全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
PLOS ONE  2007 

An Expanded Set of Amino Acid Analogs for the Ribosomal Translation of Unnatural Peptides

DOI: 10.1371/journal.pone.0000972

Full-Text   Cite this paper   Add to My Lib

Abstract:

Background The application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. The specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. We have previously shown that over 90 unnatural amino acids can be enzymatically loaded onto tRNA. Methodology/Principal Findings We have now used a competition assay to assess the efficiency of tRNA-aminoacylation of these analogs. We have also used a series of peptide translation assays to measure the efficiency with which these analogs are incorporated into peptides. The translation apparatus tolerates most side chain derivatives, a few α,α disubstituted, N-methyl and α-hydroxy derivatives, but no β-amino acids. We show that over 50 unnatural amino acids can be incorporated into peptides by ribosomal translation. Using a set of analogs that are efficiently charged and translated we were able to prepare individual peptides containing up to 13 different unnatural amino acids. Conclusions/Significance Our results demonstrate that a diverse array of unnatural building blocks can be translationally incorporated into peptides. These building blocks provide new opportunities for in vitro selections with highly modified drug-like peptides.

References

[1]  Josephson K, Hartman MCT, Szostak JW (2005) Ribosomal synthesis of unnatural peptides. J Am Chem Soc 127: 11727–11735.
[2]  Forster AC, Weissbach H, Blacklow SC (2001) A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid. Anal Biochem 297: 60–70.
[3]  Forster AC, Tan Z, Nalam MN, Lin H, Qu H, et al. (2003) Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc Natl Acad Sci U S A 100: 6353–6357.
[4]  Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, et al. (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19: 751–755.
[5]  Heckler TG, Chang LH, Zama Y, Naka T, Chorghade MS, et al. (1984) T4 RNA ligase mediated preparation of novel chemically misacylated transfer-RNA Phes. Biochemistry 23: 1468–1473.
[6]  Noren CJ, J. A-CS, Griffith MC, Schultz PG (1989) A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244: 182–188.
[7]  Bain JD, Diala ES, Glabe CG, Dix TA, Chamberlin AR (1989) Biosynthetic site-specific incorporation of a non-natural amino-acid into a polypeptide. J Am Chem Soc 111: 8013–8014.
[8]  Murakami H, Ohta M, Ashigai H, Suga H (2006) A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nat Methods 3: 357–359.
[9]  Ninomiya K, Minohata T, Nishimura M, Sisido M (2004) In situ chemical aminoacylation with amino acid thioesters linked to a peptide nucleic acid. J Am Chem Soc 126: 15984–15989.
[10]  Wang L, Xie J, Schultz PG (2006) Expanding the genetic code. Annu Rev Biophys Biomol Struct 35: 225–249.
[11]  Hartman MCT, Josephson K, Szostak JW (2006) Enzymatic aminoacylation of tRNA with unnatural amino acids. Proc Natl Acad Sci U S A 103: 4356–4361.
[12]  Hohsaka T, Sato K, Sisido M, Takai K, Yokoyama S (1993) Adaptability of nonnatural aromatic amino acids to the active center of the E. coli ribosomal A site. FEBS Lett 335: 47–50.
[13]  Hohsaka T, Kajihara D, Ashizuka Y, Murakami H, Sisido M (1999) Efficient incorporation of nonnatural amino acids with large aromatic groups into streptavidin in in vitro protein synthesizing systems. J Am Chem Soc 121: 34–40.
[14]  Asahara H, Uhlenbeck OC (2005) Predicting the binding affinities of misacylated tRNAs for Thermus thermophilus EF-Tu.GTP. Biochemistry 44: 11254–11261.
[15]  Tan Z, Forster AC, Blacklow SC, Cornish VW (2004) Amino acid backbone specificity of the Escherichia coli translation machinery. J Am Chem Soc 126: 12752–12753.
[16]  Martinez JS, Zhang GP, Holt PD, Jung HT, Carrano CJ, et al. (2000) Self-assembling amphiphilic siderophores from marine bacteria. Science 287: 1245–1247.
[17]  Kilz S, Lenz C, Fuchs R, Budzikiewicz H (1999) A fast screening method for the identification of siderophores from fluorescent Pseudomonas spp. by liquid chromatography/electrospray mass spectrometry. J Mass Spectrom 34: 281–290.
[18]  Lea PJ, Fowden L (1973) Amino acid substrate specificity of asparaginyl-,aspartyl-, and glutaminyl-tRNA synthetase isolated from higher plants. Phytochemistry 12: 1903–1916.
[19]  Levengood J, Ataide SF, Roy H, Ibba M (2004) Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases. J Biol Chem 279: 17707–17714.
[20]  Christner PJ, Rosenbloom J (1971) Effects of incorporation of trans-4,5-dehydrolysine on collagen biosynthesis and extrusion in embryonic chick tibiae. J Biol Chem 246: 7551–7556.
[21]  Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR (2007) Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 3: 44–49.
[22]  Lemeignan B, Sonigo P, Marliere P (1993) Phenotypic suppression by incorporation of an alien amino acid. J Mol Biol 231: 161–166.
[23]  Sabina J, Dover N, Templeton LJ, Smulski DR, Soll D, et al. (2003) Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12. J Bacteriol 185: 6158–6170.
[24]  Hortin G, Boime I (1983) Applications of amino acid analogs for studying co and posttranslational modifications of proteins. Methods Enzymol 96: 777–784.
[25]  Murakami M, Sun Q, Ishida K, Matsuda H, Okino T, et al. (1997) Microviridins, elastase inhibitors from the cyanobacterium Nostoc Minutum (NIES-26). Photochemistry 45: 1197–1202.
[26]  Neal AL, Libman L, Smulson ME (1968) Influence of γ-glutamyl hydrazide on protein synthesis of Pseudomonas aeruginosa. Arch Biochem Biophys 127: 426–428.
[27]  Ahluwalia GS, Grem JL, Hao Z, Cooney DA (1990) Metabolism and action of amino acid analog anti-cancer agents. Pharmacol Ther 46: 243–271.
[28]  Ikeda Y, Kawahara S, Taki M, Kuno A, Hasegawa T, et al. (2003) Synthesis of a novel histidine analogue and its efficient incorporation into a protein in vivo. Protein Eng 16: 699–706.
[29]  Schlesinger S, Schlesinger MJ (1967) The effect of amino acid analogues on alkaline phosphatase formation in Escherichia coli K-12. I. Substitution of triazolealanine for histidine. J Biol Chem 242: 3369–3372.
[30]  Beiboer SH, van den Berg B, Dekker N, Cox RC, Verheij HM (1996) Incorporation of an unnatural amino acid in the active site of porcine pancreatic phospholipase A2. Substitution of histidine by 1,2,4-triazole-3-alanine yields an enzyme with high activity at acidic pH. Protein Eng 9: 345–352.
[31]  Minks C, Alefelder S, Moroder L, Huber R, Budisa N (2000) Towards new protein engineering: in vivo building and folding of protein shuttles for drug delivery and targeting by the selective pressure incorporation (SPI) method. Tetrahedron 56: 9431–9442.
[32]  Kirshenbaum K, Carrico IS, Tirrell DA (2002) Biosynthesis of proteins incorporating a versatile set of phenylalanine analogues. Chembiochem 3: 235–237.
[33]  Budisa N, Alefelder S, Bae JH, Golbik R, Minks C, et al. (2001) Proteins with beta-(thienopyrrolyl)alanines as alternative chromophores and pharmaceutically active amino acids. Protein Sci 10: 1281–1292.
[34]  Hall LE, Hegeman GD, Bosin TR (1974) Incorporation of tryptophan and its benzo(b)thiophene, 1-methylindole, and indene analogs into protein of Escherichia coli. Res Commun Chem Pathol Pharmacol 9: 145–153.
[35]  Cleland TA (1996) Inhibitory glutamate receptor channels. Mol Neurobiol 13: 97–136.
[36]  McLennan H (1983) Receptors for the excitatory amino acids in the mammalian central nervous system. Prog Neurobiol 20: 251–271.
[37]  Bain JD, Wacker DA, Kuo EE, Chamberlin AR (1991) Site-Specific Incorporation of non-natural residues into peptides: Effect of residue structure on suppression and translation efficiencies. Tetrahedron 47: 2389–2400.
[38]  Spizek J, Janacek J (1969) The effect of ethionine on the synthesis of beta galactosidase: formation of an immunologically cross-reacting protein. Biochem Biophys Res Commun 34: 17–21.
[39]  van Hest JCM, Kiick KL, Tirrell DA (2000) Efficient incorporation of unsaturated methionine analogues into proteins in vivo. J Am Chem Soc 122: 1282–1288.
[40]  Kiick KL, Saxon E, Tirrell DA, Bertozzi CR (2002) Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation. Proc Natl Acad Sci U S A 99: 19–24.
[41]  Kiick KL, Weberskirch R, Tirrell DA (2001) Identification of an expanded set of translationally active methionine analogues in Escherichia coli. FEBS Lett 502: 25–30.
[42]  Tang Y, Tirrell DA (2002) Attenuation of the editing activity of the Escerichia coli leucyl-tRNA synthetase allows incorporation of novel amino acids into proteins in vivo. Biochemistry 41: 10635–10645.
[43]  Lincecum TL Jr, Tukalo M, Yaremchuk A, Mursinna RS, Williams AM, et al. (2003) Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase. Mol Cell 11: 951–963.
[44]  Suchanek M, Radzikowska A, Thiele C (2005) Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells. Nat Methods 2: 261–267.
[45]  Busiello V, di Girolamo M, Cini C, De Marco C (1979) Action of thiazolidine-2-carboxylic acid, a proline analog, on protein synthesizing systems. Biochim Biophys Acta 564: 311–321.
[46]  Papas TS, Mehler AH (1970) Analysis of the amino acid binding to the proline transfer ribonucleic acid synthetase of Escherichia coli. J Biol Chem 245: 1588–1595.
[47]  Morris H, Schlesinger MJ (1972) Effects of proline analogues on the formation of alkaline phosphatase in Escherichia coli. J Bacteriol 111: 203–210.
[48]  Fowden L, Neale S, Tristram H (1963) Effect of 3,4-dehydro-DL-proline on growth and protein synthesis. Nature 199: 35–38.
[49]  Deming TJ, Fournier MJ, Mason TL, Tirrell DA (1996) Structural modification of a periodic polypeptide through biosynthetic replacement of proline with azetidine-2-carboxylic acid. Macromolecules 29: 1442–1444.
[50]  Roesser JR, Xu C, Payne RC, Surratt CK, Hecht SM (1989) Preparation of misacylated aminoacyl-tRNA(Phe)'s useful as probes of the ribosomal acceptor site. Biochemistry 28: 5185–5195.
[51]  Ellman JA, Mendel D, Schultz PG (1992) Site-specific incorporation of novel backbone structures into proteins. Science 255: 197–200.
[52]  Heckler TG, Roesser JR, Xu C, Chang PI, Hecht SM (1988) Ribosomal binding and dipeptide formation by misacylated tRNA(Phe)'s. Biochemistry 27: 7254–7262.
[53]  Sando S, Abe K, Sato N, Shibata T, Mizusawa K, et al. (2007) Unexpected preference of the E. coli translation system for the ester bond during incorporation of backbone-elongated substrates. J Am Chem Soc 129: 6180–6186.
[54]  Soutourina J, Plateau P, Blanquet S (2000) Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells. J Biol Chem 275: 32535–32542.
[55]  Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, et al. (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45: 2615–2623.
[56]  Fahnestock S, Rich A (1971) Ribosome-catalyzed polyester formation. Science 173: 340–343.
[57]  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: 11314–11322.
[58]  Millward SW, Takahashi TT, Roberts RW (2005) A general route for post-translational cyclization of mRNA-displayed libraries. J Am Chem Soc 127: 14142–14143.
[59]  Mursinna RS, Lee KW, Briggs JM, Martinis SA (2004) Molecular dissection of a critical specificity determinant within the amino acid editing domain of leucyl-tRNA synthetase. Biochemistry 43: 155–165.
[60]  Sever S, Rogers K, Rogers MJ, Carter C Jr, Soll D (1996) Escherichia coli tryptophanyl-tRNA synthetase mutants selected for tryptophan auxotrophy implicate the dimer interface in optimizing amino acid binding. Biochemistry 35: 32–40.
[61]  Tsao M-L, Summerer D, Ryu Y, Schultz PG (2006) The genetic incorporation of a distance probe into proteins in Escherichia coli. J Am Chem Soc 128: 4572–4573.
[62]  Fahnestock S, Neumann H, Rich A (1974) Assay of ester and polyester formation by the ribosomal peptidyltransferase. Methods Enzymol 30: 489–497.
[63]  Merryman C, Green R (2004) Transformation of aminoacyl tRNAs for the in vitro selection of “drug-like” molecules. Chem Biol 11: 575–582.
[64]  O'Farrell PH (1978) The suppression of defective translation by ppGpp and its role in the stringent response. Cell 14: 545–557.
[65]  Mayer C, Kohrer C, Kenny E, Prusko C, RajBhandary UL (2003) Anticodon sequence mutants of Escherichia coli initiator tRNA: effects of overproduction of aminoacyl-tRNA synthetases, methionyl-tRNA formyltransferase, and initiation factor 2 on activity in initiation. Biochemistry 42: 4787–4799.
[66]  Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A 94: 12297–12302.
[67]  Hanes J, Pluckthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A 94: 4937–4942.
[68]  Mattheakis LC, Bhatt RR, Dower WJ (1994) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci U S A 91: 9022–9026.
[69]  Bemis GW, Murcko MA (1999) Properties of known drugs. 2. Side chains. J Med Chem 42: 5095–5099.
[70]  Schweizer EE, Berninger CJ, Crouse DM, Davis RA, Logothetis RS (1968) Reactions of Phosphorus Compounds. XIX. Reactions of 3-(o-formylphenoxy)propyltriphenylphosph?oniumbromide and 3-(p-formylphenoxy)propyltriphenylphosph?oniumbromide). J Org Chem 34: 207–212.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133