for incorporation of nonnatural amino acids into proteins, Nucleic Acids Res. 29, 3646-3651.
38. Hohsaka, T., Ashizuka, Y., Hikaru, T., Murakami, H., and Sisido, M. (2001) Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system, Biochemistry 40, 11060-11064.
39. Magliery, T. J., Anderson, J. C., and Schultz, P. G. (2001) Expanding the genetic code: Selection of efficient suppressors of four-base codons and identification of "shifty" four-base codons with a library approach in Escherichia coli, J. Mol. Biol. 307, 755-769.
40. Anderson, J. C, Magliery, T. J., and Schultz, P. G. (2002) Exploring the limits of codon and anticodon size, Chem. Biol. 9, 237-244.
41. Anderson, J. C., and Schultz, P. G. (2003) Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression, Biochemistry 42, 9598-9608.
42. Hohsaka, T., Ashizuka, Y., and Sisido, M. (1999) Incorporation of two nonnatural amino acids into proteins through extension of the genetic code, Nucleic Acids Symp. Ser. 42, 79-80.
43. Taki, M., Hohsaka, T., Murakami, H., Taira, K., and Sisido, M. (2002) Position-specific incorporation of a fluorophore-quencher pair into a single streptavidin through orthogonal four-base codon/ anticodon pairs, J. Am. Chem. Soc. 124, 14586-14590.
44. Anderson, R. D., Zhou, J., and Hecht, S. M. (2002) Fluorescence resonace energy transfer between unnatural amino acids in a structurally modified dihydrofolate reductase, J. Am. Chem. Soc. 124, 9674-9675.
45. Nowak, M. W., Kearney, P. C., Sampson, J. R., Saks, M. E., Labarca, C. G., Silverman, S. K., Zhong, W., Thorson, J., Abelson, J. N., Davidson, N., Schultz, P. G., Dougherty, D. A., and Lester, H. A. (1995) Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells, Science 268, 439-442.
46. Ma, J. C., and Dougherty, D. A. (1997) The cation-π interaction, Chem. Rev. 97, 1303-1324.
47. Dougherty, D. A. (1996) Cation-π interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp, Science 271, 163-168.
48. Zhong, W. G., Gallivan, J. P., Zhang, Y. O., Lit, L. T., Lester, H. A., and Dougherty, D. A. (1998) From ab initio quantum mechanics to molecular neurobiology: a cation-π binding site in the nicotinic receptor, Proc. Natl. Acad. Sci. U.S.A. 95, 12088-12093.
49. Gallivan, J. P., and Dougherty, D. A. (1999) Cation-pi interactions in structural biology, Proc. Natl. Acad. Sci. U.S.A. 96, 9459-9464.
50. England, P. M., Lester, H. A., Davidson, N., and Dougherty, D. A. (1997) Site-specific, photochemical proteolysis applied to ion channels in vivo, Proc. Natl. Acad. Sci. U.S.A. 94, 11025-11030.
51. Gallivan, J. P., Lester, H. A., and Dougherty, D. A. (1997) Site-specific incorporation of biotinylated amino acids as a means to identify surface exposed residues in integral membrane proteins, Chem. Biol. 4, 739-749.
52. Ellman, J. A., Mendel, D., and Schultz, P. G. (1992) Site-specific incorporation of novel backbone structures into proteins, Science 255, 197-200.
53. Chung, H. H., Benson, D. R., and Schultz, P. G. (1993) Probing the structure and mechanism of ras protein with an expanded genetic-code, Science 259, 806-809.
54. Turcatti, G., Nemeth, K., Edgerton, M. D., Meseth, U., Talabot, F., Peitsch, M., Knowles, J., Vogel, H., and Chollet, A. (1996) Probing the structure and function of the tachykinin neurokinin-2 receptor through biosynthetic incorporation of fluorescent amino acids at specific sites, J. Biol. Chem. 271, 19991-19998.
55. Steward, L. E., Collins, C. S., Gilmore, M. A., Carlson, J. E., Ros, J. B. A., and Chamberlin, A. R. (1997) In vitro site-specific incorporation of fluorescent probes into β-galactosidase, J. Am. Chem. Soc. 119, 6-11.
56. Cohen, B. E., McAnaney, T. B., Park, E. S., Jany, Y. N., Boxer, S. G., and Jan, L. Y. (2002) Probing protein electrostatics with a synthetic fluorescent amino acid, Science 296, 1700-1703.
57. Martoglio, B., Hofmann, M. W., Brunnere, J., and Dobberstein, B. (1995) The protein-conducting channel in the membrane of the endoplasmic reticulum is open laterally toward the lipid bilayer, Cell 81, 207-214.
58. Kanamori, T., Nishikawa, S.-I., Shin, I., Schultz, P. G., and Endo, T. (1997) Probing the environment along the protein import pathways in yeast mitochondria by site-specific photo-cross-linking, Proc. Natl. Acad. Sci. U.S.A. 94, 485-490.
59. Chin, J. W., Martin, A. B., King, D. S., Wang, L., and Schultz, P. G. (2002) Addition of a photo-cross-linking amino acid to the genetic code of Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 99, 11020-11024.
60. Chin, J. W., and Schultz, P. G. (2002) In vivo photo-cross-linking with unnatural amino acid mutagenesis, ChemBloChem 3, 1135-1137.
61. 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.
62. Wang, L., Brock, A., Herberich, B., and Schultz, P. G. (2001) Expanding the genetic code of Escherichia coli, Science 292, 498-500.
63. Chin, J. W., Cropp, T. A., Anderson, J. C., Mukherji, M., Zhang, Z. W., and Schultz, P. G. (2003) An expanded eukaryotic genetic code, Science 301, 964-967.
64. Pastrnak, M., Magliery, T. J., and Schultz, P. G. (2000) A new orthogonal suppressor tRNA/aminoacyl-tRNA synthetase pair for evolving an organism with an expanded genetic code, Helv. Chim. Acta 83, 2277-2286.
65. 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.
66. 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.
67. Chin, J. W., Cropp, T. A., Chu, S., Meggers, E., and Schultz, P. G. (2003) Progress toward an expanded eukaryotic genetic code, Chem. Biol. 10, 511-519.
68. Wang, L., Brock, A., and Schultz, P. G. (2002) Adding L-3-(2-naphthyl)alanine to the genetic code of E. coli, J. Am. Chem. Soc. 124, 1836-1837.
69. Deiters, A., Cropp, T. A., Mukherji, M., Chin, J. W., Anderson, J. C., and Schultz, P. G. (2003) Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae, J. Am. Chem. Soc. 125, 11782-11783.
70. Wang, L., Zhang, Z. W., Brock, A., and Schultz, P. G. (2003) Addition of the keto functional group to the genetic code of Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 100, 56-61.
71. Anderson, J. C., Wu, N., Santoro, S. W., Lakshman, V., King, D. S., and Schultz, P. G. (2004) An expanded genetic code with a functional quadruplet codon, Proc. Natl. Acad. Sci. U.S.A. 101, 7566-7571.
72. 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.
73. Zhang, Z. W., Smith, B. A. C., Wang, L, Brock, A., Cho, C., and Schultz, P. G. (2003) A new strategy for the site-specific modification of proteins in vivo, Biochemistry 42, 6735-6746.
74. Kohrer, C., Xie, L., Kellerer, S., Varshney, U., and RajBhandary, U. L. (2001) Import of amber and ochre suppressor tRNAs into mammalian cells: A general approach to site-specific insertion of amino acid analogues into proteins, Proc. Natl. Acad. Sci. U.S.A. 98, 14310-14315.
75. Kohrer, C., Yoo, J.-H., Bennett, M. V., Schaack, J., and RajB-handary, U. L. (2003) A possible approach to site-specific insertion of two different unnatural amino acids into proteins in mammalian cells via nonsense suppression, Chem. Biol. 10, 1095-1102.
76. Monahan, S. L., Lester, H. A., and Dougherty, D. A. (2003) Site-specific incorporation of unnatural amino acids into receptors expressed in mammalian cells, Chem. Biol. 10, 573-580.