51
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Chin JW, Cropp TA, Chu S, Meggers E, Schultz PG. Progress toward an expanded eukaryotic genetic code. CHEMISTRY & BIOLOGY 2003; 10:511-9. [PMID: 12837384 DOI: 10.1016/s1074-5521(03)00123-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expanding the eukaryotic genetic code to include unnatural amino acids with novel properties would provide powerful tools for manipulating protein function in eukaryotic cells. Toward this goal, a general approach with potential for isolating aminoacyl-tRNA synthetases that incorporate unnatural amino acids with high fidelity into proteins in Saccharomyces cerevisiae is described. The method is based on activation of GAL4-responsive HIS3, URA3, or lacZ reporter genes by suppression of amber codons in GAL4. The optimization of GAL4 reporters is described, and the positive and negative selection of active Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNA(CUA) is demonstrated. Importantly, both selections can be performed on a single cell and with a range of stringencies. This method will facilitate the isolation of a range of aminoacyl-tRNA synthetase (aaRS)/tRNA(CUA) activities from large libraries of mutant synthetases.
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Affiliation(s)
- Jason W Chin
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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52
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Petersson EJ, Brandt GS, Zacharias NM, Dougherty DA, Lester HA. Caging proteins through unnatural amino acid mutagenesis. Methods Enzymol 2003; 360:258-73. [PMID: 12622154 DOI: 10.1016/s0076-6879(03)60114-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The caging of specific residues of proteins is a powerful tool. This discussion attempts to alert the reader to the considerations that must be made in preparing and analyzing a caged protein through nonsense suppression. Although the suppression methodology is conceptually straightforward, it not possible to provide a failsafe "cook book" method for using caged unnaturals. We have emphasized the preparation of caged receptors expressed in Xenopus oocytes, but these approaches can clearly be adapted to many other systems.
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Affiliation(s)
- E James Petersson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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53
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Takahashi TT, Austin RJ, Roberts RW. mRNA display: ligand discovery, interaction analysis and beyond. Trends Biochem Sci 2003; 28:159-65. [PMID: 12633996 DOI: 10.1016/s0968-0004(03)00036-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In vitro peptide and protein selection using mRNA display enables the discovery and directed evolution of new molecules from combinatorial libraries. These selected molecules can serve as tools to control and understand biological processes, enhance our understanding of molecular interactions and potentially treat disease in therapeutic applications. In mRNA display, mRNA molecules are covalently attached to the peptide or protein they encode. These mRNA-protein fusions enable in vitro selection of peptide and protein libraries of >10(13) different sequences. mRNA display has been used to discover novel peptide and protein ligands for RNA, small molecules and proteins, as well as to define cellular interaction partners of proteins and drugs. In addition, several unique applications are possible with mRNA display, including self-assembling protein chips and library construction with unnatural amino acids and chemically modified peptides.
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Affiliation(s)
- Terry T Takahashi
- Department of Biochemistry and Molecular Biophysics, Pasadena, California 91125, USA
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54
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Hirao I, Ohtsuki T, Fujiwara T, Mitsui T, Yokogawa T, Okuni T, Nakayama H, Takio K, Yabuki T, Kigawa T, Kodama K, Yokogawa T, Nishikawa K, Yokoyama S. An unnatural base pair for incorporating amino acid analogs into proteins. Nat Biotechnol 2002; 20:177-82. [PMID: 11821864 DOI: 10.1038/nbt0202-177] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An unnatural base pair of 2-amino-6-(2-thienyl)purine (denoted by s) and pyridin-2-one (denoted by y) was developed to expand the genetic code. The ribonucleoside triphosphate of y was site-specifically incorporated into RNA, opposite s in a template, by T7 RNA polymerase. This transcription was coupled with translation in an Escherichia coli cell-free system. The yAG codon in the transcribed ras mRNA was recognized by the CUs anticodon of a yeast tyrosine transfer RNA (tRNA) variant, which had been enzymatically aminoacylated with an unnatural amino acid, 3-chlorotyrosine. Site-specific incorporation of 3-chlorotyrosine into the Ras protein was demonstrated by liquid chromatography-mass spectrometry (LC-MS) analysis of the products. This coupled transcription-translation system will permit the efficient synthesis of proteins with a tyrosine analog at the desired position.
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Affiliation(s)
- Ichiro Hirao
- Yokoyama CytoLogic Project, ERATO, JST, c/o RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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55
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Philipson KD, Gallivan JP, Brandt GS, Dougherty DA, Lester HA. Incorporation of caged cysteine and caged tyrosine into a transmembrane segment of the nicotinic ACh receptor. Am J Physiol Cell Physiol 2001; 281:C195-206. [PMID: 11401842 DOI: 10.1152/ajpcell.2001.281.1.c195] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nonsense codon suppression technique was used to incorporate o-nitrobenzyl cysteine or o-nitrobenzyl tyrosine (caged Cys or Tyr) into the 9' position of the M2 transmembrane segment of the gamma-subunit of the muscle nicotinic ACh receptor expressed in Xenopus oocytes. The caged amino acids replaced an endogenous Leu residue that has been implicated in channel gating. ACh-induced current increased substantially after ultraviolet (UV) irradiation to remove the caging group. This represents the first successful incorporation of caged Cys into a protein in vivo and the first incorporation of caged amino acids within a transmembrane segment of a membrane protein. The bulky nitrobenzyl group does not prevent the synthesis, assembly, or trafficking of the ACh receptor. When side chains were decaged using 1-ms UV light flashes, the channels with caged Cys or caged Tyr responded with strikingly different kinetics. The increase in current upon photolysis of caged Cys was too rapid for resolution by the voltage-clamp circuit [time constant (tau) <10 ms], whereas the increase in current upon photolysis of caged Tyr was dominated by a phase with tau approximately 500 ms. Apparently, the presence of a bulky o-nitrobenzyl Tyr residue distorts the receptor into an abnormal conformation. Upon release of the caging group, the receptor relaxes, with tau approximately 500 ms, into a conformation that allows the channel to open. Tyr at the 9' position of the gamma-subunit greatly increases the ability of ACh to block the channel by binding within the channel pore. This is manifested in two ways. 1) A "rebound," or increase in current, occurs upon removal of ACh from the bathing medium; and 2) at ACh concentrations >400 microM, inward currents are decreased through the mutated channel. The ability to incorporate caged amino acids into proteins should have widespread utility.
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Affiliation(s)
- K D Philipson
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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56
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Lu T, Ting AY, Mainland J, Jan LY, Schultz PG, Yang J. Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter. Nat Neurosci 2001; 4:239-46. [PMID: 11224539 DOI: 10.1038/85080] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Potassium channels selectively conduct K+ ions across cell membranes, and use diverse mechanisms to control their gating. We studied ion permeation and gating of an inwardly rectifying K+ channel by individually changing the amide carbonyls of two conserved glycines lining the selectivity filter to ester carbonyls using nonsense suppression. Surprisingly, these backbone mutations do not significantly alter ion selectivity. However, they dramatically change the kinetics of single-channel gating and produce distinct subconductance levels. The mutation at the glycine closer to the inner mouth of the pore also abolishes high-affinity binding of Ba2+ to the channel, indicating the importance of this position in ion stabilization in the selectivity filter. Our results demonstrate that K+ ion selectivity can be retained even with significant reduction of electronegativity in the selectivity filter, and that conformational changes of the filter arising from interactions between permeant ions and the backbone carbonyls contribute directly to channel gating.
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Affiliation(s)
- T Lu
- Department of Biological Sciences, 915 Fairchild Center, MC2462, Columbia University, New York, New York 10027, USA
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57
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58
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Tong Y, Brandt GS, Li M, Shapovalov G, Slimko E, Karschin A, Dougherty DA, Lester HA. Tyrosine decaging leads to substantial membrane trafficking during modulation of an inward rectifier potassium channel. J Gen Physiol 2001; 117:103-18. [PMID: 11158164 PMCID: PMC2217249 DOI: 10.1085/jgp.117.2.103] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tyrosine side chains participate in several distinct signaling pathways, including phosphorylation and membrane trafficking. A nonsense suppression procedure was used to incorporate a caged tyrosine residue in place of the natural tyrosine at position 242 of the inward rectifier channel Kir2.1 expressed in Xenopus oocytes. When tyrosine kinases were active, flash decaging led both to decreased K(+) currents and also to substantial (15-26%) decreases in capacitance, implying net membrane endocytosis. A dominant negative dynamin mutant completely blocked the decaging-induced endocytosis and partially blocked the decaging-induced K(+) channel inhibition. Thus, decaging of a single tyrosine residue in a single species of membrane protein leads to massive clathrin-mediated endocytosis; in fact, membrane area equivalent to many clathrin-coated vesicles is withdrawn from the oocyte surface for each Kir2.1 channel inhibited. Oocyte membrane proteins were also labeled with the thiol-reactive fluorophore tetramethylrhodamine-5-maleimide, and manipulations that decreased capacitance also decreased surface membrane fluorescence, confirming the net endocytosis. In single-channel studies, tyrosine kinase activation decreased the membrane density of active Kir2.1 channels per patch but did not change channel conductance or open probability, in agreement with the hypothesis that tyrosine phosphorylation results in endocytosis of Kir2.1 channels. Despite the Kir2.1 inhibition and endocytosis stimulated by tyrosine kinase activation, neither Western blotting nor (32)P labeling produced evidence for direct tyrosine phosphorylation of Kir2.1. Therefore, it is likely that tyrosine phosphorylation affects Kir2.1 function indirectly, via interactions between clathrin adaptor proteins and a tyrosine-based sorting motif on Kir2.1 that is revealed by decaging the tyrosine side chain. These interactions inhibit a fraction of the Kir2.1 channels, possibly via direct occlusion of the conduction pathway, and also lead to endocytosis, which further decreases Kir2.1 currents. These data establish that side chain decaging can provide valuable time-resolved data about intracellular signaling systems.
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Affiliation(s)
- Yanhe Tong
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - Gabriel S. Brandt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena California 91125
| | - Ming Li
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - George Shapovalov
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - Eric Slimko
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - Andreas Karschin
- Department of Physiology, University of Würzburg, Würzburg, Germany D-97070
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena California 91125
| | - Henry A. Lester
- Division of Biology, California Institute of Technology, Pasadena California 91125
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59
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Li L, Zhong W, Zacharias N, Gibbs C, Lester HA, Dougherty DA. The tethered agonist approach to mapping ion channel proteins--toward a structural model for the agonist binding site of the nicotinic acetylcholine receptor. CHEMISTRY & BIOLOGY 2001; 8:47-58. [PMID: 11182318 DOI: 10.1016/s1074-5521(00)00055-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The integral membrane proteins of neurons and other excitable cells are generally resistant to high resolution structural tools. Structure-function studies, especially those enhanced by the nonsense suppression methodology for unnatural amino acid incorporation, constitute one of the most powerful probes of ion channels and related structures. The nonsense suppression methodology can also be used to incorporate functional side chains designed to deliver novel structural probes to membrane proteins. In this vein, we sought to generalize a potentially powerful tool - the tethered agonist approach - for mapping the agonist binding site of ligand-gated ion channels. RESULTS Using the in vivo nonsense suppression method for unnatural amino acid incorporation, a series of tethered quaternary ammonium derivatives of tyrosine have been incorporated into the nicotinic acetylcholine receptor. At three sites a constitutively active receptor results, but the pattern of activation as a function of chain length is different. At position alpha149, there is a clear preference for a three-carbon tether, while at position alpha93 tethers of 2-5 carbons are comparably effective. At position gamma55/delta57 all tethers except the shortest one can activate the receptor. Based on these and other data, a model for the receptor binding site can be developed by analogy to the acetylcholine esterase crystal structure. CONCLUSION Through the use of nonsense suppression techniques, the tethered agonist approach has been made into a general tool for probing receptor structures. When applied to the nicotinic receptor, the method places new restrictions on developing models for the agonist binding site.
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Affiliation(s)
- L Li
- Division of Chemistry and Chemical Engineering. California Institute of Technology, Pasadena 91125, USA
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60
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Moore B, Nelson CC, Persson BC, Gesteland RF, Atkins JF. Decoding of tandem quadruplets by adjacent tRNAs with eight-base anticodon loops. Nucleic Acids Res 2000; 28:3615-24. [PMID: 10982884 PMCID: PMC110719 DOI: 10.1093/nar/28.18.3615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To expand the genetic code for specification of multiple non-natural amino acids, unique codons for these novel amino acids are needed. As part of a study of the potential of quadruplets as codons, the decoding of tandem UAGA quadruplets by an engineered tRNA(Leu) with an eight-base anticodon loop, has been investigated. When GCC is the codon immediately 5' of the first UAGA quadruplet, and release factor 1 is partially inactivated, the tandem UAGAs specify two leucines with an overall efficiency of at least 10%. The presence of a purine at anticodon loop position 32 of the tRNA decoding the codon 5' to the first UAGA seems to influence translation of the following codon. Another finding is intraribosomal dissociation of anticodons from codons and their re-pairing to mRNA at overlapping or nearby codons. In one case where GCC is replaced by CGG, only a single Watson-Crick base pair can form upon re-pairing when decoding is resumed. This has implications for the mechanism of some cases of programmed frameshifting.
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Affiliation(s)
- B Moore
- Department of Human Genetics, University of Utah, 15 N. 2030 E. Room 7410, Salt Lake City, UT 84112-5330, USA
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61
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Middendorf TR, Aldrich RW, Baylor DA. Modification of cyclic nucleotide-gated ion channels by ultraviolet light. J Gen Physiol 2000; 116:227-52. [PMID: 10919869 PMCID: PMC2229495 DOI: 10.1085/jgp.116.2.227] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We irradiated cyclic nucleotide-gated ion channels in situ with ultraviolet light to probe the role of aromatic residues in ion channel function. UV light reduced the current through excised membrane patches from Xenopus oocytes expressing the alpha subunit of bovine retinal cyclic nucleotide-gated channels irreversibly, a result consistent with permanent covalent modification of channel amino acids by UV light. The magnitude of the current reduction depended only on the total photon dose delivered to the patches, and not on the intensity of the exciting light, indicating that the functionally important photochemical modification(s) occurred from an excited state reached by a one-photon absorption process. The wavelength dependence of the channels' UV light sensitivity (the action spectrum) was quantitatively consistent with the absorption spectrum of tryptophan, with a small component at long wavelengths, possibly due to cystine absorption. This spectral analysis suggests that UV light reduced the currents at most wavelengths studied by modifying one or more "target" tryptophans in the channels. Comparison of the channels' action spectrum to the absorption spectrum of tryptophan in various solvents suggests that the UV light targets are in a water-like chemical environment. Experiments on mutant channels indicated that the UV light sensitivity of wild-type channels was not conferred exclusively by any one of the 10 tryptophan residues in a subunit. The similarity in the dose dependences of channel current reduction and tryptophan photolysis in solution suggests that photochemical modification of a small number of tryptophan targets in the channels is sufficient to decrease the currents.
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Affiliation(s)
- Thomas R. Middendorf
- Neurobiology Department, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, California 94305
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, California 94305
| | - Richard W. Aldrich
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, California 94305
| | - Denis A. Baylor
- Neurobiology Department, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, California 94305
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62
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Moore B, Persson BC, Nelson CC, Gesteland RF, Atkins JF. Quadruplet codons: implications for code expansion and the specification of translation step size. J Mol Biol 2000; 298:195-209. [PMID: 10764591 DOI: 10.1006/jmbi.2000.3658] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
One of the requirements for engineering expansion of the genetic code is a unique codon which is available for specifying the new amino acid. The potential of the quadruplet UAGA in Escherichia coli to specify a single amino acid residue in the presence of a mutant tRNA(Leu) molecule containing the extra nucleotide, U, at position 33.5 of its anticodon loop has been examined. With this mRNA-tRNA combination and at least partial inactivation of release factor 1, the UAGA quadruplet specifies a leucine residue with an efficiency of 13 to 26 %. The decoding properties of tRNA(Leu) with U at position 33.5 of its eight-membered anticodon loop, and a counterpart with A at position 33.5, strongly suggest that in both cases their anticodon loop bases stack in alternative conformations. The identity of the codon immediately 5' of the UAGA quadruplet influences the efficiency of quadruplet translation via the properties of its cognate tRNA. When there is the potential for the anticodon of this tRNA to dissociate from pairing with its codon and to re-pair to mRNA at a nearby 3' closely matched codon, the efficiency of quadruplet translation at UAGA is reduced. Evidence is presented which suggests that when there is a purine base at position 32 of this 5' flanking tRNA, it influences decoding of the UAGA quadruplet.
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MESH Headings
- Amino Acid Sequence
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- Codon/chemistry
- Codon/genetics
- Codon/metabolism
- Codon, Terminator/genetics
- Evolution, Molecular
- Frameshifting, Ribosomal/genetics
- Genes, Reporter/genetics
- Genetic Code/genetics
- Mass Spectrometry
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Biosynthesis/genetics
- Proteins/chemistry
- Proteins/genetics
- RNA Probes/chemistry
- RNA Probes/genetics
- RNA Probes/metabolism
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- Sequence Analysis, Protein
- Suppression, Genetic/genetics
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Affiliation(s)
- B Moore
- Department of Human Genetics, University of Utah, 15N 2030E Rm 7410, Salt Lake City, UT 84112-5330, USA
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63
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van Hest JCM, Kiick KL, Tirrell DA. Efficient Incorporation of Unsaturated Methionine Analogues into Proteins in Vivo. J Am Chem Soc 2000. [DOI: 10.1021/ja992749j] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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64
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65
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Sisido M, Hohsaka T. Extension of Protein Functions by the Incorporation of Nonnatural Amino Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.1409] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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66
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England PM, Zhang Y, Dougherty DA, Lester HA. Backbone mutations in transmembrane domains of a ligand-gated ion channel: implications for the mechanism of gating. Cell 1999; 96:89-98. [PMID: 9989500 DOI: 10.1016/s0092-8674(00)80962-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
An approach to identify backbone conformational changes underlying nicotinic acetylcholine receptor (nAChR) gating was developed. Specific backbone peptide bonds were replaced with an ester, which disrupts backbone hydrogen bonds at the site of mutation. At a conserved proline residue (alphaPro221) in the first transmembrane (M1) domain, the amide-to-ester mutation provides receptors with near-normal sensitivity, although the natural amino acids tested other than Pro produce receptors that gate with a much larger EC50 than normal. Therefore, a backbone hydrogen bond at this site may interfere with normal gating. In the alphaM2 domain, the amide-to-ester mutation yielded functional receptors at 15 positions, 3 of which provided receptors with >10-fold lower EC50 than wild type. These results support a model for gating that includes significant changes of backbone conformation within the M2 domain.
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Affiliation(s)
- P M England
- Division of Biology, California Institute of Technology, Pasadena 91125, USA
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67
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Nowak MW, Gallivan JP, Silverman SK, Labarca CG, Dougherty DA, Lester HA. In vivo incorporation of unnatural amino acids into ion channels in Xenopus oocyte expression system. Methods Enzymol 1998; 293:504-29. [PMID: 9711626 DOI: 10.1016/s0076-6879(98)93031-2] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A general method for the incorporation of unnatural amino acids into ion channels and membrane receptors using a Xenopus oocyte expression system has been described. A large number of unnatural amino acids have been incorporated into the nAChR, GIRK, and Shaker K+ channels. Continuing efforts focus on incorporating unnatural amino acids that differ substantially from the natural amino acids, for example, residues that include fluorophores. In addition, we are addressing the feasibility of incorporating unnatural amino acids into ion channels and membrane receptors in mammalian cells.
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MESH Headings
- Amino Acids/chemistry
- Amino Acids/metabolism
- Animals
- Base Sequence
- Codon
- Female
- Gene Expression
- In Vitro Techniques
- Ion Channels/biosynthesis
- Ion Channels/chemistry
- Molecular Sequence Data
- Molecular Structure
- Nucleic Acid Conformation
- Oligodeoxyribonucleotides
- Oocytes/physiology
- Point Mutation
- Potassium Channels/biosynthesis
- Potassium Channels/chemistry
- Promoter Regions, Genetic
- RNA, Transfer, Gln/chemistry
- RNA, Transfer, Gln/genetics
- RNA, Transfer, Gln/metabolism
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/chemistry
- Receptors, Nicotinic/biosynthesis
- Receptors, Nicotinic/chemistry
- Shaker Superfamily of Potassium Channels
- Suppression, Genetic
- Thermus thermophilus/genetics
- Transcription, Genetic
- Xenopus laevis
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Affiliation(s)
- M W Nowak
- Department of Psychiatry, Medical University of South Carolina, Charleston 29425, USA
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68
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Liu Y, Shah K, Yang F, Witucki L, Shokat KM. A molecular gate which controls unnatural ATP analogue recognition by the tyrosine kinase v-Src. Bioorg Med Chem 1998; 6:1219-26. [PMID: 9784863 DOI: 10.1016/s0968-0896(98)00099-6] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Engineered proteins with specificity for unnatural substrates or ligands are useful tools for studying or manipulating complex biological systems. We have engineered the prototypical tyrosine kinase v-Src to accept an unnatural ATP analogue N6-(benzyl) ATP in order to identify v-Src's direct cellular substrates. Here we have used molecular modeling to analyze the binding mode of N6-(benzyl) ATP. Based on this modeling we proposed that a new ATP analogue (N6-(2-phenethyl) ATP might be a better substrate than N6-(benzyl) ATP for the I338G mutant of v-Src. In fact the newly proposed analogue (N6-(2-phenethyl) ATP is a somewhat improved substrate for the engineered kinase (kcat = 0.6 min-1, KM = 8 microM). We also synthesized and screened three analogues of N6-(benzyl) ATP: N6-(2-methylbenzyl), ATP N6-(3-methylbenzyl), and ATP N6-(4-methylbenzyl) ATP to further probe the dimensions and shape of the introduced pocket. Results from screening newly synthesized ATP analogues agreed well with our modeling predictions. We conclude that rather than engineering a 'new' pocket by mutation of Ile 338 in v-Src to the smaller Ala or Gly residues, the I338G and I338A mutants possess a 'path' for the N6 substituent on ATP to gain access to an existing pocket in the ATP binding site. We expect to be able to extend the engineering of v-Src's ATP specificity to other kinase families based on our understanding of the binding modes of ATP analogues to engineered kinases.
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Affiliation(s)
- Y Liu
- Department of Chemistry, Princeton University, NJ 08544, USA
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69
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70
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Miller JC, Silverman SK, England PM, Dougherty DA, Lester HA. Flash decaging of tyrosine sidechains in an ion channel. Neuron 1998; 20:619-24. [PMID: 9581754 DOI: 10.1016/s0896-6273(00)81001-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A nonsense codon suppression technique was employed to incorporate ortho-nitrobenzyl tyrosine, "caged tyrosine," in place of tyrosine at any of three positions (93, 127, or 198) in the alpha subunit of the muscle nicotinic ACh receptor (nAChR) expressed in Xenopus oocytes. The ortho-nitrobenzyl group was then removed by 1 ms flashes at 300-350 nm to yield tyrosine itself while macroscopic currents were recorded during steady ACh exposure. Responses to multiple flashes showed (1) that each flash decages up to 17% of the tyrosines and (2) that two tyrosines must be decaged per receptor for a response. The conductance relaxations showed multiple kinetic components; rate constants (<0.1 s(-1) to 10(3) s(-1)) depended on pH and the site of incorporation, and relative amplitudes depended on the number of prior flashes. This method, which is potentially quite general, (1) provides a time-resolved assay for the behavior of a protein when a mutant sidechain is abruptly changed to the wild-type residue and (2) will also allow for selective decaging of sidechains that are candidates for covalent modification (such as phosphorylation) in specific proteins in intact cells.
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Affiliation(s)
- J C Miller
- Division of Biology, California Institute of Technology, Pasadena 91125, USA
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71
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Killian JA, Van Cleve MD, Shayo YF, Hecht SM. Ribosome-Mediated Incorporation of Hydrazinophenylalanine into Modified Peptide and Protein Analogues. J Am Chem Soc 1998. [DOI: 10.1021/ja974066e] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer A. Killian
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Mark D. Van Cleve
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Yuda F. Shayo
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Sidney M. Hecht
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
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72
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Lodder M, Golovine S, Laikhter AL, Karginov VA, Hecht SM. Misacylated Transfer RNAs Having a Chemically Removable Protecting Group. J Org Chem 1998; 63:794-803. [PMID: 11672075 DOI: 10.1021/jo971692l] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 4-pentenoyl group and a number of derivatives have been studied as protecting groups for N(alpha) of the aminoacyl moiety in misacylated tRNAs. The unsubstituted 4-pentenoyl group itself was found to function as efficiently as any of the derivatives studied. Four different N-(4-pentenoyl)aminoacyl-tRNA(CUA)s were prepared and shown to undergo deprotection readily upon admixture of aqueous iodine; the derived misacylated tRNAs all functioned well as suppressors of a nonsense codon in an in vitro protein biosynthesizing system. Also prepared were four N(alpha)-(4-pentenoyl)aspartyl-tRNA(CUA)s that were protected on the side chain carboxylate as the nitroveratryl ester. Following treatment with aqueous iodine, the misacylated suppressor tRNAs incorporated the aspartate derivatives into position 27 of dihydrofolate reductase by suppression of a UAG codon in the mRNA. The suppression yields were significantly better than those obtained when side chain protection was absent. The resulting "caged proteins" were inactive, but full catalytic potential was restored by irradiation under conditions sufficient to effect deprotection of the side chain carboxylate moiety.
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Affiliation(s)
- Michiel Lodder
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
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73
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Dougherty DA. Stereochemical issues in studies of ion channel proteins. Chirality 1998. [DOI: 10.1002/chir.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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74
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Gallivan JP, Lester HA, Dougherty DA. Site-specific incorporation of biotinylated amino acids to identify surface-exposed residues in integral membrane proteins. CHEMISTRY & BIOLOGY 1997; 4:739-49. [PMID: 9375252 DOI: 10.1016/s1074-5521(97)90312-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND A key structural issue for all integral membrane proteins is the exposure of individual residues to the intracellular or extracellular media. This issue involves the basic transmembrane topology as well as more subtle variations in surface accessibility. Direct methods to evaluate the degree of exposure for residues in functional proteins expressed in living cells would be highly valuable. We sought to develop a new experimental method to determine highly surface-exposed residues, and thus transmembrane topology of membrane proteins expressed in Xenopus oocytes. RESULTS We have used the in vivo nonsense suppression technique to incorporate biotinylated unnatural amino acids into functional ion channels expressed in Xenopus oocytes. Binding of 125I-streptavidin to biotinylated receptors was used to determine the surface exposure of individual amino acids. In particular, we studied the main immunogenic region of the nicotinic acetylcholine receptor. The biotin-containing amino acid biocytin was efficiently incorporated into five sites in the main immunogenic region and extracellular streptavidin bound to one residue in particular, alpha 70. The position of alpha 70 as highly exposed on the receptor surface was thus established. CONCLUSIONS The in vivo nonsense suppression technique has been extended to provide the first in a potential series of methods to identify exposed residues and to assess their relative exposure in functional proteins expressed in Xenopus oocytes.
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Affiliation(s)
- J P Gallivan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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75
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England PM, Lester HA, Davidson N, Dougherty DA. Site-specific, photochemical proteolysis applied to ion channels in vivo. Proc Natl Acad Sci U S A 1997; 94:11025-30. [PMID: 9380753 PMCID: PMC23572 DOI: 10.1073/pnas.94.20.11025] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A method for site-specific, nitrobenzyl-induced photochemical proteolysis of diverse proteins expressed in living cells has been developed based on the chemistry of the unnatural amino acid (2-nitrophenyl)glycine (Npg). Using the in vivo nonsense codon suppression method for incorporating unnatural amino acids into proteins expressed in Xenopus oocytes, Npg has been incorporated into two ion channels: the Drosophila Shaker B K+ channel and the nicotinic acetylcholine receptor. Functional studies in vivo show that irradiation of proteins containing an Npg residue does lead to peptide backbone cleavage at the site of the novel residue. Using this method, evidence is obtained for an essential functional role of the "signature" Cys128-Cys142 disulfide loop of the nAChR alpha subunit.
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Affiliation(s)
- P M England
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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76
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Kearney PC, Zhang H, Zhong W, Dougherty DA, Lester HA. Determinants of nicotinic receptor gating in natural and unnatural side chain structures at the M2 9' position. Neuron 1996; 17:1221-9. [PMID: 8982168 DOI: 10.1016/s0896-6273(00)80252-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A nonsense suppression method was employed to incorporate a total of four natural and six unnatural residues at the 9' position of the M2 region in the beta, gamma, and delta subunits of muscle nicotinic receptors. In 33 pairwise comparisons of functional properties as influenced by structural features including side chain length, branching, and substitution of oxygen for methylene carbons, it is concluded that increased polarity in the side chains at the 9' position consistently increases the sensitivity to acetylcholine. In addition, the stereochemistry of the side chain can have marked influences on the EC50, primarily because of changes in the single-channel open time. For the case of isoleucine versus allo-isoleucine in the delta subunit, these changes are themselves modified by mutations at the 9' position in other subunits. The data suggest an especially strong interaction between the beta and delta subunits in the pore region, leading in turn to a suggested arrangement of subunits within the pentamer.
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Affiliation(s)
- P C Kearney
- Division of Biology, California Institute of Technology, Pasadena 91125, USA
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77
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Cload ST, Liu DR, Froland WA, Schultz PG. Development of improved tRNAs for in vitro biosynthesis of proteins containing unnatural amino acids. CHEMISTRY & BIOLOGY 1996; 3:1033-8. [PMID: 9000011 DOI: 10.1016/s1074-5521(96)90169-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Chemically aminoacylated suppressor tRNAs have previously been used in vitro to generate mutant proteins in which unnatural amino acids are incorporated site-specifically. Although the existing methodology often provides adequate quantities of mutant proteins, the suppression efficiencies of some unnatural amino acids are not high enough to yield useful amounts of protein. In an effort to make this useful mutagenesis strategy more general, we report here the results of a search to find alternative tRNAs as a way of increasing suppression efficiencies. RESULTS Three suppressor tRNAs have been generated by runoff transcription and their ability to deliver unnatural amino acids site-specifically into proteins has been assessed in an E. coli-derived in vitro transcription/translation system. Analysis of their ability to insert both polar and nonpolar residues in response to an amber codon in two proteins suggests that an E. coli tRNAAsn-derived suppressor offers a significant improvement in suppression efficiency over other previously used tRNAs. CONCLUSIONS Use of an E. coli tRNAAsn-derived suppressor may provide substantially higher yields of proteins containing unnatural amino acids, in addition to offering a broader tolerance for polar amino acids. A comparison of suppressor tRNAs derived from tRNAAsn, tRNAGln or tRNAAsp with that derived from tRNAPhe supports emerging evidence that the identity of an amino acid may be important in message recognition.
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Affiliation(s)
- S T Cload
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, CA 94720, USA
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