XB-ART-51303
Adv Exp Med Biol
2015 Jan 01;869:119-51. doi: 10.1007/978-1-4939-2845-3_7.
Show Gene links
Show Anatomy links
Incorporation of Non-Canonical Amino Acids.
Leisle L
,
Valiyaveetil F
,
Mehl RA
,
Ahern CA
.
???displayArticle.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.
???displayArticle.pubmedLink??? 26381943
???displayArticle.pmcLink??? PMC6005199
???displayArticle.link??? Adv Exp Med Biol
???displayArticle.grants??? [+]
R01 GM106569 NIGMS NIH HHS , R01 GM114653 NIGMS NIH HHS , R21 AR066802 NIAMS NIH HHS , R01 GM087546 NIGMS NIH HHS
Genes referenced: mt-tr trna
References [+] :
Adesnik,
Photoinactivation of native AMPA receptors reveals their real-time trafficking.
2005, Pubmed
Adesnik, Photoinactivation of native AMPA receptors reveals their real-time trafficking. 2005, Pubmed
Ahern, Electrostatic contributions of aromatic residues in the local anesthetic receptor of voltage-gated sodium channels. 2008, Pubmed , Xenbase
Ai, Probing protein-protein interactions with a genetically encoded photo-crosslinking amino acid. 2011, Pubmed
Amrani, Early nonsense: mRNA decay solves a translational problem. 2006, Pubmed
Anderson, Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression. 2003, Pubmed
Anderson, An expanded genetic code with a functional quadruplet codon. 2004, Pubmed
Barrett, Evolved orthogonal ribosome purification for in vitro characterization. 2010, Pubmed
Beene, Cation-pi interactions in ligand recognition by serotonergic (5-HT3A) and nicotinic acetylcholine receptors: the anomalous binding properties of nicotine. 2002, Pubmed , Xenbase
Beene, Tyrosine residues that control binding and gating in the 5-hydroxytryptamine3 receptor revealed by unnatural amino acid mutagenesis. 2004, Pubmed , Xenbase
Bianco, Expanding the genetic code of Drosophila melanogaster. 2012, Pubmed
Blight, Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. 2004, Pubmed
Boos, Phosphorylation-dependent binding of cyclin B1 to a Cdc6-like domain of human separase. 2008, Pubmed
Braig, Two cooperating helices constitute the lipid-binding domain of the bacterial SRP receptor. 2009, Pubmed
Brick, Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. 1989, Pubmed
Cashin, Chemical-scale studies on the role of a conserved aspartate in preorganizing the agonist binding site of the nicotinic acetylcholine receptor. 2007, Pubmed , Xenbase
Cellitti, In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy. 2008, Pubmed
Cha, Characterizing voltage-dependent conformational changes in the Shaker K+ channel with fluorescence. 1997, Pubmed , Xenbase
Chang, Light-induced protein translocation by genetically encoded unnatural amino acid in Caenorhabditis elegans. 2013, Pubmed
Chatterjee, A versatile platform for single- and multiple-unnatural amino acid mutagenesis in Escherichia coli. 2013, Pubmed
Chatterjee, A tryptophanyl-tRNA synthetase/tRNA pair for unnatural amino acid mutagenesis in E. coli. 2013, Pubmed
Chatterjee, Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. 2012, Pubmed
Chen, A facile system for encoding unnatural amino acids in mammalian cells. 2009, Pubmed
Chen, An improved system for the generation and analysis of mutant proteins containing unnatural amino acids in Saccharomyces cerevisiae. 2007, Pubmed
Chin, Addition of a photocrosslinking amino acid to the genetic code of Escherichiacoli. 2002, Pubmed
Chin, An expanded eukaryotic genetic code. 2003, Pubmed
Chin, Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. 2002, Pubmed
Chin, Progress toward an expanded eukaryotic genetic code. 2003, Pubmed
Cload, Development of improved tRNAs for in vitro biosynthesis of proteins containing unnatural amino acids. 1996, Pubmed
Coin, Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. 2013, Pubmed
Coin, Photo-cross-linkers incorporated into G-protein-coupled receptors in mammalian cells: a ligand comparison. 2011, Pubmed
Cooley, Gleaning unexpected fruits from hard-won synthetases: probing principles of permissivity in non-canonical amino acid-tRNA synthetases. 2014, Pubmed
Cropp, Reprogramming the amino-acid substrate specificity of orthogonal aminoacyl-tRNA synthetases to expand the genetic code of eukaryotic cells. 2007, Pubmed
Daggett, Site-specific in vitro and in vivo incorporation of molecular probes to study G-protein-coupled receptors. 2011, Pubmed
Davis, Designer proteins: applications of genetic code expansion in cell biology. 2012, Pubmed
Devaraneni, Semisynthetic K+ channels show that the constricted conformation of the selectivity filter is not the C-type inactivated state. 2013, Pubmed
Dormán, Benzophenone photophores in biochemistry. 1994, Pubmed
Dougherty, Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. 1996, Pubmed
Dougherty, In vivo incorporation of non-canonical amino acids by using the chemical aminoacylation strategy: a broadly applicable mechanistic tool. 2014, Pubmed , Xenbase
Duca, Aminoacylation of transfer RNAs with one and two amino acids. 2008, Pubmed
Edwards, A bacterial amber suppressor in Saccharomyces cerevisiae is selectively recognized by a bacterial aminoacyl-tRNA synthetase. 1990, Pubmed
England, Backbone mutations in transmembrane domains of a ligand-gated ion channel: implications for the mechanism of gating. 1999, Pubmed , Xenbase
Farrell, Photo-cross-linking interacting proteins with a genetically encoded benzophenone. 2005, Pubmed
Furter, Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. 1998, Pubmed
Galli, Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. 1981, Pubmed , Xenbase
Gallivan, Cation-pi interactions in structural biology. 1999, Pubmed
Gautier, Genetically encoded photocontrol of protein localization in mammalian cells. 2010, Pubmed
Greiss, Expanding the genetic code of an animal. 2011, Pubmed
Grunbeck, Mapping the ligand-binding site on a G protein-coupled receptor (GPCR) using genetically encoded photocrosslinkers. 2011, Pubmed
Grunbeck, Genetically encoded photo-cross-linkers map the binding site of an allosteric drug on a G protein-coupled receptor. 2012, Pubmed
Hammill, Preparation of site-specifically labeled fluorinated proteins for 19F-NMR structural characterization. 2007, Pubmed
Hao, A new UAG-encoded residue in the structure of a methanogen methyltransferase. 2002, Pubmed
Haslberger, M domains couple the ClpB threading motor with the DnaK chaperone activity. 2007, Pubmed
Hecht, "Chemical aminoacylation" of tRNA's. 1978, Pubmed
Hino, Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells. 2011, Pubmed
Hohsaka, Incorporation of two nonnatural amino acids into proteins through extension of the genetic code. 1999, Pubmed
Hsieh, Recognition and silencing of repeated DNA. 2000, Pubmed
Huang, A convenient method for genetic incorporation of multiple noncanonical amino acids into one protein in Escherichia coli. 2010, Pubmed
Ibba, Aminoacyl-tRNA synthesis. 2000, Pubmed
Isaacs, Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. 2011, Pubmed
James, The amber codon in the gene encoding the monomethylamine methyltransferase isolated from Methanosarcina barkeri is translated as a sense codon. 2001, Pubmed
Johnson, RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. 2011, Pubmed
Kaiser, Real-time observation of trigger factor function on translating ribosomes. 2006, Pubmed
Kalstrup, Dynamics of internal pore opening in K(V) channels probed by a fluorescent unnatural amino acid. 2013, Pubmed , Xenbase
Kang, In vivo expression of a light-activatable potassium channel using unnatural amino acids. 2013, Pubmed
Klippenstein, Photoinactivation of glutamate receptors by genetically encoded unnatural amino acids. 2014, Pubmed
Kobayashi, Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. 2003, Pubmed
Kowal, 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. 2001, Pubmed
Krzycki, The direct genetic encoding of pyrrolysine. 2005, Pubmed
Lajoie, Probing the limits of genetic recoding in essential genes. 2013, Pubmed
Lakshmipathy, Identification of nascent chain interaction sites on trigger factor. 2007, Pubmed
Lee, Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae. 2009, Pubmed
Li, Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs. 2009, Pubmed
Liu, Recombinant expression of selectively sulfated proteins in Escherichia coli. 2006, Pubmed
Liu, Adding new chemistries to the genetic code. 2010, Pubmed
Liu, Structural basis for the recognition of para-benzoyl-L-phenylalanine by evolved aminoacyl-tRNA synthetases. 2007, Pubmed
Liu, Coupled chaperone action in folding and assembly of hexadecameric Rubisco. 2010, Pubmed
Liu, Efficient expression of tyrosine-sulfated proteins in E. coli using an expanded genetic code. 2009, Pubmed
Liu, Genetic incorporation of unnatural amino acids into proteins in mammalian cells. 2007, Pubmed
Lodder, The N-pentenoyl protecting group for aminoacyl-tRNAs. 2005, Pubmed
Lu, Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter. 2001, Pubmed , Xenbase
Lummis, Two amino acid residues contribute to a cation-π binding interaction in the binding site of an insect GABA receptor. 2011, Pubmed , Xenbase
Lummis, A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor. 2005, Pubmed
Ma, The Cationminus signpi Interaction. 1997, Pubmed
Majmudar, Impact of nonnatural amino acid mutagenesis on the in vivo function and binding modes of a transcriptional activator. 2009, Pubmed
Mannuzzu, Direct physical measure of conformational rearrangement underlying potassium channel gating. 1996, Pubmed , Xenbase
Maquat, Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. 2004, Pubmed
Matulef, Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels. 2013, Pubmed
Melançon, One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases. 2009, Pubmed
Mohibullah, Site-specific cross-linking of TBP in vivo and in vitro reveals a direct functional interaction with the SAGA subunit Spt3. 2008, Pubmed
Muir, Expressed protein ligation: a general method for protein engineering. 1998, Pubmed
Muir, Semisynthesis of proteins by expressed protein ligation. 2003, Pubmed
Mukai, Codon reassignment in the Escherichia coli genetic code. 2010, Pubmed
Mukai, Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. 2008, Pubmed
Neumann, Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. 2010, Pubmed
Neumann, De novo generation of mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. 2010, Pubmed
Neumann, Rewiring translation - Genetic code expansion and its applications. 2012, Pubmed
Noren, A general method for site-specific incorporation of unnatural amino acids into proteins. 1989, Pubmed
Nowak, In vivo incorporation of unnatural amino acids into ion channels in Xenopus oocyte expression system. 1998, Pubmed , Xenbase
Ohno, Co-expression of yeast amber suppressor tRNATyr and tyrosyl-tRNA synthetase in Escherichia coli: possibility to expand the genetic code. 1998, Pubmed
Okuda, Model of mouth-to-mouth transfer of bacterial lipoproteins through inner membrane LolC, periplasmic LolA, and outer membrane LolB. 2009, Pubmed
Padgett, Unnatural amino acid mutagenesis of the GABA(A) receptor binding site residues reveals a novel cation-pi interaction between GABA and beta 2Tyr97. 2007, Pubmed , Xenbase
Pantoja, Single-molecule imaging of a fluorescent unnatural amino acid incorporated into nicotinic receptors. 2009, Pubmed , Xenbase
Peeler, Site-specific incorporation of unnatural amino acids as probes for protein conformational changes. 2012, Pubmed
Pentelute, Selective desulfurization of cysteine in the presence of Cys(Acm) in polypeptides obtained by native chemical ligation. 2007, Pubmed
Peters, Photocleavage of the polypeptide backbone by 2-nitrophenylalanine. 2009, Pubmed
Pless, Contributions of conserved residues at the gating interface of glycine receptors. 2011, Pubmed
Pless, Molecular basis for class Ib anti-arrhythmic inhibition of cardiac sodium channels. 2011, Pubmed
Pless, Hydrogen bonds as molecular timers for slow inactivation in voltage-gated potassium channels. 2013, Pubmed
Pless, Contributions of counter-charge in a potassium channel voltage-sensor domain. 2011, Pubmed , Xenbase
Pless, Asymmetric functional contributions of acidic and aromatic side chains in sodium channel voltage-sensor domains. 2014, Pubmed , Xenbase
Pless, A cation-pi interaction in the binding site of the glycine receptor is mediated by a phenylalanine residue. 2008, Pubmed , Xenbase
Pless, Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences. 2013, Pubmed
Pless, A cation-π interaction at a phenylalanine residue in the glycine receptor binding site is conserved for different agonists. 2011, Pubmed , Xenbase
Polycarpo, An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. 2004, Pubmed
Polycarpo, Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase. 2006, Pubmed
Puskar, Two neuronal nicotinic acetylcholine receptors, alpha4beta4 and alpha7, show differential agonist binding modes. 2011, Pubmed , Xenbase
Rackham, A network of orthogonal ribosome x mRNA pairs. 2005, Pubmed
Rhee, Photolytic control and infrared probing of amide I mode in the dipeptide backbone-caged with the 4,5-dimethoxy-2-nitrobenzyl group. 2008, Pubmed
Rodriguez, Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 2: evaluating suppression efficiency. 2007, Pubmed , Xenbase
Rodriguez, In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression. 2006, Pubmed , Xenbase
Rodriguez, Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 1: minimizing misacylation. 2007, Pubmed , Xenbase
Rothman, Caged phosphoproteins. 2005, Pubmed
Rydén, A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors. 1984, Pubmed
Ryu, Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. 2006, Pubmed
Sakamoto, Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. 2002, Pubmed
Saks, An engineered Tetrahymena tRNAGln for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression. 1996, Pubmed , Xenbase
Santarelli, Calcium block of single sodium channels: role of a pore-lining aromatic residue. 2007, Pubmed
Santoro, An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. 2003, Pubmed
Santoro, An efficient system for the evolution of aminoacyl-tRNA synthetase specificity. 2002, Pubmed
Sato, Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid. 2011, Pubmed
Schlieker, Substrate recognition by the AAA+ chaperone ClpB. 2004, Pubmed
Shen, Genetically encoding unnatural amino acids in neural stem cells and optically reporting voltage-sensitive domain changes in differentiated neurons. 2011, Pubmed
Shiota, In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work. 2011, Pubmed
Sprinzl, Compilation of tRNA sequences and sequences of tRNA genes. 2005, Pubmed
Sprinzl, Compilation of tRNA sequences and sequences of tRNA genes. 1996, Pubmed
Srinivasan, Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. 2002, Pubmed
Summerer, A genetically encoded fluorescent amino acid. 2006, Pubmed
Takimoto, Esterification of an unnatural amino acid structurally deviating from canonical amino acids promotes its uptake and incorporation into proteins in mammalian cells. 2010, Pubmed
Tamura, Tim23-Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import. 2009, Pubmed
Tippmann, A genetically encoded diazirine photocrosslinker in Escherichia coli. 2007, Pubmed
Tracy, Acute knockdown of AMPA receptors reveals a trans-synaptic signal for presynaptic maturation. 2011, Pubmed
Umanah, Incorporation of the unnatural amino acid p-benzoyl-L-phenylalanine (Bpa) into a G protein-coupled receptor in its native context. 2009, Pubmed
Valiyaveetil, Semisynthesis and folding of the potassium channel KcsA. 2002, Pubmed
Valiyaveetil, Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation. 2006, Pubmed
Wan, A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli. 2010, Pubmed
Wang, Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. 2007, Pubmed
Wang, New methods enabling efficient incorporation of unnatural amino acids in yeast. 2008, Pubmed
Wang, Genetically encoding unnatural amino acids for cellular and neuronal studies. 2007, Pubmed
Wang, A general approach for the generation of orthogonal tRNAs. 2001, Pubmed
Wang, Expanding the genetic code of Escherichia coli. 2001, Pubmed
Wang, Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. 2014, Pubmed
Wang, Programming cells by multiplex genome engineering and accelerated evolution. 2009, Pubmed
Wang, Expanding the genetic code for biological studies. 2009, Pubmed
Wu, Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. 2010, Pubmed
Wu, A genetically encoded photocaged amino acid. 2004, Pubmed
Xiu, Nicotine binding to brain receptors requires a strong cation-pi interaction. 2009, Pubmed , Xenbase
Yamano, Tom7 regulates Mdm10-mediated assembly of the mitochondrial import channel protein Tom40. 2010, Pubmed
Ye, Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. 2010, Pubmed
Ye, FTIR analysis of GPCR activation using azido probes. 2009, Pubmed
Ye, Expanding the genetic code in Xenopus laevis oocytes. 2013, Pubmed , Xenbase
Young, An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity. 2011, Pubmed
Zacharias, Cation-pi interactions in ligand recognition and catalysis. 2002, Pubmed
Zhang, The selective incorporation of alkenes into proteins in Escherichia coli. 2002, Pubmed
Zhang, Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. 2005, Pubmed
Zhong, From ab initio quantum mechanics to molecular neurobiology: a cation-pi binding site in the nicotinic receptor. 1998, Pubmed