151
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Wiltschi B, Merkel L, Budisa N. Fine tuning the N-terminal residue excision with methionine analogues. Chembiochem 2009; 10:217-20. [PMID: 19067457 DOI: 10.1002/cbic.200800605] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Birgit Wiltschi
- Max Planck Institute of Biochemistry, Molecular Biotechnology, Am Klopferspitz 18, 82152 Martinsried, Germany
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152
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Affiliation(s)
- David P Gamblin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
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153
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Ross TL, Honer M, Lam PYH, Mindt TL, Groehn V, Schibli R, Schubiger PA, Ametamey SM. Fluorine-18 click radiosynthesis and preclinical evaluation of a new 18F-labeled folic acid derivative. Bioconjug Chem 2009; 19:2462-70. [PMID: 19053298 DOI: 10.1021/bc800356r] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The folate receptor (FR) is highly expressed on most epithelial cancer cells, while normal cells show only restricted expression of FR. As a result, the FR is an ideal target for receptor-based molecular imaging and therapy of cancer and has become a promising target in oncology. To date, several folate-based chemotherapeutics and imaging probes such as radiopharmaceuticals for single photon emission computed tomography (SPECT) have been developed. However, an (18)F-labeled folic acid derivative suitable for positron emission tomography (PET) imaging that can be routinely applied is still lacking. In this study, a new fluorinated and radiofluorinated folic acid derivative, (18/19)F-click folate, was synthesized using click chemistry. In a convenient and very efficient two-step radiosynthesis, the isolated (18)F-click folate was obtained in good radiochemical yields of 25-35% with a specific activity of 160+/-70 GBq/micromol after <or=90 min synthesis time. The new compound was pharmacologically evaluated in vitro and in vivo. The affinity of the non-radioactive (19)F-click folate to the FR was determined in displacement studies with FR expressing KB tumor cells using (3)H-folic acid. In these in vitro binding studies, a nanomolar affinity with a K(i) of 9.76+/-3.13 nM was found for (19)F-click folate. The (18)F-labeled click folate derivative was then applied for in vivo PET studies and ex vivo biodistribution experiments using nude mice bearing KB tumor xenografts. The post mortem dissection experiments showed a high specific uptake of (18)F-click folate derivative in FR-expressing tissues. Uptake in KB tumor xenografts and kidneys (FR-positive tissue) amounted to 3.13%ID/g (94% specific blockade) and 16.53%ID/g (75% specific blockade), respectively. PET imaging using (18)F-click folate permitted a visualization of KB tumors, and blockade studies confirmed the specific accumulation of the radiotracer in vivo. However, strong hepatobiliary excretion of the new tracer led to elevated accumulation of radioactivity in the abdominal region. In conclusion, the click chemistry approach is convenient to accomplish and provided high radiochemical yields of (18)F-click folate. The new tracer showed good in vitro but limited in vivo properties. Ultimately, the (18)F-click folate emphasizes the potential of (18)F-labeled folates for receptor-based tumor PET imaging.
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Affiliation(s)
- Tobias L Ross
- Animal Imaging Center-PET, Center for Pharmaceutical Science of ETH, PSI and USZ, 8093 Zurich, Switzerland.
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154
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155
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Agnew HD, Rohde RD, Millward SW, Nag A, Yeo WS, Hein JE, Pitram SM, Tariq AA, Burns VM, Krom RJ, Fokin VV, Sharpless KB, Heath JR. Iterative in situ click chemistry creates antibody-like protein-capture agents. Angew Chem Int Ed Engl 2009; 48:4944-8. [PMID: 19301344 PMCID: PMC3716464 DOI: 10.1002/anie.200900488] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Special agents for protein capture: Iterative in situ click chemistry (see scheme for the tertiary ligand screen) and the one-bead-one-compound method for the creation of a peptide library enable the fragment-based assembly of selective high-affinity protein-capture agents. The resulting ligands are water-soluble and stable chemically, biochemically, and thermally. They can be produced in gram quantities through copper(I)-catalyzed cycloaddition.
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Affiliation(s)
- Heather D. Agnew
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Rosemary D. Rohde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Steven W. Millward
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Woon-Seok Yeo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Jason E. Hein
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Suresh M. Pitram
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Abdul Ahad Tariq
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Vanessa M. Burns
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Russell J. Krom
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Valery V. Fokin
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - K. Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - James R. Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA), Fax: (+1)626-395-2355, Homepage: http://www.its.caltech.edu/~heathgrp
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156
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2333] [Impact Index Per Article: 155.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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157
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Teeuwen RLM, van Berkel SS, van Dulmen THH, Schoffelen S, Meeuwissen SA, Zuilhof H, de Wolf FA, van Hest JCM. “Clickable” elastins: elastin-like polypeptides functionalized with azide or alkyne groups. Chem Commun (Camb) 2009:4022-4. [DOI: 10.1039/b903903a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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158
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Abstract
The development of novel methodology for bond-forming processes that are compatible with biomolecules allows the assembly, alteration, or modification of proteins. Such synthetic proteins allow precise insight and investigation of function in a manner that has the potential for almost unlimited diversity.
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159
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van Dongen SFM, Teeuwen RLM, Nallani M, van Berkel SS, Cornelissen JJLM, Nolte RJM, van Hest JCM. Single-step azide introduction in proteins via an aqueous diazo transfer. Bioconjug Chem 2009; 20:20-3. [PMID: 19099498 DOI: 10.1021/bc8004304] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The controlled introduction of azides in proteins provides targetable handles for selective protein manipulation. We present here an efficient diazo transfer protocol that can be applied in an aqueous solution, leading to the facile introduction of azides in the side chains of lysine residues and at the N-terminus of enzymes, e.g. horseradish peroxidase (HRP) and the red fluorescent protein DsRed. The effective introduction of azides was verified by mass spectrometry, after which the azido-proteins were used in Cu(I)-catalyzed [3 + 2] cycloaddition reactions. Azido-HRP retained its catalytic activity after conjugation of a small molecule. This modified protein could also be successfully immobilized on the surface of an acetylene-covered polymersome. Azido-DsRed was coupled to an acetylene-bearing protein allowing it to act as a fluorescent label, demonstrating the wide applicability of the diazo transfer procedure.
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Affiliation(s)
- Stijn F M van Dongen
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
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160
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Beatty KE, Tirrell DA. Two-color labeling of temporally defined protein populations in mammalian cells. Bioorg Med Chem Lett 2008; 18:5995-9. [PMID: 18774715 PMCID: PMC3182832 DOI: 10.1016/j.bmcl.2008.08.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Revised: 08/11/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022]
Abstract
The proteome undergoes complex changes in response to disease, drug treatment, and normal cellular signaling processes. Characterization of such changes requires methods for time-resolved protein identification and imaging. Here, we describe the application of two reactive methionine (Met) analogues, azidohomoalanine (Aha) and homopropargylglycine (Hpg), to label two protein populations in fixed cells. Reactive lissamine rhodamine (LR), 7-dimethylaminocoumarin (DMAC), and bodipy-630 (BDPY) dyes were prepared and examined for use in selective dye-labeling of newly synthesized proteins in Rat-1 fibroblasts. The LR and DMAC, but not BDPY, fluorophores were found to enable selective, efficient labeling of subsets of the proteome; cells labeled with Aha and Hpg exhibited fluorescence emission three- to sevenfold more intense than that of control cells treated with Met. We also examined simultaneous and sequential pulse-labeling of cells with Aha and Hpg. After pulse-labeling, cells were treated with reactive LR and DMAC dyes, and labeled cells were imaged by fluorescence microscopy and analyzed by flow cytometry. The results of these studies demonstrate that amino acid labeling can be used to achieve selective two-color imaging of temporally defined protein populations in mammalian cells.
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Affiliation(s)
- Kimberly E. Beatty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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161
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Le Chevalier Isaad A, Barbetti F, Rovero P, D'Ursi AM, Chelli M, Chorev M, Papini AM. Nα-Fmoc-Protected ω-Azido- and ω-Alkynyl-L-amino Acids as Building Blocks for the Synthesis of “Clickable” Peptides. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800717] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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162
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Wiltschi B, Wenger W, Nehring S, Budisa N. Expanding the genetic code ofSaccharomyces cerevisiaewith methionine analogues. Yeast 2008; 25:775-86. [DOI: 10.1002/yea.1632] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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163
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Dong S, Merkel L, Moroder L, Budisa N. Convenient syntheses of homopropargylglycine. J Pept Sci 2008; 14:1148-50. [DOI: 10.1002/psc.1065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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164
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Merkel L, Beckmann HSG, Wittmann V, Budisa N. Efficient N-Terminal Glycoconjugation of Proteins by the N-End Rule. Chembiochem 2008; 9:1220-4. [DOI: 10.1002/cbic.200800050] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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165
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Schoffelen S, Lambermon MHL, van Eldijk MB, van Hest JCM. Site-specific modification of Candida antarctica lipase B via residue-specific incorporation of a non-canonical amino acid. Bioconjug Chem 2008; 19:1127-31. [PMID: 18461981 DOI: 10.1021/bc800019v] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to modify proteins in a controlled way, new functionalities need to be introduced in a defined manner. One way to accomplish this is by the incorporation of a non-natural amino acid of which the side chain can selectively be reacted to other molecules. We have investigated whether the relatively simple method of residue-specific replacement of methionine by azidohomoalanine can be used to achieve monofunctionalization of the model enzyme Candida antarctica lipase B. A protein variant was engineered with one additional methionine residue. Due to the high hydrophobicity and low abundance of methionine, this was the only residue out of five that was exposed to the solvent. The use of the Cu (I)-catalyzed [3 + 2] cycloaddition under native conditions resulted in a monofunctionalized enzyme which retained hydrolytic activity. The strategy can be considered a convenient tool to modify proteins at a single position as long as one solvent-exposed methionine is available.
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Affiliation(s)
- Sanne Schoffelen
- Department of Bioorganic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands
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166
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Strable E, Prasuhn DE, Udit AK, Brown S, Link AJ, Ngo JT, Lander G, Quispe J, Potter CS, Carragher B, Tirrell DA, Finn MG. Unnatural amino acid incorporation into virus-like particles. Bioconjug Chem 2008; 19:866-75. [PMID: 18318461 PMCID: PMC2713011 DOI: 10.1021/bc700390r] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Virus-like particles composed of hepatitis B virus (HBV) or bacteriophage Qbeta capsid proteins have been labeled with azide- or alkyne-containing unnatural amino acids by expression in a methionine auxotrophic strain of E. coli. The substitution does not affect the ability of the particles to self-assemble into icosahedral structures indistinguishable from native forms. The azide and alkyne groups were addressed by Cu(I)-catalyzed [3 + 2] cycloaddition: HBV particles were decomposed by the formation of more than 120 triazole linkages per capsid in a location-dependent manner, whereas Qbeta suffered no such instability. The marriage of these well-known techniques of sense-codon reassignment and bioorthogonal chemical coupling provides the capability to construct polyvalent particles displaying a wide variety of functional groups with near-perfect control of spacing.
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167
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Gamblin DP, van Kasteren SI, Chalker JM, Davis BG. Chemical approaches to mapping the function of post-translational modifications. FEBS J 2008; 275:1949-59. [DOI: 10.1111/j.1742-4658.2008.06347.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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168
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Song W, Wang Y, Qu J, Madden M, Lin Q. A Photoinducible 1,3-Dipolar Cycloaddition Reaction for Rapid, Selective Modification of Tetrazole-Containing Proteins. Angew Chem Int Ed Engl 2008; 47:2832-5. [DOI: 10.1002/anie.200705805] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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169
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Song W, Wang Y, Qu J, Madden M, Lin Q. A Photoinducible 1,3-Dipolar Cycloaddition Reaction for Rapid, Selective Modification of Tetrazole-Containing Proteins. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705805] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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170
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Wang A, Winblade Nairn N, Johnson RS, Tirrell DA, Grabstein K. Processing of N-terminal unnatural amino acids in recombinant human interferon-beta in Escherichia coli. Chembiochem 2008; 9:324-30. [PMID: 18098265 DOI: 10.1002/cbic.200700379] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Incorporation of unnatural amino acids into recombinant proteins represents a powerful tool for protein engineering and protein therapeutic development. While the processing of the N-terminal methionine (Met) residues in proteins is well studied, the processing of unnatural amino acids used for replacing the N-terminal Met remains largely unknown. Here we report the effects of the penultimate residue (the residue after the initiator Met) on the processing of two unnatural amino acids, L-azidohomoalanine (AHA) and L-homopropargylglycine (HPG), at the N terminus of recombinant human interferon-beta in E. coli. We have identified specific amino acids at the penultimate position that can be used to efficiently retain or remove N-terminal AHA or HPG. Retention of N-terminal AHA or HPG can be achieved by choosing amino acids with large side chains (such as Gln, Glu, and His) at the penultimate position, while Ala can be selected for the removal of N-terminal AHA or HPG. Incomplete processing of N-terminal AHA and HPG (in terms of both deformylation and cleavage) was observed with Gly or Ser at the penultimate position.
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Affiliation(s)
- Aijun Wang
- Allozyne Inc., 1616 Eastlake Ave E., Seattle, WA 98102, USA.
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171
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Connor RE, Piatkov K, Varshavsky A, Tirrell DA. Enzymatic N-terminal Addition of Noncanonical Amino Acids to Peptides and Proteins. Chembiochem 2008; 9:366-9. [DOI: 10.1002/cbic.200700605] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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172
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Prasuhn DE, Singh P, Strable E, Brown S, Manchester M, Finn M. Plasma clearance of bacteriophage Qbeta particles as a function of surface charge. J Am Chem Soc 2008; 130:1328-34. [PMID: 18177041 PMCID: PMC2657921 DOI: 10.1021/ja075937f] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-assembled protein capsids have gained attention as a promising class of nanoparticles for biomedical applications due to their monodisperse nature and versatile genetic and chemical tailorability. To determine the plasma clearance and tissue distribution in mice of the versatile capsid of bacteriophage Qbeta, the particles were decorated with gadolinium complexes using the CuI-mediated azide-alkyne cycloaddition reaction. Interior surface labeling was engineered by the introduction of an azide-containing unnatural amino acid into the coat protein for the first time. Clearance rates were conveniently monitored by quantitative detection of Gd using inductively coupled plasma optical emission spectroscopy and were found to be inversely proportional to the number of complexes attached to the exterior surface of the particle. This phenomenon was correlated to changes in exterior surface charge brought about by acylation of surface-exposed amine groups in the initial step of the bioconjugation protocol. When primary amine groups were reintroduced by azide-alkyne coupling, the circulation time increased accordingly. These results show that nanoparticle trafficking may be tailored in predictable ways by chemical and genetic modifications that modulate surface charge.
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Affiliation(s)
- Duane E. Prasuhn
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - Pratik Singh
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - Erica Strable
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - Steven Brown
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - Marianne Manchester
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - M.G. Finn
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
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173
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Kas OY, Charati MB, Rothberg LJ, Galvin ME, Kiick KL. Regulation of electronic behavior via confinement of PPV-based oligomers on peptide scaffolds. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b800860d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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174
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Merkel L, Cheburkin Y, Wiltschi B, Budisa N. In Vivo Chemoenzymatic Control of N-Terminal Processing in Recombinant Human Epidermal Growth Factor. Chembiochem 2007; 8:2227-32. [DOI: 10.1002/cbic.200700540] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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175
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van Kasteren SI, Kramer HB, Gamblin DP, Davis BG. Site-selective glycosylation of proteins: creating synthetic glycoproteins. Nat Protoc 2007; 2:3185-94. [DOI: 10.1038/nprot.2007.430] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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176
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Hartman MCT, Josephson K, Lin CW, Szostak JW. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2007; 2:e972. [PMID: 17912351 PMCID: PMC1989143 DOI: 10.1371/journal.pone.0000972] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 09/12/2007] [Indexed: 11/23/2022] Open
Abstract
Background The application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. The specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. We have previously shown that over 90 unnatural amino acids can be enzymatically loaded onto tRNA. Methodology/Principal Findings We have now used a competition assay to assess the efficiency of tRNA-aminoacylation of these analogs. We have also used a series of peptide translation assays to measure the efficiency with which these analogs are incorporated into peptides. The translation apparatus tolerates most side chain derivatives, a few α,α disubstituted, N-methyl and α-hydroxy derivatives, but no β-amino acids. We show that over 50 unnatural amino acids can be incorporated into peptides by ribosomal translation. Using a set of analogs that are efficiently charged and translated we were able to prepare individual peptides containing up to 13 different unnatural amino acids. Conclusions/Significance Our results demonstrate that a diverse array of unnatural building blocks can be translationally incorporated into peptides. These building blocks provide new opportunities for in vitro selections with highly modified drug-like peptides.
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Affiliation(s)
- Matthew C. T. Hartman
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kristopher Josephson
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Chi-Wang Lin
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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177
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178
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van Kasteren SI, Kramer HB, Jensen HH, Campbell SJ, Kirkpatrick J, Oldham NJ, Anthony DC, Davis BG. Expanding the diversity of chemical protein modification allows post-translational mimicry. Nature 2007; 446:1105-9. [PMID: 17460675 DOI: 10.1038/nature05757] [Citation(s) in RCA: 251] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 03/16/2007] [Indexed: 11/10/2022]
Abstract
One of the most important current scientific paradoxes is the economy with which nature uses genes. In all higher animals studied, we have found many fewer genes than we would have previously expected. The functional outputs of the eventual products of genes seem to be far more complex than the more restricted blueprint. In higher organisms, the functions of many proteins are modulated by post-translational modifications (PTMs). These alterations of amino-acid side chains lead to higher structural and functional protein diversity and are, therefore, a leading contender for an explanation for this seeming incongruity. Natural protein production methods typically produce PTM mixtures within which function is difficult to dissect or control. Until now it has not been possible to access pure mimics of complex PTMs. Here we report a chemical tagging approach that enables the attachment of multiple modifications to bacterially expressed (bare) protein scaffolds: this approach allows reconstitution of functionally effective mimics of higher organism PTMs. By attaching appropriate modifications at suitable distances in the widely-used LacZ reporter enzyme scaffold, we created protein probes that included sensitive systems for detection of mammalian brain inflammation and disease. Through target synthesis of the desired modification, chemistry provides a structural precision and an ability to retool with a chosen PTM in a manner not available to other approaches. In this way, combining chemical control of PTM with readily available protein scaffolds provides a systematic platform for creating probes of protein-PTM interactions. We therefore anticipate that this ability to build model systems will allow some of this gene product complexity to be dissected, with the aim of eventually being able to completely duplicate the patterns of a particular protein's PTMs from an in vivo assay into an in vitro system.
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Affiliation(s)
- Sander I van Kasteren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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180
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181
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Beatty KE, Liu JC, Xie F, Dieterich DC, Schuman EM, Wang Q, Tirrell DA. Fluorescence Visualization of Newly Synthesized Proteins in Mammalian Cells. Angew Chem Int Ed Engl 2006; 45:7364-7. [PMID: 17036290 DOI: 10.1002/anie.200602114] [Citation(s) in RCA: 250] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kimberly E Beatty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
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182
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Hartman MCT, Josephson K, Szostak JW. Enzymatic aminoacylation of tRNA with unnatural amino acids. Proc Natl Acad Sci U S A 2006; 103:4356-61. [PMID: 16537388 PMCID: PMC1450175 DOI: 10.1073/pnas.0509219103] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Indexed: 11/18/2022] Open
Abstract
The biochemical flexibility of the cellular translation apparatus offers, in principle, a simple route to the synthesis of drug-like modified peptides and novel biopolymers. However, only approximately 75 unnatural building blocks are known to be fully compatible with enzymatic tRNA acylation and subsequent ribosomal synthesis of modified peptides. Although the translation system can reject substrate analogs at several steps along the pathway to peptide synthesis, much of the specificity resides at the level of the aminoacyl-tRNA synthetase (AARS) enzymes that are responsible for charging tRNAs with amino acids. We have developed an AARS assay based on mass spectrometry that can be used to rapidly identify unnatural monomers that can be enzymatically charged onto tRNA. By using this assay, we have found 59 previously unknown AARS substrates. These include numerous side-chain analogs with useful functional properties. Remarkably, many beta-amino acids, N-methyl amino acids, and alpha,alpha-disubstituted amino acids are also AARS substrates. These previously unidentified AARS substrates will be useful in studies of the specificity of subsequent steps in translation and may significantly expand the number of analogs that can be used for the ribosomal synthesis of modified peptides.
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Affiliation(s)
- Matthew C. T. Hartman
- Department of Molecular Biology and Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114
| | - Kristopher Josephson
- Department of Molecular Biology and Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114
| | - Jack W. Szostak
- Department of Molecular Biology and Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114
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183
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Löwik DWPM, Ayres L, Smeenk JM, Van Hest JCM. Synthesis of Bio-Inspired Hybrid PolymersUsing Peptide Synthesis and Protein Engineering. PEPTIDE HYBRID POLYMERS 2006. [DOI: 10.1007/12_081] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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184
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Abstract
Dissecting complex cellular processes requires the ability to track biomolecules as they function within their native habitat. Although genetically encoded tags such as GFP are widely used to monitor discrete proteins, they can cause significant perturbations to a protein's structure and have no direct extension to other classes of biomolecules such as glycans, lipids, nucleic acids and secondary metabolites. In recent years, an alternative tool for tagging biomolecules has emerged from the chemical biology community--the bioorthogonal chemical reporter. In a prototypical experiment, a unique chemical motif, often as small as a single functional group, is incorporated into the target biomolecule using the cell's own biosynthetic machinery. The chemical reporter is then covalently modified in a highly selective fashion with an exogenously delivered probe. This review highlights the development of bioorthogonal chemical reporters and reactions and their application in living systems.
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Affiliation(s)
- Jennifer A Prescher
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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185
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Datta D, Vaidehi N, Zhang D, Goddard WA. Selectivity and specificity of substrate binding in methionyl-tRNA synthetase. Protein Sci 2005; 13:2693-705. [PMID: 15388861 PMCID: PMC2286561 DOI: 10.1110/ps.04792204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl-tRNA synthetases (aaRS). This paper describes the application of the HierDock computational method to study the molecular basis of amino acid binding to the Escherichia coli methionyl tRNA synthetase (MetRS). Starting with the protein structure from the MetRS cocrystal, the HierDock calculations predict the binding site of methionine in MetRS to a root mean square deviation in coordinates (CRMS) of 0.55 A for all the atoms, compared with the crystal structure. The MetRS conformation in the cocrystal structure shows good discrimination between cognate and the 19 noncognate amino acids. In addition, the calculated binding energies of a set of five methionine analogs show a good correlation (R(2) = 0.86) to the relative free energies of binding derived from the measured in vitro kinetic parameters, K(m) and k(cat). Starting with the crystal structure of MetRS without the methionine (apo-MetRS), the putative binding site of methionine was predicted. We demonstrate that even the apo-MetRS structure shows a preference for binding methionine compared with the 19 other natural amino acids. On comparing the calculated binding energies of the 20 natural amino acids for apo-MetRS with those for the cocrystal structure, we observe that the discrimination against the noncognate substrate increases dramatically in the second step of the physical binding process associated with the conformation change in the protein.
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Affiliation(s)
- Deepshikha Datta
- Materials and Process Simulation Center (MC 139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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186
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Abstract
Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.
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Affiliation(s)
- Lei Wang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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188
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Kaiser J, Kinderman SS, van Esseveldt BCJ, van Delft FL, Schoemaker HE, Blaauw RH, Rutjes FPJT. Synthetic applications of aliphatic unsaturated α-H-α-amino acids. Org Biomol Chem 2005; 3:3435-67. [PMID: 16172678 DOI: 10.1039/b507973j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article provides an overview of the literature concerning synthetic applications of unsaturated aliphatic amino acids in the period May 2000 to December 2004.
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Affiliation(s)
- Jasper Kaiser
- Radboud University Nijmegen, Institute for Molecules and Materials, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
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189
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Budisa N. Prolegomena zum experimentellen Engineering des genetischen Codes durch Erweiterung seines Aminosäurerepertoires. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200300646] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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190
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Budisa N. Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire. Angew Chem Int Ed Engl 2004; 43:6426-63. [PMID: 15578784 DOI: 10.1002/anie.200300646] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Junior Research Group "Moleculare Biotechnologie", Am Klopferspitz 18a, 82152 Martinsried bei München, Germany.
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191
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Large scale enantiomeric synthesis, purification, and characterization of ω-unsaturated amino acids via a Gly-Ni(II)-BPB-complex. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.06.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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192
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Wu Z, Alexandratos J, Ericksen B, Lubkowski J, Gallo RC, Lu W. Total chemical synthesis of N-myristoylated HIV-1 matrix protein p17: structural and mechanistic implications of p17 myristoylation. Proc Natl Acad Sci U S A 2004; 101:11587-92. [PMID: 15280532 PMCID: PMC511025 DOI: 10.1073/pnas.0404649101] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 matrix protein p17, excised proteolytically from the N terminus of the Gag polyprotein, forms a protective shell attached to the inner surface of the plasma membrane of the virus. During the late stages of the HIV-1 replication cycle, the N-terminally myristoylated p17 domain targets the Gag polyprotein to the host-cell membrane for particle assembly. In the early stages of HIV-1 replication, however, some p17 molecules dissociate from the viral membrane to direct the preintegration complex to the host-cell nucleus. These two opposing targeting functions of p17 require that the protein be capable of reversible membrane interaction. It is postulated that a significant structural change in p17 triggered by proteolytic cleavage of the Gag polyprotein sequesters the N-terminal myristoyl group, resulting in a weaker membrane binding by the matrix protein than the Gag precursor. To test this "myristoyl switch" hypothesis, we obtained highly purified synthetic HIV-1 p17 of 131 amino acid residues and its N-myristoylated form in large quantity. Both forms of p17 were characterized by circular dichroism spectroscopy, protein chemical denaturation, and analytical centrifugal sedimentation. Our results indicate that although N-myristoylation causes no spectroscopically discernible conformational change in p17, it stabilizes the protein by 1 kcal/mol and promotes protein trimerization in solution. These findings support the premise that the myristoyl switch in p17 is triggered not by a structural change associated with proteolysis, but rather by the destabilization of oligomeric structures of membrane-bound p17 in the absence of downstream Gag subdomains.
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Affiliation(s)
- Zhibin Wu
- Institute of Human Virology, University of Maryland Biotechnology Institute, and School of Medicine, University of Maryland, 725 West Lombard Street, Baltimore, MD 21201, USA
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193
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Cirino PC, Tang Y, Takahashi K, Tirrell DA, Arnold FH. Global incorporation of norleucine in place of methionine in cytochrome P450 BM-3 heme domain increases peroxygenase activity. Biotechnol Bioeng 2003; 83:729-34. [PMID: 12889037 DOI: 10.1002/bit.10718] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study we have replaced all 13 methionine residues in the cytochrome P450 BM-3 heme domain (463 amino acids) with the isosteric methionine analog norleucine. This experiment has provided a means of testing the functional limits of globally incorporating into an enzyme an unnatural amino acid in place of its natural analog, and also an efficient way to test whether inactivation during peroxide-driven P450 catalysis involves methionine oxidation. Although there was no increase in the stability of the P450 under standard reaction conditions (in 10 mM hydrogen peroxide), complete substitution with norleucine resulted in nearly two-fold-increased peroxygenase activity. Thermostability was significantly reduced. The fact that the enzyme can tolerate such extensive amino acid replacement suggests that we can engineer enzymes with unique chemical properties via incorporation of unnatural amino acids while retaining or improving catalytic properties. This system also provides a platform for directing enzyme evolution using an extended set of protein building blocks.
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Affiliation(s)
- Patrick C Cirino
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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194
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Pál G, Santamaria F, Kossiakoff AA, Lu W. The first semi-synthetic serine protease made by native chemical ligation. Protein Expr Purif 2003; 29:185-92. [PMID: 12767808 DOI: 10.1016/s1046-5928(03)00022-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Selective incorporation of non-natural amino acid residues into proteins is a powerful approach to delineate structure-function relationships. Although many methodologies are available for chemistry-based protein engineering, more facile methods are needed to make this approach suitable for routine laboratory practice. Here, we describe a new strategy and provide a proof of concept for engineering semi-synthetic proteins. We chose a serine protease Streptomyces griseus trypsin (SGT) for this study to show that it is possible to efficiently couple a synthetic peptide containing a catalytically critical residue to a recombinant fragment containing the other active site residues. The 223-residue hybrid SGT molecule was prepared by fusing a chemically synthesized N-terminal peptide to a large C-terminal fragment of recombinant origin using native chemical ligation. This C-terminal polypeptide was produced from full-length SGT by cyanogen bromide cleavage at a genetically engineered Met57 position. This semi-synthetic hybrid trypsin is fully active, showing kinetics identical to the wild-type enzyme. Thus, we believe that it is an ideal model enzyme for studying the catalytic mechanisms of serine proteases by providing a straightforward approach to incorporate non-natural amino acids in the N-terminal region of the protein. In particular, this strategy will allow for replacement of the catalytic His57 residue and the buried N-terminus, which is thought to help align the active site, with synthetic analogs. Our approach relies on readily available recombinant proteins and small synthetic peptides, thus having general applications in chemical engineering of large proteins where the N-terminal region is the focal interest.
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Affiliation(s)
- Gábor Pál
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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195
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Tang Y, Tirrell DA. Attenuation of the editing activity of the Escherichia coli leucyl-tRNA synthetase allows incorporation of novel amino acids into proteins in vivo. Biochemistry 2002; 41:10635-45. [PMID: 12186549 DOI: 10.1021/bi026130x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fidelity of translation is dependent on the specificity of the aminoacyl-tRNA synthetases (aaRSs). The aaRSs that activate the hydrophobic amino acids leucine, isoleucine, and valine employ a proofreading mechanism that hydrolyzes noncognate aminoacyl adenylates and misaminoacylated tRNAs. Discrimination between structurally similar amino acids by these AARSs is believed to operate by a double-sieve principle, wherein a separate editing domain governs hydrolysis on the basis of the size and hydrophilicity of the amino acid side chain. Leucyl-tRNA synthetase (LeuRS) relies on its editing function to correct misaminoacylation of tRNA(Leu) by isoleucine and methionine. Thr252 of Escherichia coli LeuRS has been shown previously to be important in defining the size of the editing cavity. Here we report the isolation and characterization of three LeuRS mutants with point mutations at this position (T252Y, T252L, and T252F). The proofreading activity of the synthetase is significantly impaired when an amino acid bulkier than threonine is introduced. The rate of misaminoacylation of tRNA(Leu) by isoleucine and valine increases with the increasing size of the amino acid substituent at position 252, and the noncognate amino acids norvaline and norleucine are inserted efficiently at the leucine sites of recombinant proteins under conditions of constitutive overexpression of the T252Y mutant in E. coli. In addition, the unsaturated amino acids allylglycine, homoallylglycine, homopropargylglycine, and 2-butynylalanine all support protein synthesis in E. coli hosts harboring the mutant synthetase. These results demonstrate that programmed manipulation of the editing cavity can allow in vivo incorporation of novel protein building blocks.
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Affiliation(s)
- Yi Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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196
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Zhang Z, Wang L, Brock A, Schultz PG. The selective incorporation of alkenes into proteins in Escherichia coli. Angew Chem Int Ed Engl 2002; 41:2840-2. [PMID: 12203503 DOI: 10.1002/1521-3773(20020802)41:15<2840::aid-anie2840>3.0.co;2-#] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhiwen Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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197
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MESH Headings
- Amino Acids/metabolism
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/isolation & purification
- Base Sequence
- Cloning, Molecular/methods
- Directed Molecular Evolution/methods
- Models, Biological
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Protein Engineering/methods
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/isolation & purification
- RNA, Transfer/metabolism
- Sensitivity and Specificity
- Substrate Specificity
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198
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Zhang D, Vaidehi N, Goddard WA, Danzer JF, Debe D. Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine. Proc Natl Acad Sci U S A 2002; 99:6579-84. [PMID: 12011422 PMCID: PMC124445 DOI: 10.1073/pnas.052150499] [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] [Accepted: 03/12/2002] [Indexed: 11/18/2022] Open
Abstract
Although incorporation of amino acid analogs provides a powerful means of producing new protein structures with interesting functions, many amino acid analogs cannot be incorporated easily by using the wild-type aminoacyl-tRNA synthetase (aaRS). To be able to incorporate specific amino acid analogs site-specifically, it is useful to build a mutant aaRS that preferentially activates the analog compared with the natural amino acids. Experimental combinatorial studies to find such mutant aaRSs have been successful but can easily become costly and time-consuming. In this article, we describe the clash opportunity progressive (COP) computational method for designing a mutant aaRS to preferentially take up the analog compared with the natural amino acids. To illustrate this COP procedure, we apply it to the design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase (M.jann-TyrRS). Because the three-dimensional structure for M.jann-TyrRS was not available, we used the STRUCTFAST homology modeling procedure plus molecular dynamics with continuum solvent forces to predict the structure of wild-type M.jann-TyrRS. We validate this structure by predicting the binding site for tyrosine and calculating the binding energies of the 20 natural amino acids, which shows that tyrosine binds the strongest. With the COP design algorithm we then designed a mutant tyrosyl tRNA synthetase to activate O-methyl-l-tyrosine preferentially compared with l-tyrosine. This mutant [Y32Q, D158A] is similar to the mutant designed with combinatorial experiments, [Y32Q, D158A, E107T, L162P], by Wang et al. [Wang, L., Brock, A., Herberich, B. & Schultz, P. G. (2001) Science 292, 498-500]. We predict that the new one will have much greater activity while retaining significant discrimination between O-methyl-l-tyrosine and tyrosine.
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Affiliation(s)
- Deqiang Zhang
- Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125; and BionomiX, Pasadena, CA 91106, USA
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199
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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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200
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Kiick KL, Saxon E, Tirrell DA, Bertozzi CR. Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation. Proc Natl Acad Sci U S A 2002; 99:19-24. [PMID: 11752401 PMCID: PMC117506 DOI: 10.1073/pnas.012583299] [Citation(s) in RCA: 710] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2001] [Accepted: 10/31/2001] [Indexed: 11/18/2022] Open
Abstract
The introduction of chemically unique groups into proteins by means of non-natural amino acids has numerous applications in protein engineering and functional studies. One method to achieve this involves the utilization of a non-natural amino acid by the cell's native translational apparatus. Here we demonstrate that a methionine surrogate, azidohomoalanine, is activated by the methionyl-tRNA synthetase of Escherichia coli and replaces methionine in proteins expressed in methionine-depleted bacterial cultures. We further show that proteins containing azidohomoalanine can be selectively modified in the presence of other cellular proteins by means of Staudinger ligation with triarylphosphine reagents. Incorporation of azide-functionalized amino acids into proteins in vivo provides opportunities for protein modification under native conditions and selective labeling of proteins in the intracellular environment.
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Affiliation(s)
- Kristi L Kiick
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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