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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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2
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Torbeev V, Kent SBH. Chemical Synthesis of an Enzyme Containing an Artificial Catalytic Apparatus. Aust J Chem 2020. [DOI: 10.1071/ch19460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
With the goal of investigating electronic aspects of the catalysis of peptide bond hydrolysis, an analogue of HIV-1 protease was designed in which a non-peptide hydroxy-isoquinolinone artificial catalytic apparatus replaced the conserved Asp25–Thr26–Gly27 sequence in each 99-residue polypeptide chain of the homodimeric enzyme molecule. The enzyme analogue was prepared by total chemical synthesis and had detectable catalytic activity on known HIV-1 protease peptide substrates. Compared with uncatalyzed hydrolysis, the analogue enzyme increased the rate of peptide bond hydrolysis by ∼108-fold. Extensions of this unique approach to the study of enzyme catalysis in HIV-1 protease are discussed.
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3
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Fujino T, Murakami H. In VitroSelection Combined with Ribosomal Translation Containing Non-proteinogenic Amino Acids. CHEM REC 2016; 16:365-77. [DOI: 10.1002/tcr.201500239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Tomoshige Fujino
- Department of Chemical and Biological Engineering, School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroshi Murakami
- Department of Chemical and Biological Engineering, School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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4
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Brut M, Estève A, Landa G, Djafari Rouhani M. Toward in silico biomolecular manipulation through static modes: atomic scale characterization of HIV-1 protease flexibility. J Phys Chem B 2014; 118:2821-30. [PMID: 24568689 DOI: 10.1021/jp4113156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current computational biology for fundamental understanding and prediction of biomolecular interactions and associated functions. This paper makes use of the static mode method to study HIV-1 protease considered as a model system to investigate the full biomolecular flexibility at the atomic scale, the screening of active site biomechanical properties, the blind prediction of allosteric sites, and the design of multisite strategies to target deformations of interest. Relying on this single calculation run of static modes, we demonstrate that in silico predictive design of an infinite set of complex excitation fields is reachable, thanks to the storage of the static modes in a data bank that can be used to mimic single or multiatom contact and efficiently anticipate conformational changes arising from external stimuli. All along this article, we compare our results to data previously published and propose a guideline for efficient, predictive, and custom in silico experiments.
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Affiliation(s)
- Marie Brut
- CNRS , LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
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5
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Kawakami T, Sasaki T, Reid PC, Murakami H. Incorporation of electrically charged N-alkyl amino acids into ribosomally synthesized peptides via post-translational conversion. Chem Sci 2014. [DOI: 10.1039/c3sc52744a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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6
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Chen S, Fahmi NE, Nangreave RC, Mehellou Y, Hecht SM. Synthesis of pdCpAs and transfer RNAs activated with thiothreonine and derivatives. Bioorg Med Chem 2012; 20:2679-89. [PMID: 22405920 PMCID: PMC3575115 DOI: 10.1016/j.bmc.2012.02.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/05/2012] [Accepted: 02/08/2012] [Indexed: 11/29/2022]
Abstract
N,S-diprotected L-thiothreonine and L-allo-thiothreonine derivatives were synthesized using a novel chemical strategy, and used for esterification of the dinucleotide pdCpA. The aminoacylated dinucleotides were then employed for the preparation of activated suppressor tRNA(CUA) transcripts. Thiothreonine and allo-thiothreonine were incorporated into a predetermined position of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine, and the elaborated proteins were derivatized site-specifically at the thiothreonine residue with a fluorophore.
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Affiliation(s)
- Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Ryan C. Nangreave
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Youcef Mehellou
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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7
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Transition states of native and drug-resistant HIV-1 protease are the same. Proc Natl Acad Sci U S A 2012; 109:6543-8. [PMID: 22493227 DOI: 10.1073/pnas.1202808109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
HIV-1 protease is an important target for the treatment of HIV/AIDS. However, drug resistance is a persistent problem and new inhibitors are needed. An approach toward understanding enzyme chemistry, the basis of drug resistance, and the design of powerful inhibitors is to establish the structure of enzymatic transition states. Enzymatic transition structures can be established by matching experimental kinetic isotope effects (KIEs) with theoretical predictions. However, the HIV-1 protease transition state has not been previously resolved using these methods. We have measured primary (14)C and (15)N KIEs and secondary (3)H and (18)O KIEs for native and multidrug-resistant HIV-1 protease (I84V). We observed (14)C KIEs ((14)V/K) of 1.029 ± 0.003 and 1.025 ± 0.005, (15)N KIEs ((15)V/K) of 0.987 ± 0.004 and 0.989 ± 0.003, (18)O KIEs ((18)V/K) of 0.999 ± 0.003 and 0.993 ± 0.003, and (3)H KIEs ((3)V/K) KIEs of 0.968 ± 0.001 and 0.976 ± 0.001 for the native and I84V enzyme, respectively. The chemical reaction involves nucleophilic water attack at the carbonyl carbon, proton transfer to the amide nitrogen leaving group, and C-N bond cleavage. A transition structure consistent with the KIE values involves proton transfer from the active site Asp-125 (1.32 Å) with partial hydrogen bond formation to the accepting nitrogen (1.20 Å) and partial bond loss from the carbonyl carbon to the amide leaving group (1.52 Å). The KIEs measured for the native and I84V enzyme indicate nearly identical transition states, implying that a true transition-state analogue should be effective against both enzymes.
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8
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Shen CH, Wang YF, Kovalevsky AY, Harrison RW, Weber IT. Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. FEBS J 2010; 277:3699-714. [PMID: 20695887 DOI: 10.1111/j.1742-4658.2010.07771.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural and kinetic effects of amprenavir (APV), a clinical HIV protease (PR) inhibitor, were analyzed with wild-type enzyme and mutants with single substitutions of V32I, I50V, I54V, I54M, I84V and L90M that are common in drug resistance. Crystal structures of the APV complexes at resolutions of 1.02-1.85 Å reveal the structural changes due to the mutations. Substitution of the larger side chains in PR(V32I) , PR(I54M) and PR(L90M) resulted in the formation of new hydrophobic contacts with flap residues, residues 79 and 80, and Asp25, respectively. Mutation to smaller side chains eliminated hydrophobic interactions in the PR(I50V) and PR(I54V) structures. The PR(I84V)-APV complex had lost hydrophobic contacts with APV, the PR(V32I)-APV complex showed increased hydrophobic contacts within the hydrophobic cluster and the PR(I50V) complex had weaker polar and hydrophobic interactions with APV. The observed structural changes in PR(I84V)-APV, PR(V32I)-APV and PR(I50V)-APV were related to their reduced inhibition by APV of six-, 10- and 30-fold, respectively, relative to wild-type PR. The APV complexes were compared with the corresponding saquinavir complexes. The PR dimers had distinct rearrangements of the flaps and 80's loops that adapt to the different P1' groups of the inhibitors, while maintaining contacts within the hydrophobic cluster. These small changes in the loops and weak internal interactions produce the different patterns of resistant mutations for the two drugs.
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Affiliation(s)
- Chen-Hsiang Shen
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA, USA
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9
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Serwa R, Majkut P, Horstmann B, Swiecicki JM, Gerrits M, Krause E, Hackenberger CPR. Site-specific PEGylation of proteins by a Staudinger-phosphite reaction. Chem Sci 2010. [DOI: 10.1039/c0sc00324g] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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10
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Serwa R, Wilkening I, Del Signore G, Mühlberg M, Claußnitzer I, Weise C, Gerrits M, Hackenberger C. Chemoselektive Staudinger-Phosphit-Reaktion von Aziden für die Phosphorylierung von Proteinen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902118] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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11
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Serwa R, Wilkening I, Del Signore G, Mühlberg M, Claußnitzer I, Weise C, Gerrits M, Hackenberger C. Chemoselective Staudinger-Phosphite Reaction of Azides for the Phosphorylation of Proteins. Angew Chem Int Ed Engl 2009; 48:8234-9. [DOI: 10.1002/anie.200902118] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Kawakami T, Murakami H, Suga H. Ribosomal Synthesis of Polypeptoids and Peptoid−Peptide Hybrids. J Am Chem Soc 2008; 130:16861-3. [DOI: 10.1021/ja806998v] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takashi Kawakami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Murakami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan, and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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13
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Synthesis of pdCpAs and transfer RNAs activated with derivatives of aspartic acid and cysteine. Bioorg Med Chem 2008; 16:9023-31. [PMID: 18790645 DOI: 10.1016/j.bmc.2008.08.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/14/2008] [Accepted: 08/15/2008] [Indexed: 11/21/2022]
Abstract
Described herein is the preparation of new aminoacylated derivatives of the dinucleotide pdCpA, and of transfer RNAs. The focus of the present work is the synthesis of amino acid analogs related to aspartic acid and cysteine species that have important functional roles in many proteins. The activated aminoacyl-tRNAs prepared can be utilized for the elaboration of proteins containing modified aspartic acid and cysteine derivatives at predetermined sites. Of particular interest is definition of functional group protection strategies that can be used for the preparation of the aminoacylated pdCpAs and tRNAs.
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14
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Kawakami T, Murakami H, Suga H. Messenger RNA-Programmed Incorporation of Multiple N-Methyl-Amino Acids into Linear and Cyclic Peptides. ACTA ACUST UNITED AC 2008; 15:32-42. [DOI: 10.1016/j.chembiol.2007.12.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 11/25/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
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15
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Johnson ECB, Malito E, Shen Y, Rich D, Tang WJ, Kent SBH. Modular total chemical synthesis of a human immunodeficiency virus type 1 protease. J Am Chem Soc 2007; 129:11480-90. [PMID: 17705484 DOI: 10.1021/ja072870n] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of our ongoing studies of the human immunodeficiency virus type 1 (HIV-1) protease enzyme, we set out to develop a modular chemical synthesis of the protein from multiple peptide segments. Our initial attempts were frustrated by the insolubility of intermediate peptide products. To overcome this problem, we designed a synthetic strategy combining the solubility-enhancing properties of C-terminal (Arg)n tags and the biological phenomenon of autoprocessing of the Gag-Pol polyprotein that occurs during maturation of the HIV-1 virus in vivo. Synthesis of a 119-residue peptide chain containing 10 residues of the reverse transcriptase (RT) open reading frame plus an (Arg)(10) tag at the C-terminus was straightforward by native chemical ligation followed by conversion of the Cys residues to Ala by Raney nickel desulfurization. The product polypeptide itself completed the final synthetic step by removing the C-terminal modification under folding conditions, to give the mature 99-residue polypeptide. High-purity homodimeric HIV-1 protease protein was obtained in excellent yield and had full enzymatic activity; the structure of the synthetic enzyme was confirmed by X-ray crystallography to a resolution of 1.07 A. This efficient modular synthesis by a biomimetic autoprocessing strategy will enable the facile synthesis of unique chemical analogues of the HIV-1 protease to further elucidate the molecular basis of enzyme catalysis.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Ben-May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, USA
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16
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Röhrig CH, Retz OA, Meergans T, Schmidt RR. In vitro non-natural amino acid mutagenesis using a suppressor tRNA generated by the cis-acting hepatitis delta virus ribozyme. Biochem Biophys Res Commun 2005; 325:731-8. [PMID: 15541351 DOI: 10.1016/j.bbrc.2004.10.086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Indexed: 10/26/2022]
Abstract
In vitro non-natural amino acid mutagenesis requires aminoacyl-charged suppressor transfer RNAs which read an internal stop codon. For the synthesis of aminoacyl-tRNAs loaded with non-natural amino acids, T4 RNA ligase is used to ligate a chemically synthesised aminoacyl-dinucleotide to a truncated 74mer tRNA(-CA) lacking the two 3' end nucleotides. The 74mer tRNA(-CA) in turn is generated by run-off transcription from a linearised plasmid encoding the tRNA sequence under control of the T7 promoter. Transcripts with heterogeneous ends are commonly obtained, which interfere with subsequent reactions such as ligation or translation. Here we report an improved procedure for the generation and chromatographic purification of large amounts of homogeneous 3' end tRNA(-CA) by hepatitis delta virus ribozyme cis-cleavage and the first application of this tRNA to in vitro non-natural amino acid mutagenesis. Stop codon suppression is increased compared to conventionally synthesised suppressor tRNA; 2.5 microg of mutated protein was synthesised in a 50 microl batch reaction.
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Affiliation(s)
- Christoph H Röhrig
- Department of Chemistry, University of Konstanz, Fach M 725, D-78457 Konstanz, Germany
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17
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Rothman DM, Petersson EJ, Vázquez ME, Brandt GS, Dougherty DA, Imperiali B. Caged Phosphoproteins. J Am Chem Soc 2004; 127:846-7. [PMID: 15656617 DOI: 10.1021/ja043875c] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the chemical and biological synthesis of caged phosphoproteins using the in vitro nonsense codon suppression methodology. Specifically, phosphoamino acid analogues of serine, threonine, and tyrosine with a single photocleavable o-nitrophenylethyl caging group were synthesized as the amino acyl tRNA adducts for insertion into full-length proteins. For this purpose, a novel phosphitylating agent was developed. The successful incorporation of these bulky and charged amino acids into the alpha-subunit of the nicotinic acetyl choline receptor (nAChR) and the vasodilator-stimulated phosphoprotein (VASP) using an in vitro translation system is reported.
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Affiliation(s)
- Deborah M Rothman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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18
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Klarmann GJ, Eisenhauer BM, Zhang Y, Sitaraman K, Chatterjee DK, Hecht SM, Le Grice SFJ. Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase. Protein Expr Purif 2004; 38:37-44. [PMID: 15477080 DOI: 10.1016/j.pep.2004.07.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Revised: 07/14/2004] [Indexed: 11/24/2022]
Abstract
A highly efficient cell-free translation system has been combined with suppressor tRNA technology to substitute nor-Tyr and 3-fluoro-Tyr in place of Tyr183 at the DNA polymerase active site of p66 of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). Supplementing the wild-type HIV-1 p51 RT subunit into this translation system permitted reconstitution of the biologically relevant p66/p51 heterodimer harboring Tyr analogs exclusively on the catalytically competent p66 subunit. Addition of an affinity tag at the p66 C-terminus allowed rapid, one-step purification of reconstituted and selectively mutated heterodimer HIV-1 RT via strep-Tactin-agarose affinity chromatography. The purified enzyme was demonstrated to be free of contaminating nucleases, allowing characterization of the DNA polymerase and ribonuclease H activities associated with HIV-1 RT. Preliminary characterization of HIV-1 RT(nor-Tyr) and HIV-1 RT(m-fluoro-Tyr) is presented. The success of this strategy will facilitate detailed molecular analysis of structurally and catalytically critical amino acids via their replacement with closely related, unnatural analogs.
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Affiliation(s)
- George J Klarmann
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, MD, USA
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Quarleri JF, Rubio A, Carobene M, Turk G, Vignoles M, Harrigan RP, Montaner JSG, Salomón H, Gómez-Carrillo M. HIV type 1 BF recombinant strains exhibit different pol gene mosaic patterns: descriptive analysis from 284 patients under treatment failure. AIDS Res Hum Retroviruses 2004; 20:1100-7. [PMID: 15585101 DOI: 10.1089/aid.2004.20.1100] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Different complex structures of the pol gene have been identified in 284 HIV-1 B/F recombinant sequences obtained from a group of 587 patients under treatment failure from Argentina. To analyze the mosaic structures of these viral sequences and to determine their phylogenetic relationship, the 284 partial pol gene sequences of BF recombinant viruses were amplified by RT-PCR and sequenced. Intersubtype breakpoints were analyzed by bootscanning. Phylogenetic relationships were determined by means of neighbor-joining trees. The analysis of the sequences showed multiple phylogenetic topologies clustering within intersubtype BF reference sequences. At least three different mosaic patterns were found compared to previously described BF-type viruses with unequal distribution in the studied population. The analysis also showed that HIV-1 BF recombinant viruses with diverse mosaic structures are phylogenetically related in their F segments and in selected B fragments with the F1 subtype and with BF recombinant viruses from Brazil, respectively, suggesting a common recombinant ancestor. No association was observed between the prevalence of each mosaic pattern and the frequency of major drug-resistance mutations in PR and RT.
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Affiliation(s)
- Jorge F Quarleri
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, 1121 Buenos Aires, Argentina.
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20
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Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Mol Biol 2003; 10:425-32. [PMID: 12754495 DOI: 10.1038/nsb934] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 04/22/2003] [Indexed: 11/09/2022]
Abstract
The archaeal/eukaryotic tyrosyl-tRNA synthetase (TyrRS)-tRNA(Tyr) pairs do not cross-react with their bacterial counterparts. This 'orthogonal' condition is essential for using the archaeal pair to expand the bacterial genetic code. In this study, the structure of the Methanococcus jannaschii TyrRS-tRNA(Tyr)-L-tyrosine complex, solved at a resolution of 1.95 A, reveals that this archaeal TyrRS strictly recognizes the C1-G72 base pair, whereas the bacterial TyrRS recognizes the G1-C72 in a different manner using different residues. These diverse tRNA recognition modes form the basis for the orthogonality. The common tRNA(Tyr) identity determinants (the discriminator, A73 and the anticodon residues) are also recognized in manners different from those of the bacterial TyrRS. Based on this finding, we created a mutant TyrRS that aminoacylates the amber suppressor tRNA with C34 65 times more efficiently than does the wild-type enzyme.
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Affiliation(s)
- Takatsugu Kobayashi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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21
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Koo JC, Lam JS, Chass GA, Torday LL, Varro A, Papp JG. Conformational dependence of the intrinsic acidity of the aspartic acid residue sidechain in N-acetyl-l-aspartic acid-N′-methylamide. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(02)00639-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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How reliable could economic Hartree–Fock computations be in studying large, folded peptides? A comparative HF and DFT case study on N- and C-protected aspartic acid. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00579-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H, Soma A, Kobayashi T, Kitabatake M, Takio K, Saito K, Shirouzu M, Hirao I, Yokoyama S. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 2002; 30:4692-9. [PMID: 12409460 PMCID: PMC135798 DOI: 10.1093/nar/gkf589] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Revised: 08/23/2002] [Accepted: 08/23/2002] [Indexed: 11/13/2022] Open
Abstract
A suppressor tRNA(Tyr) and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-L-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNA(Tyr) gene was mutated, at three positions in the D arm, to generate the internal promoter for expression. However, this tRNA, together with the cognate TyrRS, failed to exhibit suppressor activity in mammalian cells. Then, we found that amber suppression can occur with the heterologous pair of E.coli TyrRS and Bacillus stearothermophilus suppressor tRNA(Tyr), which naturally contains the promoter sequence. Furthermore, the efficiency of this suppression was significantly improved when the suppressor tRNA was expressed from a gene cluster, in which the tRNA gene was tandemly repeated nine times in the same direction. For incorporation of 3-iodo-L-tyrosine, its specific E.coli TyrRS variant, TyrRS(V37C195), which we recently created, was expressed in mammalian cells, together with the B.stearothermophilus suppressor tRNA(Tyr), while 3-iodo-L-tyrosine was supplied in the growth medium. 3-Iodo-L-tyrosine was thus incorporated into the proteins at amber positions, with an occupancy of >95%. Finally, we demonstrated conditional 3-iodo-L-tyrosine incorporation, regulated by inducible expression of the TyrRS(V37C195) gene from a tetracycline-regulated promoter.
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Affiliation(s)
- Kensaku Sakamoto
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Anderson RD, Zhou J, Hecht SM. Fluorescence resonance energy transfer between unnatural amino acids in a structurally modified dihydrofolate reductase. J Am Chem Soc 2002; 124:9674-5. [PMID: 12175203 DOI: 10.1021/ja0205939] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cleavage of a substrate protein by HIV-1 protease has been monitored in real time by the use of a dihydrofolate reductase fusion protein in which a fluorescence donor and a fluorescence acceptor were introduced into sites flanking the HIV-1 protease cleavage site. The amino acids 7-azatryptophan and dabcyl-1,2-diaminopropionic acid were introduced into specific sites of the DHFR fusion protein in an in vitro protein biosynthesizing system using two misacylated suppressor tRNAs, each of which recognized a specific, unique codon introduced into the mRNA. Excitation of the fluorescence acceptor in the initially expressed protein afforded no light production, consistent with quenching by fluorescence resonance energy transfer. Treatment of the elaborated protein with HIV-1 protease cleaved the protein between the fluorescence donor and acceptor, affording a time-dependent increase in fluorescence that was equal in magnitude to that produced by admixture of a stoichiometric amount of free 7-azatryptophan to the solution containing the intact protein.
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Affiliation(s)
- Raymond D Anderson
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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25
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Koo JCP, Chass GA, Perczel A, Farkas Ö, Torday LL, Varro A, Papp JG, Csizmadia IG. Exploration of the Four-Dimensional-Conformational Potential Energy Hypersurface of N-Acetyl-l-aspartic Acid N‘-Methylamide with Its Internally Hydrogen Bonded Side-Chain Orientation. J Phys Chem A 2002. [DOI: 10.1021/jp014514b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph C. P. Koo
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Gregory A. Chass
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Andras Perczel
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Ödon Farkas
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Ladislaus L. Torday
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Andras Varro
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Julius Gy. Papp
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
| | - Imre G. Csizmadia
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6, Velocet R & D, 210 Dundas Street West, Suite 810, Toronto, Ontario, Canada M5G 2E8, Department of Organic Chemistry, Eotvos University, H-1117, Budapest, Hungary, Department of Pharmacology and Pharmacotherapy, Szeged University, Dóm tér 12, H-6701, Szeged, Hungary, and Division of Cardiovascular Pharmacology, Hungarian Academy of Sciences and Szeged University, Dóm tér 12, H-6701, Szeged, Hungary
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26
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Avram S, Movileanu L, Mihailescu D, Flonta ML. Comparative study of some energetic and steric parameters of the wild type and mutants HIV-1 protease: a way to explain the viral resistance. J Cell Mol Med 2002; 6:251-60. [PMID: 12169210 PMCID: PMC6740297 DOI: 10.1111/j.1582-4934.2002.tb00192.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Because, in vivo, the HIV-1 PR ( HIV-1 protease) present a high mutation rate we performed a comparative study of the energetic behaviors of the wild type HIV-1 PR and four type of mutants: Val82/Asn; Val82/Asp; Gln7/Lys, Leu33/Ile, Leu63/Ile; Ala71/Thr, Val82/Ala. We suggest that the energetic fluctuation (electrostatic, van der Waals and torsion energy) of the mutants and the solvent accessible surface (SAS) values can be useful to explain the viral resistance process developed by HIV-1 PR. The number and localization of enzyme mutations induce important modifications of the van der Waals and torsional energy, while the electrostatic energy has an insignificant fluctuation. We showed that the viral resistance can be explored if the solvent accessible surfaces of the active site for the mutant structures are calculated. In this paper we have obtained the solvent accessible surface for a group of 15 mutants (11 mutants obtained by Protein Data Bank (PDB) file, 4 mutants modeled by CHARMM software) and for the wild type HIV-1 PR). Our study try to show that the number and localization of the mutations are factors which induce the HIV-1 PR viral resistance. The larger solvent accessible surface could be recorded for the point mutant Val 82/Phe.
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Affiliation(s)
- Speranta Avram
- Department of Physiology and Biophysics, University of Bucharest, Faculty of Biology, Splaiul Independentei 91-95, Bucharest, R-76201, Romania.
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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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