Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adesnik H, Nicoll RA, England PM (2005) Photoinactivation of native AMPA receptors reveals their real-time trafficking. Neuron 48:977–985. doi:10.1016/j.neuron.2005.11.030
Ahern CA, Eastwood AL, Dougherty DA, Horn R (2008) Electrostatic contributions of aromatic residues in the local anesthetic receptor of voltage-gated sodium channels. Circ Res 102:86–94. doi:10.1161/CIRCRESAHA.107.160663
Ai H-W, Shen W, Sagi A et al (2011) Probing protein–protein interactions with a genetically encoded photo-crosslinking amino acid. Chembiochem 12:1854–1857
Amrani N, Sachs MS, Jacobson A (2006) Early nonsense: mRNA decay solves a translational problem. Nat Rev Mol Cell Biol 7:415–425. doi:10.1038/nrm1942
Anderson JC, Schultz PG (2003) Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression. Biochemistry (Mosc) 42:9598–9608. doi:10.1021/bi034550w
Anderson JC, Wu N, Santoro SW et al (2004) An expanded genetic code with a functional quadruplet codon. Proc Natl Acad Sci U S A 101:7566–7571. doi:10.1073/pnas.0401517101
Barrett OPT, Chin JW (2010) Evolved orthogonal ribosome purification for in vitro characterization. Nucleic Acids Res 38:2682–2691. doi:10.1093/nar/gkq120
Beene DL, Brandt GS, Zhong W et al (2002) Cation-pi interactions in ligand recognition by serotonergic (5-HT3A) and nicotinic acetylcholine receptors: the anomalous binding properties of nicotine. Biochemistry (Mosc) 41:10262–10269
Beene DL, Price KL, Lester HA et al (2004) Tyrosine residues that control binding and gating in the 5-hydroxytryptamine3 receptor revealed by unnatural amino acid mutagenesis. J Neurosci Off J Soc Neurosci 24:9097–9104. doi:10.1523/JNEUROSCI.2429-04.2004
Bianco A, Townsley FM, Greiss S et al (2012) Expanding the genetic code of Drosophila melanogaster. Nat Chem Biol 8:748–750. doi:10.1038/nchembio.1043
Blight SK, Larue RC, Mahapatra A et al (2004) Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431:333–335. doi:10.1038/nature02895
Boos D, Kuffer C, Lenobel R et al (2008) Phosphorylation-dependent binding of cyclin B1 to a Cdc6-like domain of human separase. J Biol Chem 283:816–823. doi:10.1074/jbc.M706748200
Braig D, Bar C, Thumfart JO, Koch HG (2009) Two cooperating helices constitute the lipid-binding domain of the bacterial SRP receptor. J Mol Biol 390:401–413. doi:10.1016/j.jmb.2009.04.061
Brick P, Bhat TN, Blow DM (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol 208:83–98
Cashin AL, Torrice MM, McMenimen KA et al (2007) Chemical-scale studies on the role of a conserved aspartate in preorganizing the agonist binding site of the nicotinic acetylcholine receptor. Biochemistry (Mosc) 46:630–639. doi:10.1021/bi061638b
Cellitti SE (2008) In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy. J Am Chem Soc 130:9268–9281. doi:10.1021/ja801602q
Cha A, Bezanilla F (1997) Characterizing voltage-dependent conformational changes in the Shaker K+ channel with fluorescence. Neuron 19:1127–1140
Chang H, Han M, Huang W et al (2013) Light-induced protein translocation by genetically encoded unnatural amino acid in Caenorhabditis elegans. Protein Cell 4:883–886. doi:10.1007/s13238-013-3118-6
Chatterjee A, Xiao H, Schultz PG (2012) Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 109:14841–14846. doi:10.1073/pnas.1212454109
Chatterjee A, Sun SB, Furman JL et al (2013a) A versatile platform for single- and multiple-unnatural amino acid mutagenesis in Escherichia coli. Biochemistry (Mosc) 52:1828–1837. doi:10.1021/bi4000244
Chatterjee A, Xiao H, Yang P-Y et al (2013b) A tryptophanyl-tRNA synthetase/tRNA pair for unnatural amino acid mutagenesis in E. coli. Angew Chem Int Ed Engl 52:5106–5109. doi:10.1002/anie.201301094
Chen S, Schultz P, Brock A (2007) An improved system for the generation and analysis of mutant proteins containing unnatural amino acids in Saccharomyces cerevisiae. J Mol Biol 371:112
Chen PR, Groff D, Guo J et al (2009) A facile system for encoding unnatural amino acids in mammalian cells. Angew Chem Int Ed Engl 48:4052–4055. doi:10.1002/anie.200900683
Chin JW (2003) An expanded eukaryotic genetic code. Science 301:964–967. doi:10.1126/science.1084772
Chin JW, Martin AB, King DS et al (2002a) Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc Natl Acad Sci U S A 99:11020–11024. doi:10.1073/pnas.172226299
Chin JW, Martin AB, King DS et al (2002b) Addition of a photocrosslinking amino acid to the genetic code of Escherichiacoli. Proc Natl Acad Sci U S A 99:11020–11024. doi:10.1073/pnas.172226299
Chin JW, Santoro SW, Martin AB et al (2002c) Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J Am Chem Soc 124:9026–9027
Chin JW, Cropp TA, Chu S et al (2003) Progress toward an expanded eukaryotic genetic code. Chem Biol 10:511–519
Chou C, Uprety R, Davis L et al (2011) Genetically encoding an aliphatic diazirine for protein photocrosslinking. Chem Sci 2:480–483
Cload ST, Liu DR, Froland WA, Schultz PG (1996) Development of improved tRNAs for in vitro biosynthesis of proteins containing unnatural amino acids. Chem Biol 3:1033–1038
Coin I, Perrin MH, Vale WW, Wang L (2011) Photo-cross-linkers incorporated into G-protein-coupled receptors in mammalian cells: a ligand comparison. Angew Chem Int Ed Engl 50:8077–8081. doi:10.1002/anie.201102646
Coin I, Katritch V, Sun T et al (2013) Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. Cell 155:1258–1269. doi:10.1016/j.cell.2013.11.008
Cooley RB, Karplus PA, Mehl RA (2014) Gleaning unexpected fruits from hard-won synthetases: probing principles of permissivity in non-canonical amino acid-tRNA synthetases. Chembiochem Eur J Chem Biol 15:1810–1819. doi:10.1002/cbic.201402180
Cropp TA, Anderson JC, Chin JW (2007) Reprogramming the amino-acid substrate specificity of orthogonal aminoacyl-tRNA synthetases to expand the genetic code of eukaryotic cells. Nat Protoc 2:2590–2600. doi:10.1038/nprot.2007.378
Daggett KA, Sakmar TP (2011) Site-specific in vitro and in vivo incorporation of molecular probes to study G-protein-coupled receptors. Curr Opin Chem Biol 15:392–398. doi:10.1016/j.cbpa.2011.03.010
Davis L, Chin JW (2012) Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 13:168–182. doi:10.1038/nrm3286
Devaraneni PK, Komarov AG, Costantino CA et al (2013) Semisynthetic K+ channels show that the constricted conformation of the selectivity filter is not the C-type inactivated state. Proc Natl Acad Sci 110:15698–15703. doi:10.1073/pnas.1308699110
Dormán G, Prestwich GD (1994) Benzophenone photophores in biochemistry. Biochemistry (Mosc) 33:5661–5673
Dougherty DA (1996) Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science 271:163–168
Dougherty DA, Van Arnam EB (2014) In vivo incorporation of non-canonical amino acids by using the chemical aminoacylation strategy: a broadly applicable mechanistic tool. Chembiochem Eur J Chem Biol 15:1710–1720. doi:10.1002/cbic.201402080
Duca M, Chen S, Hecht SM (2008) Aminoacylation of transfer RNAs with one and two amino acids. Methods San Diego Calif 44:87–99. doi:10.1016/j.ymeth.2007.10.007
Edwards H, Schimmel P (1990) A bacterial amber suppressor in Saccharomyces cerevisiae is selectively recognized by a bacterial aminoacyl-tRNA synthetase. Mol Cell Biol 10:1633
England P, Zhang Y, Dougherty D, Lester H (1999) Backbone mutations in transmembrane domains of a ligand-gated ion channel: implications for the mechanism of gating. Cell 96:89
Farrell IS, Toroney R, Hazen JL et al (2005) Photo-cross-linking interacting proteins with a genetically encoded benzophenone. Nat Methods 2:377–384. doi:10.1038/nmeth0505-377
Fekner T, Li X, Chan MK (2010) Pyrrolysine analogs for translational incorporation into proteins. Eur J Org Chem 2010:4171–4179. doi:10.1002/ejoc.201000204
Furter R (1998a) Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. Protein Sci 7:419
Furter R (1998b) Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. Protein Sci Publ Protein Soc 7:419–426. doi:10.1002/pro.5560070223
Galli G, Hofstetter H, Birnstiel ML (1981) Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature 294:626–631
Gallivan JP, Dougherty DA (1999) Cation-pi interactions in structural biology. Proc Natl Acad Sci U S A 96:9459–9464
Gallivan JP, Dougherty DA (2000) A computational study of cation–p Interactions vs salt bridges in aqueous media: implications for protein engineering. J Am Chem Soc 122:870–874. doi:10.1021/ja991755c
Gautier A (2010) Genetically encoded photocontrol of protein localization in mammalian cells. J Am Chem Soc 132:4086–4088. doi:10.1021/ja910688s
Greiss S, Chin JW (2011) Expanding the genetic code of an animal. J Am Chem Soc 133:14196–14199. doi:10.1021/ja2054034
Grunbeck A, Huber T, Sachdev P, Sakmar TP (2011) Mapping the ligand-binding site on a G protein-coupled receptor (GPCR) using genetically encoded photocrosslinkers. Biochemistry (Mosc) 50:3411–3413. doi:10.1021/bi200214r
Grunbeck A, Huber T, Abrol R et al (2012) Genetically encoded photo-cross-linkers map the binding site of an allosteric drug on a G protein-coupled receptor. ACS Chem Biol 7:967–972. doi:10.1021/cb300059z
Hammill JT, Miyake-Stoner S, Hazen JL et al (2007) Preparation of site-specifically labeled fluorinated proteins for 19F-NMR structural characterization. Nat Protoc 2:2601–2607
Hao B, Gong W, Ferguson TK et al (2002) A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296:1462–1466. doi:10.1126/science.1069556
Haslberger T (2007) M domains couple the ClpB threading motor with the DnaK chaperone activity. Mol Cell 25:247–260. doi:10.1016/j.molcel.2006.11.008
Hecht S, Alford B, Kuroda Y, Kitano S (1978) “Chemical aminoacylation” of tRNA’s. J Biol Chem 253:4517
Hino N, Oyama M, Sato A et al (2011) Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells. J Mol Biol 406:343–353. doi:10.1016/j.jmb.2010.12.022
Hohsaka T, Ashizuka Y, Sisido M (1999) Incorporation of two nonnatural amino acids into proteins through extension of the genetic code. Nucleic Acids Symp Ser 79–80
Hsieh J, Fire A (2000) Recognition and silencing of repeated DNA. Annu Rev Genet 34:187–204. doi:10.1146/annurev.genet.34.1.187
Huang Y, Russell WK, Wan W et al (2010) A convenient method for genetic incorporation of multiple noncanonical amino acids into one protein in Escherichia coli. Mol Biosyst 6:683–686. doi:10.1039/b920120c
Ibba M, Soll D (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69:617–650. doi:10.1146/annurev.biochem.69.1.617
Isaacs FJ, Carr PA, Wang HH et al (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333:348–353. doi:10.1126/science.1205822
James CM, Ferguson TK, Leykam JF, Krzycki JA (2001) The amber codon in the gene encoding the monomethylamine methyltransferase isolated from Methanosarcina barkeri is translated as a sense codon. J Biol Chem 276:34252–34258. doi:10.1074/jbc.M102929200
Johnson DBF, Xu J, Shen Z et al (2011) RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol 7:779–786. doi:10.1038/nchembio.657
Kaiser CM (2006) Real-time observation of trigger factor function on translating ribosomes. Nature 444:455–460. doi:10.1038/nature05225
Kalstrup T, Blunck R (2013) Dynamics of internal pore opening in K(V) channels probed by a fluorescent unnatural amino acid. Proc Natl Acad Sci U S A 110:8272–8277. doi:10.1073/pnas.1220398110
Kang J-Y, Kawaguchi D, Coin I et al (2013) In vivo expression of a light-activatable potassium channel using unnatural amino acids. Neuron 80:358–370. doi:10.1016/j.neuron.2013.08.016
Klippenstein V, Ghisi V, Wietstruk M, Plested AJR (2014) Photoinactivation of glutamate receptors by genetically encoded unnatural amino acids. J Neurosci Off J Soc Neurosci 34:980–991. doi:10.1523/JNEUROSCI.3725–13.2014
Kobayashi T, Nureki O, Ishitani R et al (2003) Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol 10:425
Kowal AK, Kohrer C, RajBhandary UL (2001) Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria. Proc Natl Acad Sci U S A 98:2268–2273. doi:10.1073/pnas.031488298
Krzycki J (2005) The direct genetic encoding of pyrrolysine. Curr Opin Microbiol 8:706
Lajoie MJ, Kosuri S, Mosberg JA et al (2013) Probing the limits of genetic recoding in essential genes. Science 342:361–363. doi:10.1126/science.1241460
Lakshmipathy SK (2007) Identification of nascent chain interaction sites on trigger factor. J Biol Chem 282:12186–12193. doi:10.1074/jbc.M609871200
Lee HS, Guo J, Lemke EA et al (2009) Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae. J Am Chem Soc 131:12921–12923. doi:10.1021/ja904896s
Li W-T, Mahapatra A, Longstaff DG et al (2009) Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs. J Mol Biol 385:1156–1164. doi:10.1016/j.jmb.2008.11.032
Liu C (2010) Coupled chaperone action in folding and assembly of hexadecameric Rubisco. Nature 463:197–202. doi:10.1038/nature08651
Liu CC, Schultz PG (2006) Recombinant expression of selectively sulfated proteins in Escherichia coli. Nat Biotech 24:1436–1440. doi:10.1038/nbt1254
Liu CC, Schultz PG (2010) Adding new chemistries to the genetic code. Annu Rev Biochem 79:413–444. doi:10.1146/annurev.biochem.052308.105824
Liu W, Alfonta L, Mack AV, Schultz PG (2007a) Structural basis for the recognition of para-benzoyl-L-phenylalanine by evolved aminoacyl-tRNA synthetases. Angew Chem Int Ed Engl 46:6073–6075. doi:10.1002/anie.200701990
Liu W, Brock A, Chen S et al (2007b) Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat Methods 4:239
Liu C, Cellitti S, Geierstanger B, Schultz P (2009) Efficient expression of tyrosine-sulfated proteins in E. coli using an expanded genetic code. Nat Protoc 4:1784
Lodder M, Wang B, Hecht SM (2005) The N-pentenoyl protecting group for aminoacyl-tRNAs. Methods San Diego Calif 36:245–251. doi:10.1016/j.ymeth.2005.04.002
Lu T, Ting AY, Mainland J et al (2001) Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter. Nat Neurosci 4:239–246. doi:10.1038/85080
Lummis SCR, Beene D L, Harrison NJ et al (2005) A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor. Chem Biol 12:993–997. doi:10.1016/j.chembiol.2005.06.012
Lummis SCR, McGonigle I, Ashby JA, Dougherty DA (2011) Two amino acid residues contribute to a cation-p binding interaction in the binding site of an insect GABA receptor. J Neurosci Off J Soc Neurosci 31:12371–12376. doi:10.1523/JNEUROSCI.1610–11.2011
Ma JC, Dougherty DA (1997) The Cationminus signpi Interaction. Chem Rev 97:1303–1324
Majmudar CY, Lee LW, Lancia JK et al (2009) Impact of nonnatural amino acid mutagenesis on the in vivo function and binding modes of a transcriptional activator. J Am Chem Soc 131:14240–14242. doi:10.1021/ja904378z
Mannuzzu LM, Moronne MM, Isacoff EY (1996) Direct physical measure of conformational rearrangement underlying potassium channel gating. Science 271:213–216
Maquat LE (2004) Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 5:89–99. doi:10.1038/nrm1310
Matulef K, Komarov AG, Costantino CA, Valiyaveetil FI (2013) Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels. Proc Natl Acad Sci U S A 110:17886–17891. doi:10.1073/pnas.1314356110
Melancon C, Schultz P (2009) One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases. Bioorg Med Chem Lett 19:3845
Mohibullah N, Hahn S (2008) Site-specific cross-linking of TBP in vivo and in vitro reveals a direct functional interaction with the SAGA subunit Spt3. Genes Dev 22:2994–3006. doi:10.1101/gad.1724408
Muir T (2003) Semisynthesis of proteins by expressed protein ligation. Annu Rev Biochem 72:249
Muir TW, Sondhi D, Cole PA (1998) Expressed protein ligation: a general method for protein engineering. Proc Natl Acad Sci U S A 95:6705–6710
Mukai T, Kobayashi T, Hino N et al (2008) Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochem Biophys Res Commun 371:818–822. doi:10.1016/j.bbrc.2008.04.164
Mukai T, Hayashi A, Iraha F et al (2010) Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res 38:8188–8195. doi:10.1093/nar/gkq707
Neumann H (2012) Rewiring translation—Genetic code expansion and its applications. FEBS Lett 586:2057–2064. doi:10.1016/j.febslet.2012.02.002
Neumann H, Slusarczyk AL, Chin JW (2010a) De novo generation of mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. J Am Chem Soc 132:2142–2144. doi:10.1021/ja9068722
Neumann H, Wang K, Davis L et al (2010b) Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464:441–444. doi:10.1038/nature08817
Noren C, Anthony-Cahill S, Griffith M, Schultz P (1989) A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244:182
Nowak MW, Gallivan JP, Silverman SK et al (1998) In vivo incorporation of unnatural amino acids into ion channels in Xenopus oocyte expression system. Methods Enzymol 293:504–529
Ohno S, Yokogawa T, Fujii I et al (1998) Co-expression of yeast amber suppressor tRNATyr and tyrosyl-tRNA synthetase in Escherichia coli: possibility to expand the genetic code. J Biochem (Tokyo) 124:1065–1068
Okuda S, Tokuda H (2009) Model of mouth-to-mouth transfer of bacterial lipoproteins through inner membrane LolC, periplasmic LolA, and outer membrane LolB. Proc Natl Acad Sci U S A 106:5877–5882. doi:10.1073/pnas.0900896106
Padgett CL, Hanek AP, Lester HA et al (2007) Unnatural amino acid mutagenesis of the GABA(A) receptor binding site residues reveals a novel cation-pi interaction between GABA and beta 2Tyr97. J Neurosci Off J Soc Neurosci 27:886–892. doi:10.1523/JNEUROSCI.4791-06.2007
Pantoja R, Rodriguez EA, Dibas MI et al (2009) Single-molecule imaging of a fluorescent unnatural amino acid incorporated into nicotinic receptors. Biophys J 96:226–237. doi:10.1016/j.bpj.2008.09.034
Peeler JC, Mehl RA (2012) Site-specific incorporation of unnatural amino acids as probes for protein conformational changes. Methods Mol Biol Clifton NJ 794:125–134. doi:10.1007/978-1-61779-331-88
Pentelute BL, Kent SBH (2007) Selective desulfurization of cysteine in the presence of Cys(Acm) in polypeptides obtained by native chemical ligation. Org Lett 9:687–690. doi:10.1021/ol0630144
Peters F, Brock A, Wang J, Schultz P (2009) Chem Biol 16:148
Pless SA, Ahern CA (2013) Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences. Annu Rev Pharmacol Toxicol 53:211–229. doi:10.1146/annurev-pharmtox-011112-140343
Pless SA, Millen KS, Hanek AP et al (2008) A cation-pi interaction in the binding site of the glycine receptor is mediated by a phenylalanine residue. J Neurosci Off J Soc Neurosci 28:10937–10942. doi:10.1523/JNEUROSCI.2540-08.2008
Pless SA, Galpin JD, Frankel A, Ahern CA (2011a) Molecular basis for class Ib anti-arrhythmic inhibition of cardiac sodium channels. Nat Commun 2:351. doi:10.1038/ncomms1351
Pless SA, Galpin JD, Niciforovic AP, Ahern CA (2011b) Contributions of counter-charge in a potassium channel voltage-sensor domain. Nat Chem Biol 7:617–623. doi:10.1038/nchembio.622
Pless SA, Hanek AP, Price KL et al (2011c) A cation-p interaction at a phenylalanine residue in the glycine receptor binding site is conserved for different agonists. Mol Pharmacol 79:742–748. doi:10.1124/mol.110.069583
Pless SA, Leung AWY, Galpin JD, Ahern CA (2011d) Contributions of conserved residues at the gating interface of glycine receptors. J Biol Chem 286:35129–35136. doi:10.1074/jbc.M111.269027
Pless SA, Galpin JD, Niciforovic AP et al (2013) Hydrogen bonds as molecular timers for slow inactivation in voltage-gated potassium channels. eLife 2:e01289. doi:10.7554/eLife.01289
Pless SA, Elstone FD, Niciforovic AP et al (2014) Asymmetric functional contributions of acidic and aromatic side chains in sodium channel voltage-sensor domains. J Gen Physiol 143:645–656. doi:10.1085/jgp.201311036
Polycarpo C, Ambrogelly A, Bérubé A et al (2004) An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc Natl Acad Sci U S A 101:12450–12454. doi:10.1073/pnas.0405362101
Polycarpo C, Herring S, Berube A et al (2006) Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase. FEBS Lett 580:6695
Puskar NL, Xiu X, Lester HA, Dougherty DA (2011) Two neuronal nicotinic acetylcholine receptors, alpha4beta4 and alpha7, show differential agonist binding modes. J Biol Chem 286:14618–14627. doi:10.1074/jbc.M110.206565
Rackham O, Chin JW (2005) A network of orthogonal ribosome x mRNA pairs. Nat Chem Biol 1:159–166. doi:10.1038/nchembio719
Rhee H, Lee J-S, Lee J et al (2008) Photolytic control and infrared probing of amide I mode in the dipeptide backbone-caged with the 4,5-dimethoxy-2-nitrobenzyl group. J Phys Chem B 112:2128–2135. doi:10.1021/jp074776z
Robertson SA, Ellman JA, Schultz PG (1991) A general and efficient route for chemical aminoacylation of transfer RNAs. J Am Chem Soc 113:2722–2729. doi:10.1021/ja00007a055
Rodriguez E, Lester H, Dougherty D (2006) In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression. Proc Natl Acad Sci U S A 103:8650
Rodriguez EA, Lester HA, Dougherty DA (2007a) Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 1: minimizing misacylation. RNA N Y N 13:1703–1714. doi:10.1261/rna.666807
Rodriguez EA, Lester HA, Dougherty DA (2007b) Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 2: evaluating suppression efficiency. RNA N Y N 13:1715–1722. doi:10.1261/rna.667607
Rothman DM, Petersson EJ, Vázquez ME et al (2005) Caged phosphoproteins. J Am Chem Soc 127:846–847. doi:10.1021/ja043875c
Rydén SM, Isaksson LA (1984) A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors. Mol Gen Genet MGG 193:38–45
Ryu Y, Schultz PG (2006) Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. Nat Methods 3:263–265. doi:10.1038/nmeth864
Sakamoto K, Hayashi A, Sakamoto A et al (2002) Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 30:4692
Saks M, Sampson J, Nowak M et al (1996) An engineered Tetrahymena tRNAGln for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression. J Biol Chem 271:23169
Santarelli VP, Eastwood AL, Dougherty DA et al (2007) Calcium block of single sodium channels: role of a pore-lining aromatic residue. Biophys J 93:2341–2349. doi:10.1529/biophysj.107.106856
Santoro S, Wang L, Herberich B et al (2002) An efficient system for the evolution of aminoacyl-tRNA synthetase specificity. Nat Biotechnol 20:1044
Santoro SW, Anderson JC, Lakshman V, Schultz PG (2003) An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acids Res 31:6700–6709
Sato S, Mimasu S, Sato A et al (2011) Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid. Biochemistry (Mosc) 50:250–257. doi:10.1021/bi1016183
Schlieker C (2004) Substrate recognition by the AAA+ chaperone ClpB. Nat Struct Mol Biol 11:607–615. doi:10.1038/nsmb787
Shen B, Xiang Z, Miller B et al (2011) Genetically encoding unnatural amino acids in neural stem cells and optically reporting voltage-sensitive domain changes in differentiated neurons. Stem Cells Dayt Ohio 29:1231–1240. doi:10.1002/stem.679
Shiota T, Mabuchi H, Tanaka-Yamano S et al (2011) In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work. Proc Natl Acad Sci U S A 108:15179–15183. doi:10.1073/pnas.1105921108
Sprinzl M, Vassilenko KS (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 33:D139–D140. doi:10.1093/nar/gki012
Sprinzl M, Steegborn C, Hübel F, Steinberg S (1996) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 24:68–72
Srinivasan G, James CM, Krzycki JA (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296:1459–1462. doi:10.1126/science.1069588
Summerer D, Chen S, Wu N et al (2006) A genetically encoded fluorescent amino acid. Proc Natl Acad Sci U S A 103:9785
Takimoto JK, Xiang Z, Kang J-Y, Wang L (2010) Esterification of an unnatural amino acid structurally deviating from canonical amino acids promotes its uptake and incorporation into proteins in mammalian cells. Chembiochem Eur J Chem Biol 11:2268–2272. doi:10.1002/cbic.201000436
Tamura Y, Harada Y, Shiota T et al (2009) Tim23-Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import. J Cell Biol 184:129–141. doi:10.1083/jcb.200808068
Tippmann EM, Liu W, Summerer D et al (2007) A genetically encoded diazirine photocrosslinker in Escherichia coli. Chembiochem 8:2210–2214. doi:10.1002/cbic.200700460
Tracy TE, Yan JJ, Chen L (2011) Acute knockdown of AMPA receptors reveals a trans-synaptic signal for presynaptic maturation. EMBO J 30:1577–1592. doi:10.1038/emboj.2011.59
Umanah G, Huang L-Y, Schultz PG et al (2009) Incorporation of the unnatural amino acid p-benzoyl-L-phenylalanine (Bpa) into a G protein-coupled receptor in its native context. Adv Exp Med Biol 611:333–335
Valiyaveetil FI, MacKinnon R, Muir TW (2002) Semisynthesis and folding of the potassium channel KcsA. J Am Chem Soc 124:9113–9120
Valiyaveetil FI, Leonetti M, Muir TW, Mackinnon R (2006) Ion selectivity in a semisynthetic K + channel locked in the conductive conformation. Science 314:1004–1007. doi:10.1126/science.1133415
Wan W, Huang Y, Wang Z et al (2010) A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli. Angew Chem Int Ed Engl 49:3211–3214. doi:10.1002/anie.201000465
Wang L, Schultz P (2001) A general approach for the generation of orthogonal tRNAs. Chem Biol 8:883
Wang Q, Wang L (2008) New methods enabling efficient incorporation of unnatural amino acids in yeast. J Am Chem Soc 130:6066–6067. doi:10.1021/ja800894n
Wang L, Brock A, Herberich B, Schultz P (2001) Expanding the genetic code of Escherichia coli. Science 292:498
Wang K, Neumann H, Peak-Chew SY, Chin JW (2007a) Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat Biotechnol 25:770–777. doi:10.1038/nbt1314
Wang W, Takimoto J, Louie G et al (2007b) Genetically encoding unnatural amino acids for cellular and neuronal studies. Nat Neurosci 10:1063
Wang HH, Isaacs FJ, Carr PA et al (2009a) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894–898. doi:10.1038/nature08187
Wang Q, Parrish AR, Wang L (2009b) Expanding the genetic code for biological studies. Chem Biol 16:323–336. doi:10.1016/j.chembiol.2009.03.001
Wang K, Sachdeva A, Cox DJ et al (2014) Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat Chem 6:393–403. doi:10.1038/nchem.1919
Wu N, Deiters A, Cropp TA et al (2004) A genetically encoded photocaged amino acid. J Am Chem Soc 126:14306–14307. doi:10.1021/ja040175z
Wu B, Chien EYT, Mol CD et al (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330:1066–1071. doi:10.1126/science.1194396
Xiu X, Puskar NL, Shanata JAP et al (2009) Nicotine binding to brain receptors requires a strong cation-pi interaction. Nature 458:534–537. doi:10.1038/nature07768
Yamano K, Tanaka-Yamano S, Endo T (2010) Tom7 regulates Mdm10-mediated assembly of the mitochondrial import channel protein Tom40. J Biol Chem 285:41222–41231. doi:10.1074/jbc.M110.163238
Ye SX (2010) Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature 464:1386–1389. doi:10.1038/nature08948
Ye SX, Huber T, Vogel R, Sakmar TP (2009) FTIR analysis of GPCR activation using azido probes. Nat Chem Biol 5:397–399. doi:10.1038/nchembio.167
Ye S, Riou M, Carvalho S, Paoletti P (2013) Expanding the genetic code in Xenopus laevis oocytes. Chembiochem Eur J Chem Biol 14:230–235. doi:10.1002/cbic.201200515
Young DD, Young TS, Jahnz M et al (2011) An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity. Biochemistry (Mosc) 50:1894–1900. doi:10.1021/bi101929e
Zacharias N, Dougherty DA (2002) Cation-pi interactions in ligand recognition and catalysis. Trends Pharmacol Sci 23:281–287
Zhang Z, Wang L, Brock A, Schultz P (2002) The selective incorporation of alkenes into proteins in Escherichia coli. Angew Chem Int Ed Engl 41:2840
Zhang Y, Wang L, Schultz PG, Wilson IA (2005) Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. Protein Sci Publ Protein Soc 14:1340–1349. doi:10.1110/ps.041239305
Zhong W, Gallivan JP, Zhang Y et al (1998) From ab initio quantum mechanics to molecular neurobiology: a cation-pi binding site in the nicotinic receptor. Proc Natl Acad Sci U S A 95:12088–12093
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this chapter
Cite this chapter
Leisle, L., Valiyaveetil, F., Mehl, R., Ahern, C. (2015). Incorporation of Non-Canonical Amino Acids. In: Ahern, C., Pless, S. (eds) Novel Chemical Tools to Study Ion Channel Biology. Advances in Experimental Medicine and Biology, vol 869. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2845-3_7
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2845-3_7
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4939-2844-6
Online ISBN: 978-1-4939-2845-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)