Adding new chemistries to the genetic code

Annual Review of Biochemistry

Volumn 79, Issue , 2010, Pages 413-444

  Liu, Chang C ^a   Schultz, Peter G ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

aminoacyl tRNA synthetase; protein engineering; protein evolution; translation

Indexed keywords

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; BACTERIAL RNA; TRANSFER RNA;

BACTERIAL GENETICS; CODON; CRYSTAL STRUCTURE; ESCHERICHIA COLI; FUNGAL GENETICS; GENETIC CODE; MAMMAL CELL; MOLECULAR PROBE; MOLECULAR RECOGNITION; NONHUMAN; PHOTOLYSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; RNA TRANSLATION; YEAST; ANIMAL; CHEMISTRY; GENETICS; METABOLISM; PROTEIN ENGINEERING; SACCHAROMYCES CEREVISIAE;

ESCHERICHIA COLI; MAMMALIA;

AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; ANIMALS; ESCHERICHIA COLI; GENETIC CODE; PROTEIN ENGINEERING; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE;

EID: 77953643054     PISSN: 00664154     EISSN: 00664154     Source Type: Book Series    
DOI: 10.1146/annurev.biochem.052308.105824     Document Type: Review

References (183)

1. Silverman RB. 2002. Organic Chemistry of Enzyme-Catalyzed Reactions. London/San Diego: Academic. 800 pp.
2. Walsh CT. 2005. Posttranslational Modification of Proteins: Expanding Nature's Inventory. Englewood, CO: Roberts. 490 pp.
3. Chalker JM, Bernardes GJ, Lin YA, Davis BG. 2009. Chemical modification of proteins at cysteine: opportunities in chemistry and biology. Chem. Asian J. 4:630-40
4. Bernardes GJ, Chalker JM, Errey JC, Davis BG. 2008. Facile conversion of cysteine and alkyl cysteines to dehydroalanine on protein surfaces: versatile and switchable access to functionalized proteins. J. Am. Chem. Soc. 130:5052-53
5. Merrifield RB. 1969. Solid-phase peptide synthesis. Adv. Enzymol. Relat. Areas Mol. Biol. 32:221-96
6. Marshall GR. 2003. Solid-phase synthesis: a paradigm shift. J. Pept. Sci. 9:534-44
7. Dawson PE, Kent SB. 2000. Synthesis of native proteins by chemical ligation. Annu. Rev. Biochem. 69:923-60
8. Muir TW. 2003. Semisynthesis of proteins by expressed protein ligation. Annu. Rev. Biochem. 72:249-89
9. Ambrogelly A, Palioura S, Söll D. 2007. Natural expansion of the genetic code. Nat. Chem. Biol. 3:29-35
10. Kimmerlin T, Seebach D. 2005. '100 years of peptide synthesis': ligation methods for peptide and protein synthesis with applications to beta-peptide assemblies. J. Pept. Res. 65:229-60
11. Baca M, Kent SB. 1993. Catalytic contribution of flap-substrate hydrogen bonds in "HIV-1 protease" explored by chemical synthesis. Proc. Natl. Acad. Sci. USA 90:11638-42
12. Kochendoerfer GG, Chen SY, Mao F, Cressman S, Traviglia S, et al. 2003. Design and chemical synthesis of a homogeneous polymer-modified erythropoiesis protein. Science 299:884-87
13. Chen SY, Cressman S, Mao F, Shao H, Low DW, et al. 2005. Synthetic erythropoietic proteins: tuning biological performance by site-specific polymer attachment. Chem. Biol. 12:371-83
14. Vazquez ME, Nitz M, Stehn J, Yaffe MB, Imperiali B. 2003. Fluorescent caged phosphoserine peptides as probes to investigate phosphorylation-dependent protein associations. J. Am. Chem. Soc. 125:10150-51
15. Flavell RR, Muir TW. 2009. Expressed protein ligation (EPL) in the study of signal transduction, ion conduction, and chromatin biology. Acc. Chem. Res. 42:107-16
16. Valiyaveetil FI, LeonettiM, Muir TW, MacKinnon R 2006. Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation. Science 314:1004-7
17. Hecht SM, Alford BL, Kuroda Y, Kitano S. 1978. "Chemical aminoacylation" of tRNA's. J. Biol. Chem. 253:4517-20
18. Phe S. Biochemistry 23:1468-73
19. Phe's useful as probes of the ribosomal acceptor site. Biochemistry 28:5185-95
20. Robertson SA, Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG 1989. The use of 5'-phospho-2 deoxyribocytidylylriboadenosine as a facile route to chemical aminoacylation of tRNA. Nucleic Acids Res. 17:9649-60
21. Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG. 1989. A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244:182-88
22. Koh JT, Cornish VW, Schultz PG. 1997. An experimental approach to evaluating the role of backbone interactions in proteins using unnatural amino acid mutagenesis. Biochemistry 36:11314-22
23. Eisenhauer BM, Hecht SM. 2002. Site-specific incorporation of (aminooxy)acetic acid into proteins. Biochemistry 41:11472-78
24. Murakami H, Hohsaka T, Ashizuka Y, Hashimoto K, Sisido M. 2000. Site-directed incorporation of fluorescent nonnatural amino acids into streptavidin for highly sensitive detection of biotin. Biomacromolecules 1:118-25
25. Taki M, Hohsaka T, Murakami H, Taira K, Sisido M. 2001. A non-natural amino acid for efficient incorporation into proteins as a sensitive fluorescent probe. FEBS Lett. 507:35-38
26. Taki M, Hohsaka T, Murakami H, Taira K, 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. 124:14586-90
27. Fahmi NE, Dedkova L, Wang B, Golovine S, Hecht SM. 2007. Site-specific incorporation of glycosylated serine and tyrosine derivatives into proteins. J. Am. Chem. Soc. 129:3586-97
28. Kanamori T, Nishikawa S, Shin I, Schultz PG, Endo T. 1997. Probing the environment along the protein import pathways in yeast mitochondria by site-specific photocrosslinking. Proc. Natl. Acad. Sci. USA 94:485-90
29. Thorson J, Chapman E, Murphy E, Judice J, Schultz P. 1995. Linear free energy analysis of hydrogen bonding in proteins. J. Am. Chem. Soc. 117:1157-58
30. Li S, Millward S, Roberts R 2002. In vitro selection of mRNA display libraries containing an unnatural amino acid. J. Am. Chem. Soc. 124:9972-73
31. Frankel A, Li S, StarckSR, Roberts RW. 2003. Unnatural RNA display libraries. Curr. Opin. Struct. Biol. 13:506-12
32. Kohrer C, Yoo JH, BennettM, SchaackJ, RajBhandaryUL. 2003. A possible approach to site-specific insertion of two different unnatural amino acids into proteins in mammalian cells via nonsense suppression. Chem. Biol. 10:1095-102
33. Rodriguez EA, Lester HA, Dougherty DA. 2006. In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression. Proc. Natl. Acad. Sci. USA 103:8650-55
34. Gln for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression. J. Biol. Chem. 271:23169-75
35. Dougherty DA. 2000. Unnatural amino acids as probes of protein structure and function. Curr. Opin. Chem. Biol. 4:645-52
36. Beene DL, Dougherty DA, Lester HA. 2003. Unnatural amino acid mutagenesis in mapping ion channel function. Curr. Opin. Neurobiol. 13:264-70
37. England PM, Zhang Y, Dougherty DA, Lester HA. 1999. Backbone mutations in transmembrane domains of a ligand-gated ion channel: implications for the mechanism of gating. Cell 96:89-98
38. Dougherty DA. 2008. Physical organic chemistry on the brain. J. Org. Chem. 73:3667-73
39. Lummis SCR, Beene DL, Lee LW, Lester HA, Broadhurst RW, Dougherty DA. 2005. Cis-trans iso-merization at a proline opens the pore of a neurotransmitter-gated ion channel. Nature 438:248-52
40. Hendrickson TL, De Crécy-Lagard V, Schimmel P. 2004. Incorporation of nonnatural amino acids into proteins. Annu. Rev. Biochem. 73:147-76
41. Link AJ, Mock ML, Tirrell DA. 2003. Non-canonical amino acids in protein engineering. Curr. Opin. Biotechnol. 14:603-9
42. Van Hest JC, Tirrell DA. 1998. Efficient introduction of alkene functionality into proteins in vivo. FEBS Lett. 428:68-70
43. Link AJ, Tirrell DA. 2003. Cell surface labeling of Escherichia coli via copper(I)-catalyzed [3+2] cycload-dition. J. Am. Chem. Soc. 125:11164-65
44. Kiick KL, Van Hest JC, Tirrell DA. 2000. Expanding the scope of protein biosynthesis by altering the methionyl-tRNA synthetase activity of a bacterial expression host. Angew. Chem. Int. Ed. Engl. 39:2148-52
45. Datta D, Wang P, Carrico IS, Mayo SL, Tirrell DA. 2002. A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins. J. Am. Chem. Soc. 124:5652-53
46. Sharma N, Furter R, Kast P, Tirrell DA. 2000. Efficient introduction of aryl bromide functionality into proteins in vivo. FEBS Lett. 467:37-40
47. Döring V, Mootz HD, Nangle LA, Hendrickson TL, De Crécy-Lagard V, et al. 2001. Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway. Science 292:501-4
48. Link AJ, Vink MK, Agard NJ, Prescher JA, Bertozzi CR, Tirrell DA. 2006. Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids. Proc. Natl. Acad. Sci. USA 103:10180-85
49. Yang W, Hendrickson WA, Crouch RJ, Satow Y. 1990. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 249:1398-405
50. Cirino PC, Tang Y, Takahashi K, Tirrell DA, Arnold FH. 2003. Global incorporation of norleucine in place of methionine in cytochrome P450 BM-3 heme domain increases peroxygenase activity. Biotechnol. Bioeng. 83:729-34
51. Montclare JK, Tirrell DA. 2006. Evolving proteins of novel composition. Angew. Chem. Int. Ed. Engl. 45:4518-21
52. Bae JH, Rubini M, Jung G, Wiegand G, Seifert MH, et al. 2003. Expansion of the genetic code enables design of a novel "gold" class of green fluorescent proteins. J. Mol. Biol. 328:1071-81
53. Budisa N, Rubini M, Bae JH, Weyher E, Wenger W, et al. 2002. Global replacement of tryptophan with aminotryptophans generates non-invasive protein-based optical pH sensors. Angew. Chem. Int. Ed. Engl. 41:4066-69
54. Beatty KE, Xie F, Wang Q, Tirrell DA. 2005. Selective dye-labeling of newly synthesized proteins in bacterial cells. J. Am. Chem. Soc. 127:14150-51
55. Beatty KE, Liu JC, Xie F, Dieterich DC, Schuman EM, et al. 2006. Fluorescence visualization of newly synthesized proteins in mammalian cells. Angew. Chem. Int. Ed. Engl. 45:7364-67
56. Ibba M, Söll D. 2000. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69:617-50
57. Ibba M, Söll D. 2004. Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev. 18:731-38
58. Giege R, Sissler M, Florentz C. 1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26:5017-35
59. Chin JW. 2006. Modular approaches to expanding the functions of living matter. Nat. Chem. Biol. 2:304-11
60. Liu DR, Schultz PG. 1999. Progress toward the evolution of an organism with an expanded genetic code. Proc. Natl. Acad. Sci. USA 96:4780-85
61. Wang L, Schultz PG. 2004. Expanding the genetic code. Angew. Chem. Int. Ed. Engl. 44:34-66 (Pubitemid 40069845)
62. Kwok Y, Wong JT. 1980. Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes. Can. J. Biochem. 58:213-18
63. Wang L, Schultz PG. 2001. A general approach for the generation of orthogonal tRNAs. Chem. Biol. 8:883-90
64. Santoro SW, Wang L, Herberich B, King DS, Schultz PG. 2002. An efficient system for the evolution of aminoacyl-tRNA synthetase specificity. Nat. Biotechnol. 20:1044-48
65. Melancon CE 3rd, Schultz PG. 2009. One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases. Bioorg. Med. Chem. Lett. 19:3845-47
66. Wang L, Zhang Z, Brock A, Schultz PG. 2003. Addition of the keto functional group to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 100:56-61
67. Zhang Z, Smith BA, Wang L, Brock A, Cho C, Schultz PG. 2003. A new strategy for the site-specific modification of proteins in vivo. Biochemistry 42:6735-46
68. Zeng H, Xie J, Schultz PG. 2006. Genetic introduction ofa diketone-containing amino acid into proteins. Bioorg. Med. Chem. Lett. 16:5356-59
69. Zhang Z, Wang L, Brock A, Schultz PG. 2002. The selective incorporation of alkenes into proteins in Escherichia coli. Angew. Chem. Int. Ed. Engl. 41:2840-42
70. Wang J, Schiller SM, Schultz PG. 2007. A biosynthetic route to dehydroalanine-containing proteins. Angew. Chem. Int. Ed. Engl. 46:6849-51
71. Deiters A, Schultz PG. 2005. In vivo incorporation of an alkyne into proteins in Escherichia coli. Bioorg. Med. Chem. Lett. 15:1521-24
72. Chin JW, Santoro SW, Martin AB, King DS, Wang L, Schultz PG. 2002. Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J. Am. Chem. Soc. 124:9026-27
73. Brustad E, Bushey ML, Lee JW, Groff D, Liu W, Schultz PG. 2008. A genetically encoded boronate-containing amino acid. Angew. Chem. Int. Ed. Engl. 47:8220-23
74. Wang L, Brock A, Herberich B, Schultz PG. 2001. Expanding the genetic code of Escherichia coli. Science 292:498-500
75. Mehl RA, Anderson JC, Santoro SW, Wang L, Martin AB, et al. 2003. Generation of a bacterium with a 21 amino acid genetic code. J. Am. Chem. Soc. 125:935-39
76. Schultz KC, Supekova L, Ryu Y, Xie J, Perera R, Schultz PG. 2006. A genetically encoded infrared probe. J. Am. Chem. Soc. 128:13984-85
77. Wang L, Xie J, Deniz AA, Schultz PG. 2003. Unnatural amino acid mutagenesis of green fluorescent protein. J. Org. Chem. 68:174-76
78. Xie J, Wang L, Wu N, Brock A, Spraggon G, Schultz PG. 2004. The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination. Nat. Biotechnol. 22:1297-301
79. Cellitti SE, Jones DH, Lagpacan L, Hao X, Zhang Q, et al. 2008. In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy. J. Am. Chem. Soc. 130:9268-81
80. Tsao ML, Summerer D, Ryu Y, Schultz PG. 2006. The genetic incorporation of a distance probe into proteins in Escherichia coli. J. Am. Chem. Soc. 128:4572-73
81. Alfonta L, Zhang Z, Uryu S, Loo JA, Schultz PG. 2003. Site-specific incorporation of a redox-active amino acid into proteins. J. Am. Chem. Soc. 125:14662-63
82. 731 in radical propagation. J. Am. Chem. Soc. 129:15060-71
83. Sakamoto K, Murayama K, Oki K, Iraha F, Kato-Murayama M, et al. 2009. Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure 17:335-44
84. Wang L, Brock A, Schultz PG. 2002. Adding L-3-(2-Naphthyl)alanine to the genetic code of E. coli. J. Am. Chem. Soc. 124:1836-37
85. Xie J, Liu W, Schultz PG. 2007. A genetically encoded bidentate, metal-binding amino acid. Angew. Chem. Int. Ed. Engl. 46:9239-42
86. Guo J, Wang J, Anderson JC, Schultz PG. 2008. Addition of an alpha-hydroxy acid to the genetic code of bacteria. Angew. Chem. Int. Ed. Engl. 47:722-25
87. Lee HS, Spraggon G, Schultz PG, Wang F. 2009. Genetic incorporation of a metal-ion chelating amino acid into proteins as a biophysical probe. J. Am. Chem. Soc. 131:2481-83
88. Chin JW, Martin AB, King DS, Wang L, Schultz PG. 2002. Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 99:11020-24
89. Deiters A, Groff D, Ryu Y, Xie J, Schultz PG. 2006. A genetically encoded photocaged tyrosine. Angew. Chem. Int. Ed. Engl. 45:2728-31
90. Peters FB, Brock A, Wang J, Schultz PG. 2009. Photocleavage of the polypeptide backbone by 2-nitrophenylalanine. Chem. Biol. 16:148-52
91. Bose M, Groff D, Xie J, Brustad E, Schultz PG. 2006. The incorporation of a photoisomerizable amino acid into proteins in E. coli. J. Am. Chem. Soc. 128:388-89
92. Tippmann EM, Liu W, Summerer D, Mack AV, Schultz PG. 2007. A genetically encoded diazirine photocrosslinker in Escherichia coli. ChemBioChem 8:2210-14
93. Wang J, Xie J, Schultz PG. 2006. A genetically encoded fluorescent amino acid. J. Am. Chem. Soc. 128:8738-39
94. Xie J, Supekova L, Schultz PG. 2007. A genetically encoded metabolically stable analogue of phospho-tyrosine in Escherichia coli. ACS Chem. Biol. 2:474-78
95. Neumann H, Hazen JL, Weinstein J, Mehl RA, Chin JW. 2008. Genetically encoding protein oxidative damage. J. Am. Chem. Soc. 130:4028-33
96. Liu CC, Schultz PG. 2006. Recombinant expression of selectively sulfated proteins in Escherichia coli. Nat. Biotechnol. 24:1436-40
97. Pastrnak M, Magliery T, Schultz PG. 2000. A new orthogonal suppressor tRNA/aminoacyl-tRNA syn-thetase pair for evolving an organism with an expanded genetic code. Helv. Chim. Acta 83:2277-86
98. Liu DR, Magliery TJ, Pastrnak M, Schultz PG. 1997. Engineering a tRNA and aminoacyl-tRNA syn-thetase for the site-specific incorporation of unnatural amino acids into proteins in vivo. Proc. Natl. Acad. Sci. USA 94:10092-97
99. Ohno S, Yokogawa T, Fujii I, Asahara H, Inokuchi H, Nishikawa K. 1998. Co-expression of yeast amber suppressor tRNATyr and tyrosyl-tRNA synthetase in Escherichia coli: possibility to expand the genetic code. J. Biochem. 124:1065-68
100. Furter R. 1998. Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. Protein Sci. 7:419-26
101. Wang L, Magliery TJ, Liu DR, Schultz PG. 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. 122:5010-11
102. Kowal AK, Kohrer C, RajBhandary UL. 2001. Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria. Proc. Natl. Acad. Sci. USA 98:2268-73
103. Santoro SW, Anderson JC, Lakshman V, Schultz PG. 2003. An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acids Res. 31:6700-9
104. Anderson JC, Wu N, Santoro SW, Lakshman V, King DS, Schultz PG. 2004. An expanded genetic code with a functional quadruplet codon. Proc. Natl. Acad. Sci. USA 101:7566-71
105. Anderson JC, Schultz PG. 2003. Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression. Biochemistry 42:9598-608
106. Wang F, Robbins S, Shen W, Schultz PG. 2010. Genetic incorporation of unnatural amino acids into proteins in Mycobacterium tuberculosis. PLoS ONE 5(2):e9354
107. Krzycki JA. 2005. The direct genetic encoding of pyrrolysine. Curr. Opin. Microbiol. 8:706-12
108. Srinivasan G, James CM, Krzycki JA. 2002. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296:1459-62
109. Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Söll D, Steitz TA. 2007. Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc. Natl. Acad. Sci. USA 104:11268-73
110. Woese CR, Olsen GJ, Ibba M, Söll D. 2000. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64:202-36
111. Blight SK, Larue RC, Mahapatra A, Longstaff DG, Chang E, et al. 2004. Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431:333-35
112. Yanagisawa T, IshiiR, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. 2008. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem. Biol. 15:1187-97
113. Pyl structure reveals the molecular basis of orthogonality. Nature 457:1163-67
114. Mukai T, Kobayashi T, Hino N, Yanagisawa T, Sakamoto K, Yokoyama S. 2008. Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochem. Biophys. Res. Commun. 371:818-22
115. Li WT, Mahapatra A, Longstaff DG, Bechtel J, Zhao G, et al. 2009. Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs. J. Mol. Biol. 385:1156-64
116. Polycarpo CR, Herring S, Berube A, Wood JL, Söll D, Ambrogelly A. 2006. Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase. FEBS Lett. 580:6695-700
117. Fekner T, Li X, Lee MM, Chan MK. 2009. A pyrrolysine analogue for protein click chemistry. Angew. Chem. Int. Ed. Engl. 48:1633-35
118. Kobayashi T, Yanagisawa T,Sakamoto K, Yokoyama S.2009. Recognition of non-alpha-amino substrates by pyrrolysyl-tRNA synthetase. J. Mol. Biol. 385:1352-60
119. Nguyen DP, Lusic H, Neumann H, Kapadnis PB, Deiters A, Chin JW.2009.Geneticencoding andlabel-ingofaliphatic azidesandalkynesinrecombinant proteins viaapyrrolysyl-tRNAsynthetase/tRNA(CUA) pair and click chemistry. J. Am. Chem. Soc. 131:8720-21
120. Chen PR, Groff D, Guo J, Ou W, Cellitti S, et al. 2009. A facile system for encoding unnatural amino acids in mammalian cells. Angew. Chem. Int. Ed. Engl. 48:4052-55
121. Neumann H, Peak-Chew SY, Chin JW. 2008. Genetically encoding N(epsilon)-acetyllysine in recom-binant proteins. Nat. Chem. Biol. 4:232-34
122. Edwards H, Schimmel P. 1990. A bacterial amber suppressor in Saccharomyces cerevisiae is selectively recognized by a bacterial aminoacyl-tRNA synthetase. Mol. Cell. Biol. 10:1633-41
123. Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG. 2003. An expanded eukaryotic genetic code. Science 301:964-67
124. Wu N, Deiters A, Cropp TA, King D, Schultz PG. 2004. A genetically encoded photocaged amino acid. J. Am. Chem. Soc. 126:14306-7
125. Deiters A, Cropp TA, Mukherji M, Chin JW, Anderson JC, Schultz PG. 2003. Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae. J. Am. Chem. Soc. 125:11782-83
126. Lee HS, Guo J, Lemke EA, Dimla RD, Schultz PG. 2009. Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae. J. Am. Chem. Soc. 131:12921-23
127. Brustad E, Bushey ML, Brock A, Chittuluru J, Schultz PG. 2008. A promiscuous aminoacyl-tRNA synthetase that incorporates cysteine, methionine, and alanine homologs into proteins. Bioorg. Med. Chem. Lett. 18:6004-6
128. Lemke EA, Summerer D, Geierstanger BH, Brittain SM, Schultz PG. 2007. Control of protein phos-phorylation with a genetically encoded photocaged amino acid. Nat. Chem. Biol. 3:769-72
129. Summerer D, Chen S, Wu N, Deiters A, Chin JW, Schultz PG. 2006. A genetically encoded fluorescent amino acid. Proc. Natl. Acad. Sci. USA 103:9785-89
130. Tippmann EM, Schultz PG. 2007. Agenetically encoded metallocene containing amino acid. Tetrahedron 63:6182-84
131. Young TS, Ahmad I, Brock A, Schultz PG. 2009. Expanding the genetic repertoire of the methylotrophic yeast Pichia pastoris. Biochemistry 48:2643-53
132. Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H, et al. 2002. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res. 30:4692-99
133. Liu W, Brock A, Chen S, Chen S, Schultz PG. 2007. Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat. Methods 4:239-44
134. Wang W, Takimoto JK, Louie GV, Baiga TJ, Noel JP, et al. 2007. Genetically encoding unnatural amino acids for cellular and neuronal studies. Nat. Neurosci. 10:1063-72
135. Kwon I, Tirrell DA. 2007. Site-specific incorporationof tryptophan analogues into recombinant proteins in bacterial cells. J. Am. Chem. Soc. 129:10431-37
136. Kwon I, Wang P, Tirrell DA. 2006. Design of a bacterial host for site-specific incorporation of p-bromophenylalanine into recombinant proteins. J. Am. Chem. Soc. 128:11778-83
137. Oki K, Sakamoto K, Kobayashi T, Sasaki HM, Yokoyama S. 2008. Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog. Proc. Natl. Acad. Sci. USA 105:13298-303
138. Liu W, Alfonta L, Mack AV, Schultz PG. 2007. Structural basis for the recognition of para-benzoyl-L-phenylalanine by evolved aminoacyl-tRNA synthetases. Angew. Chem. Int. Ed. Engl. 46:6073-75
139. Turner JM, Graziano J, Spraggon G, Schultz PG. 2006. Structural plasticity of an aminoacyl-tRNA synthetase active site. Proc. Natl. Acad. Sci. USA 103:6483-88
140. Turner JM, Graziano J, Spraggon G, Schultz PG. 2005. Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase. J. Am. Chem. Soc. 127:14976-77
141. Cusack S, Yaremchuk A, Tukalo M. 2000. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J. 19:2351-61
142. Ryu Y, Schultz PG. 2006. Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. Nat. Methods 3:263-65
143. Bossi L. 1983. Context effects: translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J. Mol. Biol. 164:73-87
144. Taira H, Hohsaka T, Sisido M 2006. In vitro selection of tRNAs for efficient four-base decoding to incorporate non-natural amino acids into proteins in an Escherichia coli cell-free translation system.Nucleic Acids Res. 34:1653-62
145. Magliery TJ, Anderson JC, Schultz PG. 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. 307:755-69
146. Kwon I, Kirshenbaum K, Tirrell DA. 2003. Breaking the degeneracy of the genetic code. J. Am. Chem. Soc. 125:7512-13
147. Kudla G, Murray AW, Tollervey D, Plotkin JB. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science 324:255-58
148. Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S. 2008. Virus attenuation by genome-scale changes in codon pair bias. Science 320:1784-87
149. Bain JD, Switzer C, Chamberlin AR, Benner SA. 1992. Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code. Nature 356:537-39
150. Hirao I, Ohtsuki T, Fujiwara T, Mitsui T, Yokogawa T, et al. 2002. An unnatural base pair for incorporating amino acid analogs into proteins. Nat. Biotechnol. 20:177-82
151. Hirao I, Harada Y, Kimoto M, Mitsui T, Fujiwara T, Yokoyama S. 2004. A two-unnatural-base-pair system toward the expansion of the genetic code. J. Am. Chem. Soc. 126:13298-305
152. Liu CC, Cellitti S, Geierstanger BH, Schultz PG. 2009. Efficient expression of tyrosine-sulfated proteins in E. coli using an expanded genetic code. Nat. Protoc. 4:1784-89
153. Chen S, Schultz PG, Brock A. 2007. An improved system for the generation and analysis of mutant proteins containing unnatural amino acids in Saccharomyces cerevisiae. J. Mol. Biol. 371:112-22
154. Wang Q, Wang L. 2008. New methods enabling efficient incorporation of unnatural amino acids in yeast. J. Am. Chem. Soc. 130:6066-67
155. Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, et al. 2003. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat. Struct. Biol. 10:425-32
156. Guo J, Melancon CE, Lee HS, Groff D, Schultz PG. 2009. Evolution of amber suppressor tRNAs for efficient bacterial production of proteins containing nonnatural amino acids. Angew. Chem. Int. Ed. Engl. 48:9148-51
157. Young TS, Ahmad I, Yin JA, Schultz PG. 2009. An enhanced system for unnatural amino acid mutagenesis in E. coli. J. Mol. Biol. 395:361-74
158. Rackham O, Chin JW. 2005. A network of orthogonal ribosome xmRNA pairs.Nat. Chem. Biol. 1:159-66
159. Wang K, Neumann H, Peak-Chew SY, Chin JW. 2007. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25:770-77
160. Doi Y, Ohtsuki T, Shimizu Y, Ueda T, Sisido M. 2007. Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system. J. Am. Chem. Soc. 129:14458-62
161. Sella G, Ardell DH. 2006. The coevolution of genes and genetic codes: Crick's frozen accident revisited. J. Mol. Evol. 63:297-313
162. Vetsigian K, Woese C, Goldenfeld N. 2006. Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA 103:10696-701
163. Lu Y, Freeland S. 2006. On the evolution of the standard amino-acid alphabet. Genome Biol. 7:102.1-.6
164. Weber AL, Miller SL. 1981. Reasons for the occurrence of the twenty coded protein amino acids. J. Mol. Evol. 17:273-84
165. Ye S, Huber T, Vogel R, Sakmar TP. 2009. FTIR analysis of GPCR activation using azido probes. Nat. Chem. Biol. 5:397-99
166. Groff D, Thielges MC, Cellitti S, Schultz PG, Romesberg FE. 2009. Efforts toward the direct experimental characterization of enzyme microenvironments: tyrosine100 in dihydrofolate reductase. Angew. Chem. Int. Ed. Engl. 48:3478-81
167. Mills JH, Lee HS, Liu CC, Wang J, Schultz PG. 2009. A genetically encoded direct sensor of antibody-antigen interactions. ChemBioChem 10:2162-64
168. Lee HS, Dimla RD, Schultz PG. 2009. Protein-DNA photo-crosslinking with a genetically encoded benzophenone-containing amino acid. Bioorg. Med. Chem. Lett. 19:5222-24
169. Hino N, Okazaki Y, Kobayashi T, Hayashi A, Sakamoto K, Yokoyama S. 2005. Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat. Methods 2:201-6
170. Grunewald J, Tsao ML, Perera R, Dong L, Niessen F, et al. 2008. Immunochemical termination of self-tolerance. Proc. Natl. Acad. Sci. USA 105:11276-80
171. Grunewald J, Hunt GS, Dong L, Niessen F, Wen BG, et al. 2009. Mechanistic studies of the immuno-chemical terminationof self-tolerance with unnatural amino acids. Proc. Natl. Acad. Sci. USA106:4337-42
172. Liu CC, Brustad E,Liu W,Schultz PG. 2007. Crystal structureofa biosynthetic sulfo-hirudin complexed to thrombin. J. Am. Chem. Soc. 129:10648-49
173. Liu H, Wang L, Brock A, Wong CH, Schultz PG. 2003. A method for the generation of glycoprotein mimetics. J. Am. Chem. Soc. 125:1702-3
174. Brustad EM, Lemke EA, Schultz PG, Deniz AA. 2008. A general and efficient method for the site-specific dual-labeling of proteins for single molecule fluorescence resonance energy transfer. J. Am. Chem. Soc. 130:17664-65
175. Ye S, Kohrer C, Huber T, Kazmi M, Sachdev P, et al. 2008. Site-specific incorporation of keto amino acids into functional G protein-coupled receptors using unnatural amino acid mutagenesis. J. Biol. Chem. 283:1525-33
176. Guo J, Wang J, Lee JS, Schultz PG. 2008. Site-specific incorporation of methyl-and acetyl-lysine analogues into recombinant proteins. Angew. Chem. Int. Ed. Engl. 47:6399-401
177. Deiters A, Cropp TA, Summerer D, Mukherji M, Schultz PG. 2004. Site-specific PEGylation of proteins containing unnatural amino acids. Bioorg. Med. Chem. Lett. 14:5743-45
178. Love KR, Swoboda JG, Noren CJ, Walker S. 2006. Enabling glycosyltransferase evolution: a facile substrate-attachment strategy for phage-display enzyme evolution. ChemBioChem 7:753-56
179. Liu CC, Mack AV, Tsao ML, Mills JH, Lee HS, et al. 2008. Protein evolution with an expanded genetic code. Proc. Natl. Acad. Sci. USA 105:17688-93
180. Liu CC, Mack AV, Brustad E, Mills JH, Groff D, et al. 2009. Evolution of proteins with genetically encoded "chemical warheads." J. Am. Chem. Soc. 131:9616-17
181. Liu CC, Choe H, Farzan M, Schultz PG. 2009. Mutagenesis and evolution of sulfated antibodies using an expanded genetic code. Biochemistry 48:8891-98
182. Donia MS, Hathaway BJ, Sudek S, Haygood MG, Rosovitz MJ, et al. 2006. Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nat. Chem. Biol. 2:729-35
183. Lee HS, Schultz PG. 2008. Biosynthesis of a site-specific DNA cleaving protein. J. Am. Chem. Soc. 130:13194-95