Site specific incorporation of keto amino acids into proteins

Schultz, Peter G; Wang, Lei

Title: Site specific incorporation of keto amino acids into proteins

Abstract

Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

Inventors:

Schultz, Peter G ^[1]; Wang, Lei ^[2]

La Jolla, CA
San Diego, CA

Issue Date:: 2011-03-22

Research Org.:: The Scripps Research Inst., La Jolla, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1016350

Patent Number(s):: 7910345

Application Number:: US Patent Application 12/228,146

Assignee:: The Scripps Research Institute (La Jolla, CA)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {

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C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C12N15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12N15/67 - General methods for enhancing the expression
C12N9/93 - {Ligases

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {
C12P21/005 - {Glycopeptides, glycoproteins}

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DOE Contract Number:: FG03-00ER45812; AC03-76SF00098

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Schultz, Peter G, and Wang, Lei. Site specific incorporation of keto amino acids into proteins.  United States: N. p., 2011. 
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                    Schultz, Peter G, & Wang, Lei. Site specific incorporation of keto amino acids into proteins.  United States.

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                    Schultz, Peter G, and Wang, Lei. Tue .  
        "Site specific incorporation of keto amino acids into proteins".  United States.  https://www.osti.gov/servlets/purl/1016350.

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@article{osti_1016350,

  title        = {Site specific incorporation of keto amino acids into proteins},

  author       = {Schultz, Peter G and Wang, Lei},

  abstractNote = {Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2011},

  month        = {3}

}

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Title: Site specific incorporation of keto amino acids into proteins

Abstract

Citation Formats

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 journal, January 2001

Engineering Chemical Reactivity on Cell Surfaces Through Oligosaccharide Biosynthesis journal, May 1997

Bio–incorporation of telluromethionine into buried residues of dihydrofolate reductase journal, May 1994

An unnatural base pair for incorporating amino acid analogs into proteins journal, February 2002

Site-specific incorporation of novel backbone structures into proteins journal, January 1992

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system journal, July 2002

In vitro protein engineering using synthetic tRNAAla with different anticodons journal, August 1993

Direct Physical Measure of Conformational Rearrangement Underlying Potassium Channel Gating journal, January 1996

An Expanded Eukaryotic Genetic Code journal, August 2003

Addition of p-Azido-L-phenylalanine to the Genetic Code of Escherichia coli journal, July 2002

An efficient system for the evolution of aminoacyl-tRNA synthetase specificity journal, September 2002

Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering journal, March 1993

Flash Decaging of Tyrosine Sidechains in an Ion Channel journal, April 1998

Synthesis of 4-substituted prolines as conformationally constrained amino acid analogs journal, April 1989

Probing the Structure and Function of the Tachykinin Neurokinin-2 Receptor through Biosynthetic Incorporation of Fluorescent Amino Acids at Specific Sites journal, August 1996

Selenocysteine: the 21st amino acid journal, March 1991

Relaxing the substrate specificity of an aminoacyl-tRNA synthetase allows in vitro and in vivo synthesis of proteins containing unnatural amino acids journal, May 1995

A set of plasmids constitutively producing different RNA levels in Escherichia coli journal, July 1999

Efforts toward Expansion of the Genetic Alphabet: Replication of DNA with Three Base Pairs journal, August 2001

Photocrosslinking of the signal sequence of nascent preprolactin to the 54-kilodalton polypeptide of the signal recognition particle. journal, November 1986

Adding l-3-(2-Naphthyl)alanine to the Genetic Code of E. coli journal, March 2002

Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. journal, May 1990

Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes journal, March 1980

[15] Biosynthetic method for introducing unnatural amino acids site-specifically into proteins book, January 1991

Human Tyrosyl-tRNA Synthetase Shares Amino Acid Sequence Homology with a Putative Cytokine journal, May 1997

Expanding tRNA recognition of a tRNA synthetase by a single amino acid change journal, May 2003

Rational Design of an Unnatural Base Pair with Increased Kinetic Selectivity journal, September 2000

Unnatural amino acids as probes of protein structure and function journal, December 2000

TRNA2Gln Su+2 mutants that increase amber suppression. journal, January 1981

Quadruplet codons: implications for code expansion and the specification of translation step size journal, April 2000

Progress toward the evolution of an organism with an expanded genetic code journal, April 1999

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet journal, January 1990

Construction of Escherichia coli amber suppressor tRNA genes: II. Synthesis of additional tRNA genes and improvement of suppressor efficiency journal, June 1990

Editing of errors in selection of amino acids for protein synthesis. journal, January 1992

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant journal, January 1998

Incorporation of Trifluoromethionine into a Phage Lysozyme: Implications and a New Marker for Use in Protein 19 F NMR † journal, March 1997

An Engineered Tetrahymena tRNA Gln for in Vivo Incorporation of Unnatural Amino Acids into Proteins by Nonsense Suppression journal, September 1996

Specific Covalent Labeling of Recombinant Protein Molecules Inside Live Cells journal, July 1998

2 .ANG. Resolution Structure of DppA, a Periplasmic Dipeptide Transport/Chemosensory Receptor journal, December 1995

Enzyme-generated intracellular fluorescence for single-cell reporter gene analysis utilizing Escherichia coli-glucuronidase journal, August 1996

Biodegradation of Aromatic Compounds by Escherichia coli journal, December 2001

Differences in Backbone Structure between Angiotensin II Agonists and Type I Antagonists journal, November 1995

Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo journal, September 1997

Protein Engineering by In Vivo Incorporation of Non-Natural Amino Acids: Control of Incorporation of Methionine Analogues by Methionyl-tRNA Synthetase journal, November 2000

Enlarging the Amino Acid Set of Escherichia coli by Infiltration of the Valine Coding Pathway journal, April 2001

Site-Directed Mutagenesis with an Expanded Genetic Code journal, June 1995

A synthetic IgG-binding domain based on staphylococcal protein A journal, January 1987

Incorporation of Two Different Nonnatural Amino Acids Independently into a Single Protein through Extension of the Genetic Code journal, December 1999

Co-Expression of Yeast Amber Suppressor tRNATyr and Tyrosyl-tRNA Synthetase in Escherichia coli: Possibility to Expand the Genetic Code journal, December 1998

Substrate Specificity Is Determined by Amino Acid Binding Pocket Size in Escherichia coli Phenylalanyl-tRNA Synthetase journal, June 1994

Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide journal, September 1989

An expanding genetic code journal, December 2004

Expanding the Genetic Code journal, January 2005

Residue-specific bioincorporation of non-natural, biologically active amino acids into proteins as possible drug carriers: Structure and stability of the per-thiaproline mutant of annexin V journal, January 1998

Synthetically modified DNAs as substrates for polymerases journal, December 2000

Programming peptidomimetic syntheses by translating genetic codes designed de novo journal, May 2003

Multicolor and Electron Microscopic Imaging of Connexin Trafficking journal, April 2002

New Photolabeling and Crosslinking Methods journal, June 1993

Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter journal, March 2001

Transmembrane protein structure: spin labeling of bacteriorhodopsin mutants journal, June 1990

Universal rules and idiosyncratic features in tRNA identity journal, November 1998

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme journal, July 1998

Absolute configuration of the enantiomers of 7-chloro-4-[[4-(diethylamino)-1-methylbutyl]amino]quinoline (chloroquine) journal, March 1988

Novel cofactors via post-translational modifications of enzyme active sites journal, July 2000

Site-Specific Protein Modification Using a Ketone Handle journal, January 1996

Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells journal, April 1995

Probing Protein Structure and Function with an Expanded Genetic Code journal, March 1995

Directed evolution of the site specificity of Cre recombinase journal, March 2002

Studying organelle physiology with fusion protein-targeted avidin and fluorescent biotin conjugates book, January 2000

Site-directed conjugation of nonpeptide groups to peptides and proteins via periodate oxidation of a 2-amino alcohol. Application to modification at N-terminal serine journal, March 1992

Highly Precise Shape Mimicry by a Difluorotoluene Deoxynucleoside, a Replication-Competent Substitute for Thymidine journal, January 1997

Site-specific incorporation of biotinylated amino acids to identify surface-exposed residues in integral membrane proteins journal, October 1997

A general approach for the generation of orthogonal tRNAs journal, September 2001

Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution: Interaction of the enzyme with the tyrosyl adenylate intermediate journal, July 1989

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase journal, December 1999

A Novel Copper-Mediated DNA Base Pair journal, November 2000

Backbone Mutations in Transmembrane Domains of a Ligand-Gated Ion Channel journal, January 1999

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
journal, January 2001

Engineering Chemical Reactivity on Cell Surfaces Through Oligosaccharide Biosynthesis
journal, May 1997

Bio–incorporation of telluromethionine into buried residues of dihydrofolate reductase
journal, May 1994

An unnatural base pair for incorporating amino acid analogs into proteins
journal, February 2002

Site-specific incorporation of novel backbone structures into proteins
journal, January 1992

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system
journal, July 2002

In vitro protein engineering using synthetic tRNAAla with different anticodons
journal, August 1993

Direct Physical Measure of Conformational Rearrangement Underlying Potassium Channel Gating
journal, January 1996

An Expanded Eukaryotic Genetic Code
journal, August 2003

Addition of p-Azido-L-phenylalanine to the Genetic Code of Escherichia coli
journal, July 2002

An efficient system for the evolution of aminoacyl-tRNA synthetase specificity
journal, September 2002

Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering
journal, March 1993

Flash Decaging of Tyrosine Sidechains in an Ion Channel
journal, April 1998

Synthesis of 4-substituted prolines as conformationally constrained amino acid analogs
journal, April 1989

Probing the Structure and Function of the Tachykinin Neurokinin-2 Receptor through Biosynthetic Incorporation of Fluorescent Amino Acids at Specific Sites
journal, August 1996

Selenocysteine: the 21st amino acid
journal, March 1991

Relaxing the substrate specificity of an aminoacyl-tRNA synthetase allows in vitro and in vivo synthesis of proteins containing unnatural amino acids
journal, May 1995

A set of plasmids constitutively producing different RNA levels in Escherichia coli
journal, July 1999

Efforts toward Expansion of the Genetic Alphabet: Replication of DNA with Three Base Pairs
journal, August 2001

Photocrosslinking of the signal sequence of nascent preprolactin to the 54-kilodalton polypeptide of the signal recognition particle.
journal, November 1986

Adding l-3-(2-Naphthyl)alanine to the Genetic Code of E. coli
journal, March 2002

Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure.
journal, May 1990

Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes
journal, March 1980

[15] Biosynthetic method for introducing unnatural amino acids site-specifically into proteins
book, January 1991

Human Tyrosyl-tRNA Synthetase Shares Amino Acid Sequence Homology with a Putative Cytokine
journal, May 1997

Expanding tRNA recognition of a tRNA synthetase by a single amino acid change
journal, May 2003

Rational Design of an Unnatural Base Pair with Increased Kinetic Selectivity
journal, September 2000

Unnatural amino acids as probes of protein structure and function
journal, December 2000

TRNA2Gln Su+2 mutants that increase amber suppression.
journal, January 1981

Quadruplet codons: implications for code expansion and the specification of translation step size
journal, April 2000

Progress toward the evolution of an organism with an expanded genetic code
journal, April 1999

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet
journal, January 1990

Construction of Escherichia coli amber suppressor tRNA genes: II. Synthesis of additional tRNA genes and improvement of suppressor efficiency
journal, June 1990

Editing of errors in selection of amino acids for protein synthesis.
journal, January 1992

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant
journal, January 1998

Incorporation of Trifluoromethionine into a Phage Lysozyme: Implications and a New Marker for Use in Protein ¹⁹ F NMR ^†
journal, March 1997

An Engineered Tetrahymena tRNA ^Gln for in Vivo Incorporation of Unnatural Amino Acids into Proteins by Nonsense Suppression
journal, September 1996

Specific Covalent Labeling of Recombinant Protein Molecules Inside Live Cells
journal, July 1998

2 .ANG. Resolution Structure of DppA, a Periplasmic Dipeptide Transport/Chemosensory Receptor
journal, December 1995

Enzyme-generated intracellular fluorescence for single-cell reporter gene analysis utilizing Escherichia coli-glucuronidase
journal, August 1996

Biodegradation of Aromatic Compounds by Escherichia coli
journal, December 2001

Differences in Backbone Structure between Angiotensin II Agonists and Type I Antagonists
journal, November 1995

Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo
journal, September 1997

Protein Engineering by In Vivo Incorporation of Non-Natural Amino Acids: Control of Incorporation of Methionine Analogues by Methionyl-tRNA Synthetase
journal, November 2000

Enlarging the Amino Acid Set of Escherichia coli by Infiltration of the Valine Coding Pathway
journal, April 2001

Site-Directed Mutagenesis with an Expanded Genetic Code
journal, June 1995

A synthetic IgG-binding domain based on staphylococcal protein A
journal, January 1987

Incorporation of Two Different Nonnatural Amino Acids Independently into a Single Protein through Extension of the Genetic Code
journal, December 1999

Co-Expression of Yeast Amber Suppressor tRNATyr and Tyrosyl-tRNA Synthetase in Escherichia coli: Possibility to Expand the Genetic Code
journal, December 1998

Substrate Specificity Is Determined by Amino Acid Binding Pocket Size in Escherichia coli Phenylalanyl-tRNA Synthetase
journal, June 1994

Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide
journal, September 1989

An expanding genetic code
journal, December 2004

Expanding the Genetic Code
journal, January 2005

Residue-specific bioincorporation of non-natural, biologically active amino acids into proteins as possible drug carriers: Structure and stability of the per-thiaproline mutant of annexin V
journal, January 1998

Synthetically modified DNAs as substrates for polymerases
journal, December 2000

Programming peptidomimetic syntheses by translating genetic codes designed de novo
journal, May 2003

Multicolor and Electron Microscopic Imaging of Connexin Trafficking
journal, April 2002

New Photolabeling and Crosslinking Methods
journal, June 1993

Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter
journal, March 2001

Transmembrane protein structure: spin labeling of bacteriorhodopsin mutants
journal, June 1990

Universal rules and idiosyncratic features in tRNA identity
journal, November 1998

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme
journal, July 1998

Absolute configuration of the enantiomers of 7-chloro-4-[[4-(diethylamino)-1-methylbutyl]amino]quinoline (chloroquine)
journal, March 1988

Novel cofactors via post-translational modifications of enzyme active sites
journal, July 2000

Site-Specific Protein Modification Using a Ketone Handle
journal, January 1996

Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells
journal, April 1995

Probing Protein Structure and Function with an Expanded Genetic Code
journal, March 1995

Directed evolution of the site specificity of Cre recombinase
journal, March 2002

Studying organelle physiology with fusion protein-targeted avidin and fluorescent biotin conjugates
book, January 2000

Site-directed conjugation of nonpeptide groups to peptides and proteins via periodate oxidation of a 2-amino alcohol. Application to modification at N-terminal serine
journal, March 1992

Highly Precise Shape Mimicry by a Difluorotoluene Deoxynucleoside, a Replication-Competent Substitute for Thymidine
journal, January 1997

Site-specific incorporation of biotinylated amino acids to identify surface-exposed residues in integral membrane proteins
journal, October 1997

A general approach for the generation of orthogonal tRNAs
journal, September 2001

Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution: Interaction of the enzyme with the tyrosyl adenylate intermediate
journal, July 1989

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase
journal, December 1999

A Novel Copper-Mediated DNA Base Pair
journal, November 2000

Backbone Mutations in Transmembrane Domains of a Ligand-Gated Ion Channel
journal, January 1999

Strategies for in vitro and in vivo translation with non-natural amino acids
journal, December 1996

A New Functional Suppressor tRNA/Aminoacyl−tRNA Synthetase Pair for the in Vivo Incorporation of Unnatural Amino Acids into Proteins
journal, May 2000

Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base
journal, December 1999