Abstract
Recently, it has become possible to reprogram the protein synthesis machinery such that numerous noncanonical amino acids can be translated into target sequences yielding tailor-made proteins. The canonical amino acid tryptophan (Trp) encoded by a single nucleotide triplet (UGG) is a particularly interesting target for protein engineering and design. Trp-residues can be substituted with a variety of analogs and surrogates generated biosynthetically or by organic chemistry. Among them, nitrogen-containing tryptophan analogs occupy a central position, as they have distinct chemical properties in comparison with aliphatic amines and imines. They resemble purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. These special properties of the analogs can be directly transmitted into related protein structures via in vivo ribosome-mediated translation. Proteins expressed in this way are further endowed with unique properties like new spectral, altered redox and titration features or might serve as useful biomaterials. We present and discuss current works and future developments in protein engineering with nitrogen-containing tryptophan analogs and related compounds as well as their relevance for academic and applicative research.
References
Ardell DH, Sella G (2001) On the evolution of redundancy in genetic codes. J Mol Evol 53:269–281
Bae JH, Alefelder S, Kaiser JT, Friedrich R, Moroder L, Huber R, Budisa N (2001) Incorporation of beta-selenolo 3,2-b pyrrolyl-alanine into proteins for phase determination in protein X-ray crystallography. J Mol Biol 309:925–936
Bae JH, Rubini M, Jung G, Wiegand G, Seifert MHJ, Azim MK, Kim JS, Zumbusch A, Holak TA, Moroder L, Huber R, Budisa N (2003) Expansion of the genetic code enables design of a novel “gold” class of green fluorescent proteins. J Mol Biol 328:1071–1081
Baldwin RL (2002) Protein folding—making a network of hydrophobic clusters. Science 295:1657–1658
Bergstrom DE (2004) Orthogonal base pairs continue to evolve. Chem Biol 11:18–20
Brawerman G, Ycas M (1957) Incorporation of the amino acid analog tryptazan into the protein of Escherichia coli. Arch Biochem Biophys 68:112–117
Budisa N (2004) Prolegomena to future efforts on genetic code engineering by expanding its amino acid repertoire. Angew Chem Angew Chem Int Ed 43:3387–3428
Budisa N (2005a) Amino acids and codons—code organisation and protein structure. In: Engineering the genetic code. Wiley, Weinheim, pp 66–90
Budisa N (2005b) A brief history of an expanded amino acid repertoire. In: Engineering the genetic code. Wiley, Weinheim, pp 13–28
Budisa N (2005c) Reprogramming the cellular translation machinery. In: Engineering the genetic code. Wiley, Weinheim, pp 90–184
Budisa N (2005d) Some practical potentials of reprogrammed cellular translation. In: Engineering the genetic code. Wiley, Weinheim, pp 213–261
Budisa N, Pal PP (2004) Designing novel spectral classes of proteins with tryptophan-expanded genetic code. Biol Chem 385:893–904
Budisa N, Minks C, Alefelder S, Wenger W, Dong FM, Moroder L, Huber R (1999) Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire. FASEB J 13:41–51
Budisa N, Alefelder S, Bae JH, Golbik R, Minks C, Huber R, Moroder L (2001) Proteins with beta-(thienopyrrolyl)alanines as alternative chromophores and pharmaceutically active amino acids. Protein Sci 10:1281–1292
Budisa N, Rubini M, Bae JH, Weyher E, Wenger W, Golbik R, Huber R, Moroder L (2002) Global replacement of tryptophan with aminotryptophans generates non-invasive protein-based optical pH sensors. Angew Chem Angew Chem Int Ed 41:4066–4069
Budisa N, Pal PP, Alefelder S, Birle P, Krywcun T, Rubini M, Wenger W, Bae JH, Steiner T (2004a) Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code. Biol Chem 385:191–202
Budisa N, Pipitone O, Slivanowiz I, Rubini M, Pal PP, Holak TA, Huber R, Gelmi ML (2004) Efforts toward the design of ‘Teflon’ proteins: in vivo translation with trifluorinated leucine and methionine analogues. Chem Biodiver 1:1465–1475
Campbell RE, Tour O, Palmer AE, Steinbach PA, Baird DA, Zacharias DA, Tsien RY (2002) A monomeric red fluorescent protein. Proc Natl Acad Sci USA 99:7877–7882
Carter CW (2004) Tryptophanyl-tRNA Synthetase. In: Ibba M, Francklyn C, Cusack S (eds) Aminoacyl-tRNA synthetases. Landes Bioscience, Austin
Chapeville F, Ehrenstein GV, Benzer S, Weisblum B, Ray WJ, Lipmann F (1962) On role of soluble ribonucleic acid in coding for amino acids. Proc Natl Acad Sci USA 48:1086–1092
Cohen GN, Munier R (1959) Effects of structural analogues of amino acids on growth and synthesis of proteins and enzymes in Escherichia coli. Biochim Biophys Acta 31:347–356
Crick FHC (1968) Origin of genetic code. J Mol Biol 38:367–379
Doublie S, Bricogne G, Gilmore C, Carter CW (1995) Tryptophanyl-transfer-Rna synthetase crystal-structure reveals an unexpected homology to tyrosyl-transfer-Rna synthetase. Structure 3:17–31
Dougherty DA (1996) Cation—interactions in chemistry and biology: a new view of Benzene, Phe, Tyr, and Trp. Science 271:163–168
Dryden DFT, Tock MR (2006) DNA mimicry by proteins. Biochem Soc Trans 34(Part 2):317–319
Evans CS, Bell EA (1980) Neuroactive plant amino acids and amines. Trends Neurosci 3:70–72
Ezekiel DH (1965) False feedback inhibition of aromatic amino acid biosynthesis by beta-2-thienylalanine. Biochim Biophys Acta 95:54–62
Hendrickson TL, de Crecy-Lagard V, Schimmel P (2004) Incorporation of nonnatural amino acids into proteins. Ann Rev Biochem 73:147–176
Hirao I, Ohtsuki T, Fujiwara T, Mitsui T, Yokogawa T, Okuni T, Nakayama H, Takio K, Yabuki T, Kigawa T, Kodama K, Nishikawa K, Yokoyama S (2002) An unnatural base pair for incorporating amino acid analogs into proteins. Nat Biotechnol 20:177–182
Hohsaka T, Sisido M (2002) Incorporation of non-natural amino acids into proteins. Curr Opin Chem Biol 6:809–815
Hohsaka T, Sato K, Sisido M, Takai K, Yokoyama S (1993) Adaptability of nonnatural aromatic amino acids to the active center of the Escherichia coli ribosomal A-site. FEBS Lett 335:47–50
Kajihara D, Hohsaka T, Sisido M (2005) Synthesis and sequence optimization of GFP mutants containing aromatic non-natural amino acids at the Tyr66 position. Protein Eng Des Sel 18:273–278
Kishi T, Tanaka M, Tanaka J (1977) Electronic absorption and fluorescence-spectra of 5-hydroxytryptamine (serotonin)—protonation in excited-state. Bull Chem Soc Jpn 50:1267–1271
Koopman G, Reutelingsperger C, Kuijten G, Keehnen R, Pals S, van Oers M (1994) Annexin V for flow cytometric detection of phosphatidylserine expression on B cells undergoing apoptosis. Blood 84:1415–1420
Labas YA, Gurskaya NG, Yanushevich YG, Fradkov AF, Lukyanov KA, Lukyanov SA, Matz MV (2002) Diversity and evolution of the green fluorescent protein family. Proc Natl Acad Sci USA 99:4256–4261
Lakowitz JR (1999) Protein fluorescence. In: Principles of fluorescence spectroscopy. Kluwer/Plenum, New York, pp 445–486
Levitt M, Gerstein M, Huang E, Subbiah S, Tsai J (1997) Protein folding: the endgame. Ann Rev Biochem 66:549–579
Martynov VI, Savitsky AP, Martynova NY, Savitsky PA, Lukyanov KA, Lukyanov SA (2001) Alternative cyclization in GFP-like proteins family. J Biol Chem 276:21012–21016
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
Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ (1996) Crystal structure of the Aequorea victoria green fluorescent protein. Science 273:1392–1395
Palm GJ, Wlodawer A (1999) Spectral variants of green fluorescent protein. In: Green fluorescent protein, vol. 302, pp 378–394
Pardee AB, Shore VG, Prestidge LS (1956) Incorporation of azatryptophan into proteins of bacteria and bacteriophage. Biochim Biophys Acta 21:406–407
Rosenthal G (1982) Plant nonprotein amino and imino acids. Biological, biochemical and toxicological properties. Academic, New York
Ross JBA, Szabo AG, Hogue CWV (1997) Enhancement of protein spectra with tryptophan analogs: fluorescence spectroscopy of protein–protein and protein–nucleic acid interactions. In: Fluorescence spectroscopy, vol 278, pp 151–190
Ross JBA, Rusinova E, Luck LA, Rousslang KW (2000) Spectral enhancement of proteins by in vivo incorporation of tryptophan analogues. In: Lakowitz JR (ed) Trends in fluorescence spectroscopy, vol 6. Plenum, New York
Rubini M, Lepthien S, Golbik R, Budisa N (2006) Aminotryptophan-containing barstar: structure–function tradeoff in protein design and engineering with an expanded genetic code. Proteomics 1764:1147–1158
Schlesinger S, Schlesinger MJ (1967) Effect of amino acid analogues on alkaline phosphatase formation in Escherichia coli K-12: substitution of triazolealanine for histidine. J Biol Chem 242:3369–3378
Shafirovich V, Geacintov NE (2005) Spectroscopic investigations of charge transfer in DNA. In: Wagenknecht HA (ed) Charge transfer in DNA, vol. Wiley, Weinheim, pp 175–193
Shaner NC, Steinbach PA, Tsien RY (2005) A guide to choosing fluorescent proteins. Nat Methods 2:905–909
Shimomura O (1979) Structure of the chromophore of aequorea green fluorescent protein. FEBS Lett 104:220–222
Sinha HK, Dogra SK, Krishnamurthy M (1987) Excited-state and ground-state proton-transfer reactions in 5-aminoindole. Bull Chem Soc Jpn 60:4401–4407
Sonneborn TM (1965) Degeneracy of the genetic code: extent, nature and genetic implications. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic, New York, pp 377–397
Sridevi K, Juneja J, Bhuyan AK, Krishnamoorthy G, Udgaonkar JB (2000) The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain. J Mol Biol 302:479–495
Swanson R, Hoben P, Sumner-Smith M, Uemura H, Watson L, Soll D (1998) Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science 242:1548–1551
Sykes BD, Weingart H, Schlesin M (1974) Fluorotyrosine alkaline-phosphatase from Escherichia coli—preparation, properties, and fluorine-19 nuclear magnetic-resonance spectrum. Proc Natl Acad Sci USA 71:469–473
Szathmary E (2003) Why are there four letters in the genetic alphabet? Nat Rev Genet 4:995–1001
Tang Y, Tirrell DA (2001) Biosynthesis of a highly stable coiled-coil protein containing hexafluoroleucine in an engineered bacterial host. J Am Chem Soc 123:11089–11090
Tidor B, Lee LP (2001) Barstar is electrostatically optimized for tight binding to barnase. Nat Struct Biol 8:73–76
Trinquier G, Sanejouand YH (1998) Which effective property of amino acids is best preserved by the genetic code? Protein Eng 11:153–169
Turesky RJ (2004) The role of genetic polymorphisms in metabolism of carcinogenic heterocyclic aromatic amines. Curr Drug Metab 5:169–180
Twine SM, Szabo AG (2003) Fluorescent amino acid analogs. Methods Enzymol 360:104–127
Vaughan M, Steinberg D (1959) The specificty of protein synthesis. In: Anfinsen CB, Anson ML, Bailey K, Edsall JT (eds) Advances in protein chemistry, vol XIV. Academic, New York and London, pp 116–173
Verkhusha VV, Lukyanov KA (2004) The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins. Nat Biotechnol 22:289–296
Wachter RM, Elsliger MA, Kallio K, Hanson GT, Remington SJ (1998) Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein. Structure 6:1267–1277
Walsh CT (2006) Posttranslational modifications of proteins: expanding nature’s inventory. Roberts, Englewood, Colorado
Weber AL, Miller SL (1981) Reasons for the occurrence of the 20 coded protein amino acids. J Mol Evol 17:273–284
Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC (1966) On fundamental nature and evolution of genetic code. Cold Spring Harbor Symp Quant Biol 31:723–736
Wolfenden R, Radzicka A (1986) How hydrophilic is tryptophan. Trends Biochem Sci 11:69–70
Wong TTF (1998) Evolution of the genetic code. Microbiol Sci 5:174–181
Xu ZJ, Love ML, Ma LYY, Blum M, Bronskill PM, Bernstein J, Grey AA, Hofmann T, Camerman N, Wong JTF (1989) Tryptophanyl-tRNA synthetase from Bacillus subtilis: characterization and role of hydrophobicity in substrate recognition. J Biol Chem 264:4304–4311
Zhang ZW, Alfonta L, Tian F, Bursulaya B, Uryu S, King DS, Schultz PG (2004) Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells. Proc Natl Acad Sci USA 101:8882–8887
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The term noncanonical amino acid refers to an amino acid that does not belong, in contrast to a canonical amino acid, to the genetically encoded, proteinogenic amino acids. The term analog defines a strict isosteric exchange of a canonical/noncanonical amino acid (e.g., tryptophan/azatryptophan), while the term surrogate defines a nonisosteric change (e.g., tryptophan/azulene). Mutant denotes a protein in which the wild-type sequence was changed by site-directed mutagenesis (codon manipulation on the DNA level) within the repertoire of the standard amino acids. Variant denotes a protein in which one or more canonical amino acids derived from a wild-type or a mutant sequence were replaced by a noncanonical one (expanded amino acid repertoire, codon reassignment on the protein translation level).
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Lepthien, S., Wiltschi, B., Bolic, B. et al. In vivo engineering of proteins with nitrogen-containing tryptophan analogs. Appl Microbiol Biotechnol 73, 740–754 (2006). https://doi.org/10.1007/s00253-006-0665-2
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DOI: https://doi.org/10.1007/s00253-006-0665-2