101
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Abstract
Peptidomimetic research is an approach to identify peptide-based drugs designed to mimic structural, conformational, and biological properties of peptides while overcoming their limitations, such as protease instability and poor cell penetration. With recent advances in ribosomal synthesis of peptides containing unnatural amino acids, this technology appears suitable for preparing large structurally diverse libraries of peptidomimetics for drug discovery screening.
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Affiliation(s)
- Roger M Freidinger
- Independent Medicinal Chemistry Consultant 744 Newport Lane, Lansdale, PA 19446 USA.
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102
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A flexizyme that selectively charges amino acids activated by a water-friendly leaving group. Bioorg Med Chem Lett 2009; 19:3892-4. [DOI: 10.1016/j.bmcl.2009.03.114] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/20/2009] [Accepted: 03/25/2009] [Indexed: 11/24/2022]
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103
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Brudno Y, Liu DR. Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers. ACTA ACUST UNITED AC 2009; 16:265-76. [PMID: 19318208 DOI: 10.1016/j.chembiol.2009.02.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/20/2009] [Accepted: 02/16/2009] [Indexed: 12/21/2022]
Abstract
Biological polymers such as nucleic acids and proteins are ubiquitous in living systems, but their ability to address problems beyond those found in nature is constrained by factors such as chemical or biological instability, limited building-block functionality, bioavailability, and immunogenicity. In principle, sequence-defined synthetic polymers based on nonbiological monomers and backbones might overcome these constraints; however, identifying the sequence of a synthetic polymer that possesses a specific desired functional property remains a major challenge. Molecular evolution can rapidly generate functional polymers but requires a means of translating amplifiable templates such as nucleic acids into the polymer being evolved. This review covers recent advances in the enzymatic and nonenzymatic templated polymerization of nonnatural polymers and their potential applications in the directed evolution of sequence-defined synthetic polymers.
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Affiliation(s)
- Yevgeny Brudno
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, 12 Oxford Street, Harvard University, Cambridge, MA 02138, USA
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104
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Nakajima E, Goto Y, Sako Y, Murakami H, Suga H. Ribosomal Synthesis of Peptides with C-Terminal Lactams, Thiolactones, and Alkylamides. Chembiochem 2009; 10:1186-92. [DOI: 10.1002/cbic.200900058] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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105
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Goto Y, Iwasaki K, Torikai K, Murakami H, Suga H. Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. Chem Commun (Camb) 2009:3419-21. [PMID: 19503890 DOI: 10.1039/b904314d] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the ribosomal synthesis of methyllanthionine-containing cyclic peptides involving a site-specific incorporation of vinylglycine under the reprogrammed genetic code, followed by the isomerization of the vinylglycine to dehydrobutyrine, and the subsequent intramolecular Michael addition of a cysteine residue placed at a downstream position of the vinylglycine.
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Affiliation(s)
- Yuki Goto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo 153-8904, Japan
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106
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Forster AC. Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome. Nucleic Acids Res 2009; 37:3747-55. [PMID: 19376831 PMCID: PMC2699524 DOI: 10.1093/nar/gkp240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Aminoacyl-transfer RNAs contain four standardized units: amino acids, an invariant 3′-terminal CCA, trinucleotide anticodons and tRNA bodies. The degree of interchangeability of the three variable modules is poorly understood, despite its role in evolution and the engineering of translation to incorporate unnatural amino acids. Here, a purified translation system is used to investigate effects of various module swaps on the efficiency of multiple ribosomal incorporations of unnatural aminoacyl-tRNA substrates per peptide product. The yields of products containing three to five adjacent l-amino acids with unnatural side chains are low and cannot be improved by optimization or explained simply by any single factor tested. Though combinations of modules that allow quantitative single unnatural incorporations are found readily, finding combinations that enable efficient synthesis of products containing multiple unnatural amino acids is challenging. This implies that assaying multiple, as opposed to single, incorporations per product is a more stringent assay of substrate activity. The unpredictability of most results illustrates the multifactorial nature of substrate recognition and the value of synthetic biology for testing our understanding of translation. Data indicate that the degree of interchangeability of the modules of aminoacyl-tRNAs is low.
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Affiliation(s)
- Anthony C Forster
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, 2222 Pierce Ave., Nashville, TN 37232, USA.
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107
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Goto Y, Suga H. Translation Initiation with Initiator tRNA Charged with Exotic Peptides. J Am Chem Soc 2009; 131:5040-1. [DOI: 10.1021/ja900597d] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuki Goto
- Research Center for Advanced Science and Technology and Department of Advanced Interdisciplinary Studies, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroaki Suga
- Research Center for Advanced Science and Technology and Department of Advanced Interdisciplinary Studies, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
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108
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Mizusawa K, Abe K, Sando S, Aoyama Y. Synthesis of puromycin derivatives with backbone-elongated substrates and associated translation inhibitory activities. Bioorg Med Chem 2009; 17:2381-7. [DOI: 10.1016/j.bmc.2009.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/05/2009] [Accepted: 02/06/2009] [Indexed: 10/21/2022]
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109
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Recognition of non-alpha-amino substrates by pyrrolysyl-tRNA synthetase. J Mol Biol 2008; 385:1352-60. [PMID: 19100747 DOI: 10.1016/j.jmb.2008.11.059] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 11/26/2008] [Indexed: 11/23/2022]
Abstract
Pyrrolysyl-tRNA synthetase (PylRS), an aminoacyl-tRNA synthetase (aaRS) recently found in some methanogenic archaea and bacteria, recognizes an unusually large lysine derivative, L-pyrrolysine, as the substrate, and attaches it to the cognate tRNA (tRNA(Pyl)). The PylRS-tRNA(Pyl) pair interacts with none of the endogenous aaRS-tRNA pairs in Escherichia coli, and thus can be used as a novel aaRS-tRNA pair for genetic code expansion. The crystal structures of the Methanosarcina mazei PylRS revealed that it has a unique, large pocket for amino acid binding, and the wild type M. mazei PylRS recognizes the natural lysine derivative as well as many lysine analogs, including N(epsilon)-(tert-butoxycarbonyl)-L-lysine (Boc-lysine), with diverse side chain sizes and structures. Moreover, the PylRS only loosely recognizes the alpha-amino group of the substrate, whereas most aaRSs, including the structurally and genetically related phenylalanyl-tRNA synthetase (PheRS), strictly recognize the main chain groups of the substrate. We report here that wild type PylRS can recognize substrates with a variety of main-chain alpha-groups: alpha-hydroxyacid, non-alpha-amino-carboxylic acid, N(alpha)-methyl-amino acid, and D-amino acid, each with the same side chain as that of Boc-lysine. In contrast, PheRS recognizes none of these amino acid analogs. By expressing the wild type PylRS and its cognate tRNA(Pyl) in E. coli in the presence of the alpha-hydroxyacid analog of Boc-lysine (Boc-LysOH), the amber codon (UAG) was recoded successfully as Boc-LysOH, and thus an ester bond was site-specifically incorporated into a protein molecule. This PylRS-tRNA(Pyl) pair is expected to expand the backbone diversity of protein molecules produced by both in vivo and in vitro ribosomal translation.
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110
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111
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Kawakami T, Murakami H, Suga H. Ribosomal Synthesis of Polypeptoids and Peptoid−Peptide Hybrids. J Am Chem Soc 2008; 130:16861-3. [DOI: 10.1021/ja806998v] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takashi Kawakami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Murakami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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112
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Goto Y, Murakami H, Suga H. Initiating translation with D-amino acids. RNA (NEW YORK, N.Y.) 2008; 14:1390-8. [PMID: 18515548 PMCID: PMC2441986 DOI: 10.1261/rna.1020708] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/30/2008] [Indexed: 05/19/2023]
Abstract
Here we report experimental evidence that the translation initiation apparatus accepts D-amino acids ((D)aa), as opposed to only L-methionine, as initiators. Nineteen (D)aa, as the stereoisomers to their natural L-amino acids, were charged onto initiator tRNA(fMet)(CAU) using flexizyme technology and tested for initiation in a reconstituted Escherichia coli translation system lacking methionine, i.e., the initiator was reprogrammed from methionine to (D)aa. Remarkably, all (D)aa could initiate translation while the efficiency of initiation depends upon the type of side chain. The peptide product initiated with (D)aa was generally in a nonformylated form, indicating that methionyl-tRNA formyltransferase poorly formylated the corresponding (D)aa-tRNA(fMet)(CAU). Although the inefficient formylation of (D)aa-tRNA(fMet)(CAU) resulted in modest expression of the corresponding peptide, preacetylation of (D)aa-tRNA(fMet)(CAU) dramatically increased expression level, implying that the formylation efficiency is one of the critical determinants of initiation efficiency with (D)aa. Our findings provide not only the experimental evidence that translation initiation tolerates (D)aa, but also a new means for the mRNA-directed synthesis of peptides capped with (D)aa or acyl-(D)aa at the N terminus.
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Affiliation(s)
- Yuki Goto
- Research Center of Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
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113
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Sako Y, Morimoto J, Murakami H, Suga H. Ribosomal synthesis of bicyclic peptides via two orthogonal inter-side-chain reactions. J Am Chem Soc 2008; 130:7232-4. [PMID: 18479111 DOI: 10.1021/ja800953c] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Here we report a new methodology for the synthesis of bicyclic peptides by using a reconstituted cell-free translation system under the reprogrammed genetic code. Cysteine (Cys) and three different nonproteinogenic amino acids, Cab, Aha, and Pgl, were simultaneously incorporated into a peptide chain. The first cyclization occurred between the chloroacetyl group of Cab and the sulfhydryl group in Cys in situ of translation, and the second cyclization on the side chains of Aha-Pgl via Cu(I)-catalyzed azide-alkyne cycloaddition was performed. This offers us a powerful means of mRNA-programmed synthesis of various peptides with uniform bicyclic scaffolds.
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Affiliation(s)
- Yusuke Sako
- Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro, Tokyo 153-8904, Japan
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114
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Sako Y, Goto Y, Murakami H, Suga H. Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond. ACS Chem Biol 2008; 3:241-9. [PMID: 18338852 DOI: 10.1021/cb800010p] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we report a new enabling technology for the synthesis of peptidase-resistant cyclic peptides by means of genetic code reprogramming involving the flexizyme (a tRNA acylation ribozyme) and PURE (a reconstituted cell-free translation) systems. In this work, we have developed a new nonproteinogenic amino acid bearing a chloroacetyl group in the side chain, which forms a physiologically stable thioether bond by intramolecular reaction with the sulfhydryl group of a Cys residue in the peptide chain upon translation. Significantly, this chemistry takes place spontaneously in situ of the translation solution, giving the corresponding cyclic peptides independent of ring sizes. We have used this method to convert human urotensin II, known as a potent vasoconstrictor, to its analogue containing a thioether bond, showing that this new analogue retains biological activity. Moreover, this peptide exhibits remarkable resistance against peptidases under reducing conditions. Thus, this technology offers a new means to accelerate the discovery of therapeutic peptidic drugs.
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Affiliation(s)
- Yusuke Sako
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Yuki Goto
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
| | - Hiroshi Murakami
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
| | - Hiroaki Suga
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo, 113-8656, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
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115
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Abstract
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N-Methyl amino acids (N-Me AAs) are a common component of nonribosomal peptides (NRPs), a class of natural products from which many clinically important therapeutics are obtained. N-Me AAs confer peptides with increased conformational rigidity, membrane permeability, and protease resistance. Hence, these analogues are highly desirable building blocks in the ribosomal synthesis of unnatural peptide libraries, from which functional, NRP-like molecules may be identified. By supplementing a reconstituted Escherichia coli translation system with specifically aminoacylated total tRNA that has been chemically methylated, we have identified three N-Me AAs (N-Me Leu, N-Me Thr, and N-Me Val) that are efficiently incorporated into peptides by the ribosome. Moreover, we have demonstrated the synthesis of peptides containing up to three N-Me AAs, a number comparable to that found in many NRP drugs. With improved incorporation efficiency and translational fidelity, it may be possible to synthesize combinatorial libraries of peptides that contain multiple N-Me AAs. Such libraries could be subjected to in vitro selection methods to identify drug-like, high-affinity ligands for protein targets of interest.
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Affiliation(s)
- Alexander O Subtelny
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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116
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Kang TJ, Suga H. Ribosomal synthesis of nonstandard peptidesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2008; 86:92-9. [DOI: 10.1139/o08-009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
It is well known that standard peptides, which comprise proteinogenic amino acids, can act as specific chemical probes to target proteins with high affinity. Despite this fact, a number of peptide drug leads have been abandoned because of their poor cell permeability and protease instability. On the other hand, nonstandard peptides isolated as natural products often exhibit remarkable pharmaco-behavior and stability in vivo. Although it is likely that numerous nonstandard therapeutic peptides capable of recognizing various targets could have been synthesized, enzymes for nonribosomal peptide syntheses are complex; therefore, it is difficult to engineer such modular enzymes to build nonstandard peptide libraries. Here we describe an emerging technology for the synthesis of nonstandard peptides that employs an integrated system of reconstituted cell-free translation and flexizymes. We summarize the historical background of this technology and discuss its current and future applications to the synthesis of nonstandard peptides and drug discovery.
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Affiliation(s)
- Taek Jin Kang
- Research Center for Advanced Science and Technology, University of Tokyo, 153-8904 Tokyo; and Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 113-8656 Tokyo, Japan
| | - Hiroaki Suga
- Research Center for Advanced Science and Technology, University of Tokyo, 153-8904 Tokyo; and Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 113-8656 Tokyo, Japan
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117
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Ohta A, Yamagishi Y, Suga H. Synthesis of biopolymers using genetic code reprogramming. Curr Opin Chem Biol 2008; 12:159-67. [PMID: 18249198 DOI: 10.1016/j.cbpa.2007.12.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 12/27/2007] [Indexed: 11/25/2022]
Abstract
Genetic code reprogramming is a new emerging methodology that enables us to synthesize non-standard peptides containing multiple non-proteinogenic amino acids using translation machinery. This review describes the historical background of this methodology and what distinguishes it from the classical 'nonsense suppression' methodology, followed by a discussion of recent developments in combining this methodology with other compatible technologies. Specifically, we discuss in detail the combination of genetic code reprogramming with flexizymes, de novo tRNA acylation ribozymes that facilitate the charging process of a variety of non-proteinogenic amino acids onto tRNAs bearing designated anticodons, and summarize some of the recent demonstrations of the synthesis of non-standard peptides with cyclic structure or/and altered backbones employing this technology.
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Affiliation(s)
- Atsushi Ohta
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan
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118
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Research highlights. Nat Chem Biol 2008. [DOI: 10.1038/nchembio0208-95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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119
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Kawakami T, Murakami H, Suga H. Messenger RNA-Programmed Incorporation of Multiple N-Methyl-Amino Acids into Linear and Cyclic Peptides. ACTA ACUST UNITED AC 2008; 15:32-42. [DOI: 10.1016/j.chembiol.2007.12.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 11/25/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
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