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Journal of Nucleic Acids
Volume 2012, Article ID 713510, 15 pages
http://dx.doi.org/10.1155/2012/713510
Review Article

Genetically Encoded Libraries of Nonstandard Peptides

Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan

Received 1 June 2012; Accepted 12 August 2012

Academic Editor: Masayasu Kuwahara

Copyright © 2012 Takashi Kawakami and Hiroshi Murakami. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. M. Miller, R. J. Simon, S. Ng, R. N. Zuckermann, J. M. Kerr, and W. H. Moos, “Comparison of the proteolytic susceptibilities of homologous L-amino acid, D-amino acid, and N-substituted glycine peptide and peptoid oligomers,” Drug Development Research, vol. 35, no. 1, pp. 20–32, 1995. View at Publisher · View at Google Scholar · View at Scopus
  2. A. Frankel, S. W. Millward, and R. W. Roberts, “Encodamers: unnatural peptide oligomers encoded in RNA,” Chemistry and Biology, vol. 10, no. 11, pp. 1043–1050, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. Y. Sako, Y. Goto, H. Murakami, and H. Suga, “Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond,” ACS Chemical Biology, vol. 3, no. 4, pp. 241–249, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. O. Ovadia, S. Greenberg, J. Chatterjee et al., “The effect of multiple N-methylation on intestinal permeability of cyclic hexapeptides,” Molecular Pharmaceutics, vol. 8, no. 2, pp. 479–487, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. Y. Yamagishi, I. Shoji, S. Miyagawa et al., “Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library,” Chemistry & Biology, vol. 18, no. 12, pp. 1562–1570, 2011. View at Google Scholar
  6. G. P. Smith, “Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface,” Science, vol. 228, no. 4705, pp. 1315–1317, 1985. View at Google Scholar · View at Scopus
  7. L. C. Mattheakis, R. R. Bhatt, and W. J. Dower, “An in vitro polysome display system for identifying ligands from very large peptide libraries,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 19, pp. 9022–9026, 1994. View at Publisher · View at Google Scholar · View at Scopus
  8. N. Nemoto, E. Miyamoto-Sato, Y. Husimi, and H. Yanagawa, “In vitro virus: bonding of mRNA bearing puromycin at the 3'-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro,” FEBS Letters, vol. 414, no. 2, pp. 405–408, 1997. View at Publisher · View at Google Scholar · View at Scopus
  9. R. W. Roberts and J. W. Szostak, “RNA-peptide fusions for the in vitro selection of peptides and proteins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 23, pp. 12297–12302, 1997. View at Publisher · View at Google Scholar · View at Scopus
  10. C. Heinis, T. Rutherford, S. Freund, and G. Winter, “Phage-encoded combinatorial chemical libraries based on bicyclic peptides,” Nature Chemical Biology, vol. 5, no. 7, pp. 502–507, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. A. Angelini, L. Cendron, S. Chen et al., “Bicyclic peptide inhibitor reveals large contact interface with a protease target,” ACS Chemical Biology, vol. 7, no. 5, pp. 817–821, 2012. View at Publisher · View at Google Scholar
  12. V. Baeriswyl, H. Rapley, L. Pollaro et al., “Bicyclic peptides with optimized ring size inhibit human plasma kallikrein and its orthologues while sparing paralogous proteases,” ChemMedChem, vol. 7, no. 7, pp. 1173–1176, 2012. View at Publisher · View at Google Scholar
  13. T. Bosma, A. Kuipers, E. Bulten, L. de Vries, R. Rink, and G. N. Moll, “Bacterial display and screening of posttranslationally thioether-stabilized peptides,” Applied and Environmental Microbiology, vol. 77, no. 19, pp. 6794–6801, 2011. View at Publisher · View at Google Scholar
  14. S. Li and R. W. Roberts, “A novel strategy for in vitro selection of peptide-drug conjugates,” Chemistry and Biology, vol. 10, no. 3, pp. 233–239, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. A. Angelini and C. Heinis, “Post-translational modification of genetically encoded polypeptide libraries,” Current Opinion in Chemical Biology, vol. 15, no. 3, pp. 355–361, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. J. D. Bain, C. G. Glabe, T. A. Dix, A. R. Chamberlin, and E. S. Diala, “Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide,” Journal of the American Chemical Society, vol. 111, no. 20, pp. 8013–8014, 1989. View at Google Scholar · View at Scopus
  17. C. J. Noren, S. J. Anthony-Cahill, M. C. Griffith, and P. G. Schultz, “A general method for site-specific incorporation of unnatural amino acids into proteins,” Science, vol. 244, no. 4901, pp. 182–188, 1989. View at Google Scholar · View at Scopus
  18. T. G. Heckler, L. H. Chang, Y. Zama, T. Naka, M. S. Chorghade, and S. M. Hecht, “T4 RNA ligase mediated preparation of novel "chemically misacylated" tRNAPheS,” Biochemistry, vol. 23, no. 7, pp. 1468–1473, 1984. View at Google Scholar · View at Scopus
  19. J. D. Bain, E. S. Diala, C. G. Glabe et al., “Site-specific incorporation of nonnatural residues during in vitro protein biosynthesis with semisynthetic aminoacyl-tRNAs,” Biochemistry, vol. 30, no. 22, pp. 5411–5421, 1991. View at Google Scholar · View at Scopus
  20. T. Hohsaka, Y. Ashizuka, H. Murakami, and M. Sisido, “Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression,” Journal of the American Chemical Society, vol. 118, no. 40, pp. 9778–9779, 1996. View at Publisher · View at Google Scholar · View at Scopus
  21. H. Murakami, T. Hohsaka, Y. Ashizuka, and M. Sisido, “Site-directed incorporation of p-nitrophenylalanine into streptavidin and site-to-site photinduced electron transfer from a pyrenyl group to a nitrophenyl group on the protein framework,” Journal of the American Chemical Society, vol. 120, no. 30, pp. 7520–7529, 1998. View at Publisher · View at Google Scholar · View at Scopus
  22. T. Hohsaka, D. Kajihara, Y. Ashizuka, H. Murakami, and M. Sisido, “Efficient incorporation of nonnatural amino acids with large aromatic groups into streptavidin in in vitro protein synthesizing systems,” Journal of the American Chemical Society, vol. 121, no. 1, pp. 34–40, 1999. View at Publisher · View at Google Scholar · View at Scopus
  23. T. Hohsaka, Y. Ashizuka, H. Taira, H. Murakami, and M. Sisido, “Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system,” Biochemistry, vol. 40, no. 37, pp. 11060–11064, 2001. View at Publisher · View at Google Scholar · View at Scopus
  24. T. Hohsaka, Y. Ashizuka, H. Murakami, and M. Sisido, “Five-base codons for incorporation of nonnatural amino acids into proteins,” Nucleic Acids Research, vol. 29, no. 17, pp. 3646–3651, 2001. View at Google Scholar · View at Scopus
  25. T. Hohsaka, Y. Ashizuka, H. Sasaki, H. Murakami, and M. Sisido, “Incorporation of two different nonnatural amino acids independently into a single protein through extension of the genetic code,” Journal of the American Chemical Society, vol. 121, no. 51, pp. 12194–12195, 1999. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Taki, T. Hohsaka, H. Murakami, K. Taira, and M. Sisido, “Position-specific incorporation of a fluorophore—quencher pair into a single streptavidin through orthogonal four-base codon/anticodon pairs,” Journal of the American Chemical Society, vol. 124, no. 49, pp. 14586–14590, 2002. View at Publisher · View at Google Scholar · View at Scopus
  27. T. Ohtsuki, T. Manabe, and M. Sisido, “Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures,” FEBS Letters, vol. 579, no. 30, pp. 6769–6774, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. D. Kajihara, R. Abe, I. Iijima, C. Komiyama, M. Sisido, and T. Hohsaka, “FRET analysis of protein conformational change through position-specific incorporation of fluorescent amino acids,” Nature Methods, vol. 3, no. 11, pp. 923–929, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. M. W. Nowak, P. C. Kearney, J. R. Sampson et al., “Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells,” Science, vol. 268, no. 5209, pp. 439–442, 1995. View at Google Scholar · View at Scopus
  30. D. L. Beene, D. A. Dougherty, and H. A. Lester, “Unnatural amino acid mutagenesis in mapping ion channel function,” Current Opinion in Neurobiology, vol. 13, no. 3, pp. 264–270, 2003. View at Publisher · View at Google Scholar · View at Scopus
  31. L. Wang, A. Brock, B. Herberich, and P. G. Schultz, “Expanding the genetic code of Escherichia coli,” Science, vol. 292, no. 5516, pp. 498–500, 2001. View at Google Scholar · View at Scopus
  32. C. C. Liu and P. G. Schultz, “Adding new chemistries to the genetic code,” Annual Review of Biochemistry, vol. 79, pp. 413–444, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. Q. Wang, A. R. Parrish, and L. Wang, “Expanding the genetic code for biological studies,” Chemistry and Biology, vol. 16, no. 3, pp. 323–336, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. L. Davis and J. W. Chin, “Designer proteins: applications of genetic code expansion in cell biology,” Nature Reviews Molecular Cell Biology, vol. 13, no. 3, pp. 168–182, 2012. View at Google Scholar
  35. C. C. Liu and P. G. Schultz, “Recombinant expression of selectively sulfated proteins in Escherichia coli,” Nature Biotechnology, vol. 24, no. 11, pp. 1436–1440, 2006. View at Publisher · View at Google Scholar · View at Scopus
  36. H. Neumann, S. Y. Peak-Chew, and J. W. Chin, “Genetically encoding Nε-acetyllysine in recombinant proteins,” Nature Chemical Biology, vol. 4, no. 4, pp. 232–234, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. D. P. Nguyen, M. M. Garcia Alai, P. B. Kapadnis, H. Neumann, and J. W. Chin, “Genetically encoding Nε-methyl-L-lysine in recombinant histones,” Journal of the American Chemical Society, vol. 131, no. 40, pp. 14194–14195, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. D. P. Nguyen, M. M. G. Alai, S. Virdee, and J. W. Chin, “Genetically directing ε-N, N-dimethyl-l-lysine in recombinant histones,” Chemistry and Biology, vol. 17, no. 10, pp. 1072–1076, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. D. Summerer, S. Chen, N. Wu, A. Deiters, J. W. Chin, and P. G. Schultz, “A genetically encoded fluorescent amino acid,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 26, pp. 9785–9789, 2006. View at Publisher · View at Google Scholar · View at Scopus
  40. J. Wang, J. Xie, and P. G. Schultz, “A genetically encoded fluorescent amino acid,” Journal of the American Chemical Society, vol. 128, no. 27, pp. 8738–8739, 2006. View at Publisher · View at Google Scholar · View at Scopus
  41. W. Wang, J. K. Takimoto, G. V. Louie et al., “Genetically encoding unnatural amino acids for cellular and neuronal studies,” Nature Neuroscience, vol. 10, no. 8, pp. 1063–1072, 2007. View at Publisher · View at Google Scholar · View at Scopus
  42. V. K. Lacey, A. R. Parrish, S. Han et al., “A fluorescent reporter of the phosphorylation status of the substrate protein STAT3,” Angewandte Chemie International Edition, vol. 50, no. 37, pp. 8692–8696, 2011. View at Publisher · View at Google Scholar
  43. H. S. Lee, J. Guo, E. A. Lemke, R. D. Dimla, and P. G. Schultz, “Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae,” Journal of the American Chemical Society, vol. 131, no. 36, pp. 12921–12923, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. N. Hino, Y. Okazaki, T. Kobayashi, A. Hayashi, K. Sakamoto, and S. Yokoyama, “Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid,” Nature Methods, vol. 2, no. 3, pp. 201–206, 2005. View at Publisher · View at Google Scholar · View at Scopus
  45. N. Hino, M. Oyama, A. Sato et al., “Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells,” Journal of Molecular Biology, vol. 406, no. 2, pp. 343–353, 2011. View at Publisher · View at Google Scholar · View at Scopus
  46. J. W. Chin, A. B. Martin, D. S. King, L. Wang, and P. G. Schultz, “Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 17, pp. 11020–11024, 2002. View at Publisher · View at Google Scholar · View at Scopus
  47. J. W. Chin, S. W. Santoro, A. B. Martin, D. S. King, L. Wang, and P. G. Schultz, “Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli,” Journal of the American Chemical Society, vol. 124, no. 31, pp. 9026–9027, 2002. View at Publisher · View at Google Scholar · View at Scopus
  48. I. S. Farell, R. Toroney, J. L. Hazen, R. A. Mehl, and J. W. Chin, “Photo-cross-linking interacting proteins with a genetically encoded benzophenone,” Nature Methods, vol. 2, no. 5, pp. 377–384, 2005. View at Publisher · View at Google Scholar · View at Scopus
  49. I. Coin, M. H. Perrin, W. W. Vale, and L. Wang, “Photo-cross-linkers incorporated into G-protein-coupled receptors in mammalian cells: a ligand comparison,” Angewandte Chemie International Edition, vol. 50, no. 35, pp. 8077–8081, 2011. View at Publisher · View at Google Scholar
  50. A. Gautier, D. P. Nguyen, H. Lusic, W. An, A. Deiters, and J. W. Chin, “Genetically encoded photocontrol of protein localization in mammalian cells,” Journal of the American Chemical Society, vol. 132, no. 12, pp. 4086–4088, 2010. View at Publisher · View at Google Scholar · View at Scopus
  51. A. Gautier, A. Deiters, and J. W. Chin, “Light-activated kinases enable temporal dissection of signaling networks in living cells,” Journal of the American Chemical Society, vol. 133, no. 7, pp. 2124–2127, 2011. View at Publisher · View at Google Scholar · View at Scopus
  52. E. Arbely, J. Torres-Kolbus, A. Deiters, and J. W. Chin, “Photocontrol of tyrosine phosphorylation in mammalian cells via genetic encoding of photocaged tyrosine,” Journal of the American Chemical Society, vol. 134, no. 29, pp. 11912–11915, 2012. View at Publisher · View at Google Scholar
  53. N. Wu, A. Deiters, T. A. Cropp, D. King, and P. G. Schultz, “A genetically encoded photocaged amino acid,” Journal of the American Chemical Society, vol. 126, no. 44, pp. 14306–14307, 2004. View at Publisher · View at Google Scholar · View at Scopus
  54. A. Deiters, D. Groff, Y. Ryu, J. Xie, and P. G. Schultz, “A genetically encoded photocaged tyrosine,” Angewandte Chemie, vol. 45, no. 17, pp. 2728–2731, 2006. View at Publisher · View at Google Scholar · View at Scopus
  55. E. A. Lemke, D. Summerer, B. H. Geierstanger, S. M. Brittain, and P. G. Schultz, “Control of protein phosphorylation with a genetically encoded photocaged amino acid,” Nature Chemical Biology, vol. 3, no. 12, pp. 769–772, 2007. View at Publisher · View at Google Scholar · View at Scopus
  56. Y. S. Wang, B. Wu, Z. Wang et al., “A genetically encoded photocaged Nepsilon-methyl-L-lysine,” Molecular bioSystems, vol. 6, no. 9, pp. 1557–1560, 2010. View at Google Scholar · View at Scopus
  57. T. Yanagisawa, R. Ishii, R. Fukunaga, T. Kobayashi, K. Sakamoto, and S. Yokoyama, “Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode Nε-(o-Azidobenzyloxycarbonyl) lysine for site-specific protein modification,” Chemistry and Biology, vol. 15, no. 11, pp. 1187–1197, 2008. View at Publisher · View at Google Scholar · View at Scopus
  58. D. P. Nguyen, H. Lusic, H. Neumann, P. B. Kapadnis, A. Deiters, and J. W. Chin, “Genetic encoding and labeling of aliphatic azides and alkynes in recombinant proteins via a pyrrolysyl-tRNA synthetase/tRNACUA pair and click chemistry,” Journal of the American Chemical Society, vol. 131, no. 25, pp. 8720–8721, 2009. View at Publisher · View at Google Scholar · View at Scopus
  59. D. P. Nguyen, T. Elliott, M. Holt, T. W. Muir, and J. W. Chin, “Genetically encoded 1,2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation,” Journal of the American Chemical Society, vol. 133, no. 30, pp. 11418–11421, 2011. View at Publisher · View at Google Scholar · View at Scopus
  60. S. Virdee, P. B. Kapadnis, T. Elliott et al., “Traceless and site-specific ubiquitination of recombinant proteins,” Journal of the American Chemical Society, vol. 133, no. 28, pp. 10708–10711, 2011. View at Publisher · View at Google Scholar · View at Scopus
  61. K. Lang, L. Davis, J. Torres-Kolbus, C. Chou, A. Deiters, and J. W. Chin, “Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction,” Nature Chemistry, vol. 4, no. 4, pp. 298–304, 2012. View at Publisher · View at Google Scholar
  62. K. Lang, L. Davis, S. Wallace et al., “Genetic encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic diels-alder reactions,” Journal of the American Chemical Society, vol. 134, no. 25, pp. 10317–10320, 2012. View at Publisher · View at Google Scholar
  63. J. L. Seitchik, J. C. Peeler, M. T. Taylor et al., “Genetically encoded tetrazine amino acid directs rapid site-specific in vivo bioorthogonal ligation with trans-cyclooctenes,” Journal of the American Chemical Society, vol. 134, no. 6, pp. 2898–2901, 2012. View at Publisher · View at Google Scholar
  64. C. Köhrer, E. L. Sullivan, and U. L. RajBhandary, “Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: concomitant suppression of three different termination codons in an mRNA in mammalian cells,” Nucleic Acids Research, vol. 32, no. 21, pp. 6200–6211, 2004. View at Publisher · View at Google Scholar · View at Scopus
  65. Z. Zhang, L. Alfonta, F. Tian et al., “Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 24, pp. 8882–8887, 2004. View at Publisher · View at Google Scholar · View at Scopus
  66. W. Wan, Y. Huang, Z. Wang et al., “A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli,” Angewandte Chemie, vol. 49, no. 18, pp. 3211–3214, 2010. View at Publisher · View at Google Scholar · View at Scopus
  67. J. C. Anderson, N. Wu, S. W. Santoro, V. Lakshman, D. S. King, and P. G. Schultz, “An expanded genetic code with a functional quadruplet codon,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 20, pp. 7566–7571, 2004. View at Publisher · View at Google Scholar · View at Scopus
  68. H. Neumann, K. Wang, L. Davis, M. Garcia-Alai, and J. W. Chin, “Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome,” Nature, vol. 464, no. 7287, pp. 441–444, 2010. View at Publisher · View at Google Scholar · View at Scopus
  69. T. S. Young, D. D. Young, I. Ahmad, J. M. Louis, S. J. Benkovic, and P. G. Schultz, “Evolution of cyclic peptide protease inhibitors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 27, pp. 11052–11056, 2011. View at Publisher · View at Google Scholar · View at Scopus
  70. C. P. Scott, E. Abel-Santos, M. Wall, D. C. Wahnon, and S. J. Benkovic, “Production of cyclic peptides and proteins in vivo,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 24, pp. 13638–13643, 1999. View at Publisher · View at Google Scholar · View at Scopus
  71. A. R. Horswill and S. J. Benkovic, “Cyclic peptides, a chemical genetics tool for biologists,” Cell Cycle, vol. 4, no. 4, pp. 552–555, 2005. View at Google Scholar · View at Scopus
  72. S. Li, S. Millward, and R. Roberts, “In vitro selection of mRNA display libraries containing an unnatural amino acid,” Journal of the American Chemical Society, vol. 124, no. 34, pp. 9972–9973, 2002. View at Publisher · View at Google Scholar · View at Scopus
  73. A. Frankel, S. Li, S. R. Starck, and R. W. Roberts, “Unnatural RNA display libraries,” Current Opinion in Structural Biology, vol. 13, no. 4, pp. 506–512, 2003. View at Publisher · View at Google Scholar · View at Scopus
  74. S. W. Millward, S. Fiacco, R. J. Austin, and R. W. Roberts, “Design of cyclic peptides that bind protein surfaces with antibody-like affinity,” ACS Chemical Biology, vol. 2, no. 9, pp. 625–634, 2007. View at Publisher · View at Google Scholar · View at Scopus
  75. N. Muranaka, T. Hohsaka, and M. Sisido, “Four-base codon mediated mRNA display to construct peptide libraries that contain multiple nonnatural amino acids,” Nucleic Acids Research, vol. 34, no. 1, p. e7, 2006. View at Publisher · View at Google Scholar · View at Scopus
  76. K. Wang, H. Neumann, S. Y. Peak-Chew, and J. W. Chin, “Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion,” Nature Biotechnology, vol. 25, no. 7, pp. 770–777, 2007. View at Publisher · View at Google Scholar · View at Scopus
  77. Y. Huang, W. K. Russell, W. Wan, P. J. Pai, D. H. Russell, and W. Liu, “A convenient method for genetic incorporation of multiple noncanonical amino acids into one protein in Escherichia coli,” Molecular BioSystems, vol. 6, no. 4, pp. 683–686, 2010. View at Publisher · View at Google Scholar · View at Scopus
  78. T. Mukai, A. Hayashi, F. Iraha et al., “Codon reassignment in the Escherichia coli genetic code,” Nucleic Acids Research, vol. 38, no. 22, pp. 8188–8195, 2010. View at Publisher · View at Google Scholar · View at Scopus
  79. T. Mukai, T. Yanagisawa, K. Ohtake et al., “Genetic-code evolution for protein synthesis with non-natural amino acids,” Biochemical and Biophysical Research Communications, vol. 411, no. 4, pp. 757–761, 2011. View at Publisher · View at Google Scholar
  80. K. Ohtake, A. Sato, T. Mukai, N. Hino, S. Yokoyama, and K. Sakamoto, “Efficient decoding of the UAG triplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli,” Journal of Bacteriology, vol. 194, no. 10, pp. 2606–2613, 2012. View at Google Scholar
  81. D. B. Johnson, J. Xu, Z. Shen et al., “RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites,” Nature Chemical Biology, vol. 7, no. 11, pp. 779–786, 2011. View at Publisher · View at Google Scholar
  82. D. B. Johnson, C. Wang, J. Xu et al., “Release factor one is nonessential in Escherichia coli,” ACS Chemical Biology, vol. 7, no. 8, pp. 1337–1344, 2012. View at Publisher · View at Google Scholar
  83. F. J. Isaacs, P. A. Carr, H. H. Wang et al., “Precise manipulation of chromosomes in vivo enables genome-wide codon replacement,” Science, vol. 333, no. 6040, pp. 348–353, 2011. View at Publisher · View at Google Scholar · View at Scopus
  84. G. F. Short III, S. Y. Golovine, and S. M. Hecht, “Effects of release factor 1 on in vitro protein translation and the elaboration of proteins containing unnatural amino acids,” Biochemistry, vol. 38, no. 27, pp. 8808–8819, 1999. View at Publisher · View at Google Scholar · View at Scopus
  85. S. Sando, A. Ogawa, T. Nishi, M. Hayami, and Y. Aoyama, “In vitro selection of RNA aptamer against Escherichia coli release factor 1,” Bioorganic and Medicinal Chemistry Letters, vol. 17, no. 5, pp. 1216–1220, 2007. View at Publisher · View at Google Scholar · View at Scopus
  86. M. Humenik, Y. Huang, I. Safronov, and M. Sprinzl, “Simultaneous and site-directed incorporation of an ester linkage and an azide group into a polypeptide by in vitro translation,” Organic and Biomolecular Chemistry, vol. 7, no. 20, pp. 4218–4224, 2009. View at Publisher · View at Google Scholar · View at Scopus
  87. S. Sando, K. Kanatani, N. Sato, H. Matsumoto, T. Hohsaka, and Y. Aoyama, “A small-molecule-based approach to sense codon-templated natural-unnatural hybrid peptides. Selective silencing and reassignment of the sense codon by orthogonal reacylation stalling at the single-codon level,” Journal of the American Chemical Society, vol. 127, no. 22, pp. 7998–7999, 2005. View at Publisher · View at Google Scholar · View at Scopus
  88. A. C. Forster, Z. Tan, M. N. L. Nalam et al., “Programming peptidomimetic syntheses by translating genetic codes designed de novo,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 11, pp. 6353–6357, 2003. View at Publisher · View at Google Scholar · View at Scopus
  89. B. Zhang, Z. Tan, L. G. Dickson, M. N. L. Nalam, V. W. Cornish, and A. C. Forster, “Specificity of translation for N-alkyl amino acids,” Journal of the American Chemical Society, vol. 129, no. 37, pp. 11316–11317, 2007. View at Publisher · View at Google Scholar · View at Scopus
  90. A. C. Forster, “Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome,” Nucleic Acids Research, vol. 37, no. 11, pp. 3747–3755, 2009. View at Publisher · View at Google Scholar · View at Scopus
  91. R. Gao and A. C. Forster, “Changeability of individual domains of an aminoacyl-tRNA in polymerization by the ribosome,” FEBS Letters, vol. 584, no. 1, pp. 99–105, 2010. View at Publisher · View at Google Scholar · View at Scopus
  92. A. C. Forster, “Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription,” Biotechnology Journal, vol. 7, no. 7, pp. 835–845, 2012. View at Publisher · View at Google Scholar
  93. K. Josephson, M. C. T. Hartman, and J. W. Szostak, “Ribosomal synthesis of unnatural peptides,” Journal of the American Chemical Society, vol. 127, no. 33, pp. 11727–11735, 2005. View at Publisher · View at Google Scholar · View at Scopus
  94. H. Koide, S. Yokoyama, G. Kawai et al., “Biosynthesis of a protein containing a nonprotein amino acid by Escherichia coli: L-2-aminohexanoic acid at position 21 in human epidermal growth factor,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 17, pp. 6237–6241, 1988. View at Google Scholar · View at Scopus
  95. N. Budisa, “Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire,” Angewandte Chemie, vol. 43, no. 47, pp. 6426–6463, 2004. View at Publisher · View at Google Scholar · View at Scopus
  96. T. L. Hendrickson, V. De Crécy-Lagard, and P. Schimmel, “Incorporation of nonnatural amino acids into proteins,” Annual Review of Biochemistry, vol. 73, pp. 147–176, 2004. View at Publisher · View at Google Scholar · View at Scopus
  97. J. A. Johnson, Y. Y. Lu, J. A. Van Deventer, and D. A. Tirrell, “Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications,” Current Opinion in Chemical Biology, vol. 14, no. 6, pp. 774–780, 2010. View at Publisher · View at Google Scholar · View at Scopus
  98. Y. Shimizu, A. Inoue, Y. Tomari et al., “Cell-free translation reconstituted with purified components,” Nature Biotechnology, vol. 19, no. 8, pp. 751–755, 2001. View at Publisher · View at Google Scholar · View at Scopus
  99. M. C. T. Hartman, K. Josephson, and J. W. Szostak, “Enzymatic aminoacylation of tRNA with unnatural amino acids,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 12, pp. 4356–4361, 2006. View at Publisher · View at Google Scholar · View at Scopus
  100. M. C. Hartman, K. Josephson, C. W. Lin, and J. W. Szostak, “An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides,” PLoS ONE, vol. 2, no. 10, p. e972, 2007. View at Publisher · View at Google Scholar · View at Scopus
  101. H. Murakami, A. Ohta, H. Ashigai, and H. Suga, “A highly flexible tRNA acylation method for non-natural polypeptide synthesis,” Nature Methods, vol. 3, no. 5, pp. 357–359, 2006. View at Publisher · View at Google Scholar · View at Scopus
  102. H. Saito, D. Kourouklis, and H. Suga, “An in vitro evolved precursor tRNA with aminoacylation activity,” EMBO Journal, vol. 20, no. 7, pp. 1797–1806, 2001. View at Publisher · View at Google Scholar · View at Scopus
  103. H. Murakami, H. Saito, and H. Suga, “A versatile tRNA aminoacylation catalyst based on RNA,” Chemistry and Biology, vol. 10, no. 7, pp. 655–662, 2003. View at Publisher · View at Google Scholar · View at Scopus
  104. H. Xiao, H. Murakami, H. Suga, and A. R. Ferré-D'Amaré, “Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme,” Nature, vol. 454, no. 7202, pp. 358–361, 2008. View at Publisher · View at Google Scholar · View at Scopus
  105. M. Ohuchi, H. Murakami, and H. Suga, “The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus,” Current Opinion in Chemical Biology, vol. 11, no. 5, pp. 537–542, 2007. View at Publisher · View at Google Scholar · View at Scopus
  106. J. Morimoto, Y. Hayashi, K. Iwasaki, and H. Suga, “Flexizymes: their evolutionary history and the origin of catalytic function,” Accounts of Chemical Research, vol. 44, no. 12, pp. 1359–1368, 2011. View at Publisher · View at Google Scholar
  107. T. J. Kang, S. Yuzawa, and H. Suga, “Expression of histone H3 tails with combinatorial lysine modifications under the reprogrammed genetic code for the investigation on epigenetic markers,” Chemistry and Biology, vol. 15, no. 11, pp. 1166–1174, 2008. View at Publisher · View at Google Scholar · View at Scopus
  108. Y. Sako, J. Morimoto, H. Murakami, and H. Suga, “Ribosomal synthesis of bicyclic peptides via two orthogonal inter-side-chain reactions,” Journal of the American Chemical Society, vol. 130, no. 23, pp. 7232–7234, 2008. View at Publisher · View at Google Scholar · View at Scopus
  109. E. Nakajima, Y. Goto, Y. Sako, H. Murakami, and H. Suga, “Ribosomal synthesis of peptides with C-terminal lactams, thiolactones, and alkylamides,” ChemBioChem, vol. 10, no. 7, pp. 1186–1192, 2009. View at Publisher · View at Google Scholar · View at Scopus
  110. Y. Yamagshi, H. Ahigai, Y. Goto, H. Murakami, and H. Suga, “Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction,” ChemBioChem, vol. 10, no. 9, pp. 1469–1472, 2009. View at Publisher · View at Google Scholar · View at Scopus
  111. Y. Goto, K. Iwasaki, K. Torikai, H. Murakami, and H. Suga, “Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides,” Chemical Communications, no. 23, pp. 3419–3421, 2009. View at Publisher · View at Google Scholar · View at Scopus
  112. T. Kawakami, H. Murakami, and H. Suga, “Messenger RNA-programmed incorporation of multiple N-Methyl-Amino acids into linear and cyclic peptides,” Chemistry and Biology, vol. 15, no. 1, pp. 32–42, 2008. View at Publisher · View at Google Scholar · View at Scopus
  113. T. Kawakami, H. Murakami, and H. Suga, “Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids,” Journal of the American Chemical Society, vol. 130, no. 50, pp. 16861–16863, 2008. View at Publisher · View at Google Scholar · View at Scopus
  114. T. Kawakami, A. Ohta, M. Ohuchi, H. Ashigai, H. Murakami, and H. Suga, “Diverse backbone-cyclized peptides via codon reprogramming,” Nature Chemical Biology, vol. 5, no. 12, pp. 888–890, 2009. View at Publisher · View at Google Scholar · View at Scopus
  115. Y. Goto, A. Ohta, Y. Sako, Y. Yamagishi, H. Murakami, and H. Suga, “Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides,” ACS Chemical Biology, vol. 3, no. 2, pp. 120–129, 2008. View at Publisher · View at Google Scholar · View at Scopus
  116. Y. Goto, H. Murakami, and H. Suga, “Initiating translation with D-amino acids,” RNA, vol. 14, no. 7, pp. 1390–1398, 2008. View at Publisher · View at Google Scholar · View at Scopus
  117. Y. Goto and H. Suga, “Translation initiation with initiator tRNA charged with exotic peptides,” Journal of the American Chemical Society, vol. 131, no. 14, pp. 5040–5041, 2009. View at Publisher · View at Google Scholar · View at Scopus
  118. Y. Ohshiro, E. Nakajima, Y. Goto et al., “Ribosomal synthesis of backbone-macrocyclic peptides containing γ-amino acids,” ChemBioChem, vol. 12, no. 8, pp. 1183–1187, 2011. View at Publisher · View at Google Scholar · View at Scopus
  119. A. Ohta, H. Murakami, E. Higashimura, and H. Suga, “Synthesis of polyester by means of genetic code reprogramming,” Chemistry and Biology, vol. 14, no. 12, pp. 1315–1322, 2007. View at Publisher · View at Google Scholar · View at Scopus
  120. A. Ohta, H. Murakami, and H. Suga, “Polymerization of alpha-hydroxy acids by ribosomes,” Chembiochem, vol. 9, no. 17, pp. 2773–2778, 2008. View at Publisher · View at Google Scholar · View at Scopus
  121. P. R. Effraim, J. Wang, M. T. Englander et al., “Natural amino acids do not require their native tRNAs for efficient selection by the ribosome,” Nature Chemical Biology, vol. 5, no. 12, pp. 947–953, 2009. View at Publisher · View at Google Scholar · View at Scopus
  122. A. C. Forster, V. W. Cornish, and S. C. Blacklow, “Pure translation display,” Analytical Biochemistry, vol. 333, no. 2, pp. 358–364, 2004. View at Publisher · View at Google Scholar · View at Scopus
  123. C. J. Hipolito and H. Suga, “Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems,” Current Opinion in Chemical Biology, vol. 16, no. 1-2, pp. 196–203, 2012. View at Publisher · View at Google Scholar
  124. A. Ohta, Y. Yamagishi, and H. Suga, “Synthesis of biopolymers using genetic code reprogramming,” Current Opinion in Chemical Biology, vol. 12, no. 2, pp. 159–167, 2008. View at Publisher · View at Google Scholar · View at Scopus
  125. K. Iwasaki, Y. Goto, T. Katoh, and H. Suga, “Selective thioether macrocyclization of peptides having the N-terminal 2-chloroacetyl group and competing two or three cysteine residues in translation,” Organic & Biomolecular Chemistry, vol. 10, no. 30, pp. 5783–5786, 2012. View at Google Scholar
  126. Y. Hayashi, J. Morimoto, and H. Suga, “In vitro selection of Anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors,” ACS Chemical Biology, vol. 7, no. 3, pp. 607–613, 2012. View at Publisher · View at Google Scholar
  127. J. Morimoto, Y. Hayashi, and H. Suga, “Discovery of macrocyclic peptides armed with a mechanism-based warhead: isoform-selective inhibition of human deacetylase SIRT2,” Angewandte Chemie, vol. 51, no. 14, pp. 3423–3427, 2012. View at Publisher · View at Google Scholar
  128. Y. V. Guillen Schlippe, M. C. Hartman, K. Josephson, and J. W. Szostak, “In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors,” Journal of the American Chemical Society, vol. 134, no. 25, pp. 10469–10477, 2012. View at Publisher · View at Google Scholar
  129. F. T. Hofmann, J. W. Szostak, and F. P. Seebeck, “In vitro selection of functional lantipeptides,” Journal of the American Chemical Society, vol. 134, no. 19, pp. 8038–8041, 2012. View at Publisher · View at Google Scholar
  130. F. P. Seebeck and J. W. Szostak, “Ribosomal synthesis of dehydroalanine-containing peptides,” Journal of the American Chemical Society, vol. 128, no. 22, pp. 7150–7151, 2006. View at Publisher · View at Google Scholar · View at Scopus
  131. F. P. Seebeck, A. Ricardo, and J. W. Szostak, “Artificial lantipeptides from in vitro translations,” Chemical Communications, vol. 47, no. 21, pp. 6141–6143, 2011. View at Publisher · View at Google Scholar · View at Scopus
  132. V. W. Cornish, D. Mendel, and P. G. Schultz, “Probing protein structure and function with an expanded genetic code,” Angewandte Chemie, vol. 34, no. 6, pp. 621–633, 1995. View at Google Scholar · View at Scopus
  133. Z. Tan, A. C. Forster, S. C. Blacklow, and V. W. Cornish, “Amino acid backbone specificity of the Escherichia coli translation machinery,” Journal of the American Chemical Society, vol. 126, no. 40, pp. 12752–12753, 2004. View at Google Scholar · View at Scopus
  134. L. M. Dedkova, N. E. Fahmi, S. Y. Golovine, and S. M. Hecht, “Enhanced D-amino acid incorporation into protein by modified ribosomes,” Journal of the American Chemical Society, vol. 125, no. 22, pp. 6616–6617, 2003. View at Publisher · View at Google Scholar · View at Scopus
  135. L. M. Dedkova, N. E. Fahmi, S. Y. Golovine, and S. M. Hecht, “Construction of modified ribosomes for incorporation of D-amino acids into proteins,” Biochemistry, vol. 45, no. 51, pp. 15541–15551, 2006. View at Publisher · View at Google Scholar · View at Scopus
  136. L. M. Dedkova, N. E. Fahmi, R. Paul et al., “beta-Puromycin selection of modified ribosomes for in vitro incorporation of beta-amino acids,” Biochemistry, vol. 51, no. 1, pp. 401–415, 2012. View at Publisher · View at Google Scholar
  137. Y. Doi, T. Ohtsuki, Y. Shimizu, T. Ueda, and M. Sisido, “Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system,” Journal of the American Chemical Society, vol. 129, no. 46, pp. 14458–14462, 2007. View at Publisher · View at Google Scholar · View at Scopus
  138. H. S. Park, M. J. Hohn, T. Umehara et al., “Expanding the genetic code of Escherichia coli with phosphoserine,” Science, vol. 333, no. 6046, pp. 1151–1154, 2011. View at Publisher · View at Google Scholar
  139. T. J. Magliery, J. C. Anderson, and P. G. Schultz, “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,” Journal of Molecular Biology, vol. 307, no. 3, pp. 755–769, 2001. View at Publisher · View at Google Scholar · View at Scopus
  140. H. Taira, T. Hohsaka, and M. Sisido, “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 Research, vol. 34, no. 5, article e44, 2006. View at Publisher · View at Google Scholar · View at Scopus
  141. J. Guo, C. E. Melançon, H. S. Lee, D. Groff, and P. G. Schultz, “Evolution of amber suppressor tRNAs for efficient bacterial production of proteins containing nonnatural amino acids,” Angewandte Chemie, vol. 48, no. 48, pp. 9148–9151, 2009. View at Publisher · View at Google Scholar · View at Scopus
  142. A. O. Subtelny, M. C. T. Hartman, and J. W. Szostak, “Ribosomal synthesis of N-methyl peptides,” Journal of the American Chemical Society, vol. 130, no. 19, pp. 6131–6136, 2008. View at Publisher · View at Google Scholar · View at Scopus
  143. A. O. Subtelny, M. C. T. Hartman, and J. W. Szostak, “Optimal codon choice can improve the efficiency and fidelity of N-methyl amino acid incorporation into peptides by in-vitro translation,” Angewandte Chemie, vol. 50, no. 14, pp. 3164–3167, 2011. View at Publisher · View at Google Scholar · View at Scopus
  144. R. Odegrip, D. Coomber, B. Eldridge et al., “CIS display: in vitro selection of peptides from libraries of protein-DNA complexes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 9, pp. 2806–2810, 2004. View at Publisher · View at Google Scholar · View at Scopus