101
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Wallat JD, Rose KA, Pokorski JK. Proteins as substrates for controlled radical polymerization. Polym Chem 2014. [DOI: 10.1039/c3py01193c] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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102
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Steen Redeker E, Ta DT, Cortens D, Billen B, Guedens W, Adriaensens P. Protein Engineering For Directed Immobilization. Bioconjug Chem 2013; 24:1761-77. [DOI: 10.1021/bc4002823] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Erik Steen Redeker
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Duy Tien Ta
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - David Cortens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Brecht Billen
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Wanda Guedens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Peter Adriaensens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
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103
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Ribeiro-Viana R, Sánchez-Navarro M, Luczkowiak J, Koeppe JR, Delgado R, Rojo J, Davis BG. Virus-like glycodendrinanoparticles displaying quasi-equivalent nested polyvalency upon glycoprotein platforms potently block viral infection. Nat Commun 2013; 3:1303. [PMID: 23250433 PMCID: PMC3535419 DOI: 10.1038/ncomms2302] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/15/2012] [Indexed: 01/08/2023] Open
Abstract
Ligand polyvalency is a powerful modulator of protein–receptor interactions. Host–pathogen infection interactions are often mediated by glycan ligand–protein interactions, yet its interrogation with very high copy number ligands has been limited to heterogenous systems. Here we report that through the use of nested layers of multivalency we are able to assemble the most highly valent glycodendrimeric constructs yet seen (bearing up to 1,620 glycans). These constructs are pure and well-defined single entities that at diameters of up to 32 nm are capable of mimicking pathogens both in size and in their highly glycosylated surfaces. Through this mimicry these glyco-dendri-protein-nano-particles are capable of blocking (at picomolar concentrations) a model of the infection of T-lymphocytes and human dendritic cells by Ebola virus. The high associated polyvalency effects (β>106, β/N ~102–103) displayed on an unprecedented surface area by precise clusters suggest a general strategy for modulation of such interactions. Host–pathogen relationships can be mediated by polyvalent glycan ligand–protein interactions. Here well-defined highly valent glycodendrimeric constructs are synthesized that can mimic pathogens, and can inhibit a model of infection by the Ebola virus.
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Affiliation(s)
- Renato Ribeiro-Viana
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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104
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Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP. Multiple Site-Selective Insertions of Noncanonical Amino Acids into Sequence-Repetitive Polypeptides. Chembiochem 2013; 14:968-78. [DOI: 10.1002/cbic.201300069] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 11/11/2022]
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105
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Krueger AT, Imperiali B. Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology. Chembiochem 2013; 14:788-99. [DOI: 10.1002/cbic.201300079] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 12/16/2022]
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106
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Li C, Glidle A, Yuan X, Hu Z, Pulleine E, Cooper J, Yang W, Yin H. Creating “Living” Polymer Surfaces to Pattern Biomolecules and Cells on Common Plastics. Biomacromolecules 2013; 14:1278-86. [DOI: 10.1021/bm4000597] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Chunyan Li
- State Key Laboratory of Chemical
Resource Engineering, Key Laboratory of Carbon Fiber and Functional
Polymers, Ministry of Education, College of Materials
Science and Engineering, Beijing University of Chemical Technology, Beijing, China 100029
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
| | - Andrew Glidle
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
| | - Xiaofei Yuan
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
| | - Zhixiong Hu
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
- Division
of Medical
and Biological Measurements, National Institute of Metrology, Beijing, China 100013
| | - Ellie Pulleine
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
| | - Jon Cooper
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
| | - Wantai Yang
- State Key Laboratory of Chemical
Resource Engineering, Key Laboratory of Carbon Fiber and Functional
Polymers, Ministry of Education, College of Materials
Science and Engineering, Beijing University of Chemical Technology, Beijing, China 100029
| | - Huabing Yin
- College of Science and Engineering,
Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United
Kingdom
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107
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Abstract
Post-translational modifications of proteins can have dramatic effect on the function of proteins. Significant research effort has gone into understanding the effect of particular modifications on protein parameters. In the present paper, I review some of the recently developed tools for the synthesis of proteins modified with single post-translational modifications at specific sites in the protein, such as amber codon suppression technologies, tag and modify, and native chemical ligation.
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108
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Szymański W, Wu B, Poloni C, Janssen DB, Feringa BL. Azobenzene Photoswitches for Staudinger-Bertozzi Ligation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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109
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Szymański W, Wu B, Poloni C, Janssen DB, Feringa BL. Azobenzene Photoswitches for Staudinger-Bertozzi Ligation. Angew Chem Int Ed Engl 2013; 52:2068-72. [DOI: 10.1002/anie.201208596] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/03/2012] [Indexed: 11/07/2022]
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110
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Duan X, Li H, Chen H, Wang Q. Discrimination of colon cancer stem cells using noncanonical amino acid. Chem Commun (Camb) 2012; 48:9035-7. [PMID: 22842824 PMCID: PMC4821495 DOI: 10.1039/c2cc33776b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer stem cells (CSCs) may be responsible for tumor recurrence. Metabolic labelling of newly synthesized proteins with non-canonical amino acids allows us to discriminate CSCs in mixed populations due to the quiescent nature of these cells.
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Affiliation(s)
- Xinrui Duan
- Department of Chemistry and Biochemistry & Nanocenter, University of South Carolina, Columbia, SC 29208 (USA)
| | - Honglin Li
- Department of Chemistry and Biochemistry & Nanocenter, University of South Carolina, Columbia, SC 29208 (USA)
| | - Hexin Chen
- Department of Biology, University of South Carolina, Columbia, SC 29208 (USA)
| | - Qian Wang
- Department of Chemistry and Biochemistry & Nanocenter, University of South Carolina, Columbia, SC 29208 (USA)
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111
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Abstract
The collection of chemical techniques that can be used to attach synthetic groups to proteins has expanded substantially in recent years. Each of these approaches allows new protein targets to be addressed, leading to advances in biological understanding, new protein-drug conjugates, targeted medical imaging agents and hybrid materials with complex functions. The protein modification reactions in current use vary widely in their inherent site selectivity, overall yields and functional group compatibility. Some are more amenable to large-scale bioconjugate production, and a number of techniques can be used to label a single protein in a complex biological mixture. This review examines the way in which experimental circumstances influence one's selection of an appropriate protein modification strategy. It also provides a simple decision tree that can narrow down the possibilities in many instances. The review concludes with example studies that examine how this decision process has been applied in different contexts.
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112
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Seim KL, Obermeyer AC, Francis MB. Oxidative modification of native protein residues using cerium(IV) ammonium nitrate. J Am Chem Soc 2011; 133:16970-6. [PMID: 21967510 DOI: 10.1021/ja206324q] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new protein modification strategy has been developed that is based on an oxidative coupling reaction that targets electron-rich amino acids. This strategy relies on cerium(IV) ammonium nitrate (CAN) as an oxidation reagent and results in the coupling of tyrosine and tryptophan residues to phenylene diamine and anisidine derivatives. The methodology was first identified and characterized on peptides and small molecules, and was subsequently adapted for protein modification by determining appropriate buffer conditions. Using the optimized procedure, native and introduced solvent-accessible residues on proteins were selectively modified with polyethylene glycol (PEG) and small peptides. This unprecedented bioconjugation strategy targets these under-utilized amino acids with excellent chemoselectivity and affords good-to-high yields using low concentrations of the oxidant and coupling partners, short reaction times, and mild conditions.
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Affiliation(s)
- Kristen L Seim
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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113
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Chalker JM, Bernardes GJL, Davis BG. A "tag-and-modify" approach to site-selective protein modification. Acc Chem Res 2011; 44:730-41. [PMID: 21563755 DOI: 10.1021/ar200056q] [Citation(s) in RCA: 295] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covalent modification can expand a protein's functional capacity. Fluorescent or radioactive labeling, for instance, allows imaging of a protein in real time. Labeling with an affinity probe enables isolation of target proteins and other interacting molecules. At the other end of this functional spectrum, protein structures can be naturally altered by enzymatic action. Protein-protein interactions, genetic regulation, and a range of cellular processes are under the purview of these post-translational modifications. The ability of protein chemists to install these covalent additions selectively has been critical for elucidating their roles in biology. Frequently the transformations must be applied in a site-specific manner, which demands the most selective chemistry. In this Account, we discuss the development and application of such chemistry in our laboratory. A centerpiece of our strategy is a "tag-and-modify" approach, which entails sequential installation of a uniquely reactive chemical group into the protein (the "tag") and the selective or specific modification of this group. The chemical tag can be a natural or unnatural amino acid residue. Of the natural residues, cysteine is the most widely used as a tag. Early work in our program focused on selective disulfide formation in the synthesis of glycoproteins. For certain applications, the susceptibility of disulfides to reduction was a limitation and prompted the development of several methods for the synthesis of more stable thioether modifications. The desulfurization of disulfides and conjugate addition to dehydroalanine are two routes to these modifications. The dehydroalanine tag has since proven useful as a general precursor to many modifications after conjugate addition of various nucleophiles; phosphorylated, glycosylated, peptidylated, prenylated, and even mimics of methylated and acetylated lysine-containing proteins are all accessible from dehydroalanine. While cysteine is a useful tag for selective modification, unnatural residues present the opportunity for bio-orthogonal chemistry. Azide-, arylhalide-, alkyne-, and alkene-containing amino acids can be incorporated into proteins genetically and can be specifically modified through various transformations. These transformations often rely on metal catalysis. The Cu-catalyzed azide-alkyne addition, Ru-catalyzed olefin metathesis, and Pd-catalyzed cross-coupling are examples of such transformations. In the course of adapting these reactions to protein modification, we learned much about the behavior of these reactions in water, and in some cases entirely new catalysts were developed. Through a combination of these bio-orthogonal transformations from the panel of tag-and-modify reactions, multiple and distinct modifications can be installed on protein surfaces. Multiple modifications are common in natural systems, and synthetic access to these proteins has enabled study of their biological role. Throughout these investigations, much has been learned in chemistry and biology. The demands of selective protein modification have revealed many aspects of reaction mechanisms, which in turn have guided the design of reagents and catalysts that allow their successful deployment in water and in biological milieu. With this ability to modify proteins, it is now possible to interrogate biological systems with precision that was not previously possible.
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Affiliation(s)
- Justin M. Chalker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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114
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Lim RKV, Lin Q. Photoinducible bioorthogonal chemistry: a spatiotemporally controllable tool to visualize and perturb proteins in live cells. Acc Chem Res 2011; 44:828-39. [PMID: 21609129 DOI: 10.1021/ar200021p] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Visualization in biology has been greatly facilitated by the use of fluorescent proteins as in-cell probes. The genes coding for these wavelength-tunable proteins can be readily fused with the DNA coding for a protein of interest, which enables direct monitoring of natural proteins in real time inside living cells. Despite their success, however, fluorescent proteins have limitations that have only begun to be addressed in the past decade through the development of bioorthogonal chemistry. In this approach, a very small bioorthogonal tag is embedded within the basic building blocks of the cell, and then a variety of external molecules can be selectively conjugated to these pretagged biomolecules. The result is a veritable palette of biophysical probes for the researcher to choose from. In this Account, we review our progress in developing a photoinducible, bioorthogonal tetrazole-alkene cycloaddition reaction ("photoclick chemistry") and applying it to probe protein dynamics and function in live cells. The work described here summarizes the synthesis, structure, and reactivity studies of tetrazoles, including their optimization for applications in biology. Building on key insights from earlier reports, our initial studies of the reaction have revealed full water compatibility, high photoactivation quantum yield, tunable photoactivation wavelength, and broad substrate scope; an added benefit is the formation of fluorescent cycloadducts. Subsequent studies have shown fast reaction kinetics (up to 11.0 M(-1) s(-1)), with the rate depending on the HOMO energy of the nitrile imine dipole as well as the LUMO energy of the alkene dipolarophile. Moreover, through the use of photocrystallography, we have observed that the photogenerated nitrile imine adopts a bent geometry in the solid state. This observation has led to the synthesis of reactive, macrocyclic tetrazoles that contain a short "bridge" between two flanking phenyl rings. This photoclick chemistry has been used to label proteins rapidly (within ∼1 min) both in vitro and in E. coli . To create an effective interface with biology, we have identified both a metabolically incorporable alkene amino acid, homoallylglycine, and a genetically encodable tetrazole amino acid, p-(2-tetrazole)phenylalanine. We demonstrate the utility of these two moieties, respectively, in spatiotemporally controlled imaging of newly synthesized proteins and in site-specific labeling of proteins. Additionally, we demonstrate the use of the photoclick chemistry to perturb the localization of a fluorescent protein in mammalian cells.
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Affiliation(s)
- Reyna K. V. Lim
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
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115
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Abstract
Proteins in living cells can be made receptive to bioorthogonal chemistries through metabolic labeling with appropriately designed noncanonical amino acids (ncAAs). In the simplest approach to metabolic labeling, an amino acid analog replaces one of the natural amino acids specified by the protein's gene (or genes) of interest. Through manipulation of experimental conditions, the extent of the replacement can be adjusted. This approach, often termed residue-specific incorporation, allows the ncAA to be incorporated in controlled proportions into positions normally occupied by the natural amino acid residue. For a protein to be labeled in this way with an ncAA, it must fulfill just two requirements: (i) the corresponding natural amino acid must be encoded within the sequence of the protein at the genetic level, and (ii) the protein must be expressed while the ncAA is in the cell. Because this approach permits labeling of proteins throughout the cell, it has enabled us to develop strategies to track cellular protein synthesis by tagging proteins with reactive ncAAs. In procedures similar to isotopic labeling, translationally active ncAAs are incorporated into proteins during a "pulse" in which newly synthesized proteins are tagged. The set of tagged proteins can be distinguished from those made before the pulse by bioorthogonally ligating the ncAA side chain to probes that permit detection, isolation, and visualization of the labeled proteins. Noncanonical amino acids with side chains containing azide, alkyne, or alkene groups have been especially useful in experiments of this kind. They have been incorporated into proteins in the form of methionine analogs that are substrates for the natural translational machinery. The selectivity of the method can be enhanced through the use of mutant aminoacyl tRNA synthetases (aaRSs) that permit incorporation of ncAAs not used by the endogenous biomachinery. Through expression of mutant aaRSs, proteins can be tagged with other useful ncAAs, including analogs that contain ketones or aryl halides. High-throughput screening strategies can identify aaRS variants that activate a wide range of ncAAs. Controlled expression of mutant synthetases has been combined with ncAA tagging to permit cell-selective metabolic labeling of proteins. Expression of a mutant synthetase in a portion of cells within a complex cellular mixture restricts labeling to that subset of cells. Proteins synthesized in cells not expressing the synthetase are neither labeled nor detected. In multicellular environments, this approach permits the identification of the cellular origins of labeled proteins. In this Account, we summarize the tools and strategies that have been developed for interrogating cellular protein synthesis through residue-specific tagging with ncAAs. We describe the chemical and genetic components of ncAA-tagging strategies and discuss how these methods are being used in chemical biology.
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Affiliation(s)
- John T. Ngo
- 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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116
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Li N, Lim RKV, Edwardraja S, Lin Q. Copper-free Sonogashira cross-coupling for functionalization of alkyne-encoded proteins in aqueous medium and in bacterial cells. J Am Chem Soc 2011; 133:15316-9. [PMID: 21899368 DOI: 10.1021/ja2066913] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioorthogonal reactions suitable for functionalization of genetically or metabolically encoded alkynes, for example, copper-catalyzed azide-alkyne cycloaddition reaction ("click chemistry"), have provided chemical tools to study biomolecular dynamics and function in living systems. Despite its prominence in organic synthesis, copper-free Sonogashira cross-coupling reaction suitable for biological applications has not been reported. In this work, we report the discovery of a robust aminopyrimidine-palladium(II) complex for copper-free Sonogashira cross-coupling that enables selective functionalization of a homopropargylglycine (HPG)-encoded ubiquitin protein in aqueous medium. A wide range of aromatic groups including fluorophores and fluorinated aromatic compounds can be readily introduced into the HPG-containing ubiquitin under mild conditions with good to excellent yields. The suitability of this reaction for functionalization of HPG-encoded ubiquitin in Escherichia coli was also demonstrated. The high efficiency of this new catalytic system should greatly enhance the utility of Sonogashira cross-coupling in bioorthogonal chemistry.
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Affiliation(s)
- Nan Li
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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117
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Thonon D, Goukens E, Kaisin G, Paris J, Flagothier J, Luxen A. Photoactivated 1,3-dipolar cycloaddition for the rapid preparation of 18F labelled radiotracers. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.05.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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118
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Abdeljabbar DM, Klein TJ, Link AJ. An engineered methionyl-tRNA synthetase enables azidonorleucine incorporation in methionine prototrophic bacteria. Chembiochem 2011; 12:1699-702. [PMID: 21671329 DOI: 10.1002/cbic.201100089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Diya M Abdeljabbar
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
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119
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van Hest JCM, van Delft FL. Protein Modification by Strain-Promoted Alkyne-Azide Cycloaddition. Chembiochem 2011; 12:1309-12. [DOI: 10.1002/cbic.201100206] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Indexed: 12/23/2022]
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120
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Grayson EJ, Bernardes GJL, Chalker JM, Boutureira O, Koeppe JR, Davis BG. A Coordinated Synthesis and Conjugation Strategy for the Preparation of Homogeneous Glycoconjugate Vaccine Candidates. Angew Chem Int Ed Engl 2011; 50:4127-32. [DOI: 10.1002/anie.201006327] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/05/2011] [Indexed: 12/26/2022]
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121
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Grayson EJ, Bernardes GJL, Chalker JM, Boutureira O, Koeppe JR, Davis BG. A Coordinated Synthesis and Conjugation Strategy for the Preparation of Homogeneous Glycoconjugate Vaccine Candidates. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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122
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Beatty KE. Chemical strategies for tagging and imaging the proteome. MOLECULAR BIOSYSTEMS 2011; 7:2360-7. [DOI: 10.1039/c1mb05040k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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123
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Top A, Kiick KL. Multivalent protein polymers with controlled chemical and physical properties. Adv Drug Deliv Rev 2010; 62:1530-40. [PMID: 20562016 PMCID: PMC3025749 DOI: 10.1016/j.addr.2010.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 05/04/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
Abstract
In this review, we describe our work on the design, characterization, and modification of a series of alanine-rich helical polypeptides with novel functions. Glycosylation of the polypeptides has permitted investigation of polymer architecture effects on multivalent interactions. One of the members of this polypeptide family exhibits polymorphological behavior that is easily manipulated via simple changes in solution pH and temperature. Polypeptide-based fibrils formed at acidic pH and high temperature were shown to direct the one-dimensional organization of gold nanoparticles via electrostatic interactions. As a precursor to fibrils, aggregates likely comprising alanine-rich cores form at low temperatures and acidic pH and reversibly dissociate into monomers upon deprotonation. PEGylation of these polypeptides does not alter the self-association or conformational behavior of the polypeptide, suggesting potential applications in the development of assembled delivery vehicles, as modification of the polypeptides should be a useful strategy for controlling assembly.
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Affiliation(s)
- Ayben Top
- Department of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark, Delaware 19716
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark, Delaware 19716
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124
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Szychowski J, Mahdavi A, Hodas JJL, Bagert JD, Ngo JT, Landgraf P, Dieterich DC, Schuman EM, Tirrell DA. Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition. J Am Chem Soc 2010; 132:18351-60. [PMID: 21141861 PMCID: PMC3016050 DOI: 10.1021/ja1083909] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The azide-alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide-alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na(2)S(2)O(4), 2% HOCH(2)CH(2)SH, 10% HCO(2)H, 95% CF(3)CO(2)H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO(2)H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies.
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Affiliation(s)
- Janek Szychowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - Alborz Mahdavi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - Jennifer J. L. Hodas
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA, 91125, USA
| | - John D. Bagert
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - John T. Ngo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
| | - Peter Landgraf
- Leibniz-Institute for Neurobiology, Research Group Neuralomics, Brenneckestraße 6, 39118 Magdeburg, Germany
| | - Daniela C. Dieterich
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA, 91125, USA
- Leibniz-Institute for Neurobiology, Research Group Neuralomics, Brenneckestraße 6, 39118 Magdeburg, Germany
| | - Erin M. Schuman
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA, 91125, USA
- Max Planck Institute for Brain Research, Deutschordenstraße 46, 60528 Frankfurt, Germany
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC 210-41, Pasadena, CA, 91125, USA
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125
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Lin YA, Davis BG. The allylic chalcogen effect in olefin metathesis. Beilstein J Org Chem 2010; 6:1219-28. [PMID: 21283554 PMCID: PMC3028527 DOI: 10.3762/bjoc.6.140] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 11/09/2010] [Indexed: 11/23/2022] Open
Abstract
Olefin metathesis has emerged as a powerful tool in organic synthesis. The activating effect of an allylic hydroxy group in metathesis has been known for more than 10 years, and many organic chemists have taken advantage of this positive influence for efficient synthesis of natural products. Recently, the discovery of the rate enhancement by allyl sulfides in aqueous cross-metathesis has allowed the first examples of such a reaction on proteins. This led to a new benchmark in substrate complexity for cross-metathesis and expanded the potential of olefin metathesis for other applications in chemical biology. The enhanced reactivity of allyl sulfide, along with earlier reports of a similar effect by allylic hydroxy groups, suggests that allyl chalcogens generally play an important role in modulating the rate of olefin metathesis. In this review, we discuss the effect of allylic chalcogens in olefin metathesis and highlight its most recent applications in synthetic chemistry and protein modifications.
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Affiliation(s)
- Yuya A Lin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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126
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Abstract
A concise and highly efficient synthetic route to L-azidohomoalanine (L-Aha) and its homologues is presented here. These chemically modified amino acids are used for the introduction of bioorthogonal handles into proteins. The described route avoids major problems of previously reported methods including expensive starting materials, low efficiency, and lack of scalability. Starting from inexpensive N-Boc-O-Bn-L-aspartic acid, gram quantities of L-Aha hydrochloride can be prepared with high purity. The reactions can be completed within 1 week and the products can be incorporated into proteins using L-methionine auxotrophs.
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127
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Wang J, Zhang W, Song W, Wang Y, Yu Z, Li J, Wu M, Wang L, Zang J, Lin Q. A biosynthetic route to photoclick chemistry on proteins. J Am Chem Soc 2010; 132:14812-8. [PMID: 20919707 PMCID: PMC2965590 DOI: 10.1021/ja104350y] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Light-induced chemical reactions exist in nature, regulating many important cellular and organismal functions, e.g., photosensing in prokaryotes and vision formation in mammals. Here, we report the genetic incorporation of a photoreactive unnatural amino acid, p-(2-tetrazole)phenylalanine (p-Tpa), into myoglobin site-specifically in E. coli by evolving an orthogonal tRNA/aminoacyl-tRNA synthetase pair and the use of p-Tpa as a bioorthogonal chemical "handle" for fluorescent labeling of p-Tpa-encoded myoglobin via the photoclick reaction. Moreover, we elucidated the structural basis for the biosynthetic incorporation of p-Tpa into proteins by solving the X-ray structure of p-Tpa-specific aminoacyl-tRNA synthetase in complex with p-Tpa. The genetic encoding of this photoreactive amino acid should make it possible in the future to photoregulate protein function in living systems.
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Affiliation(s)
- Jiangyun Wang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenjiao Song
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Yizhong Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Jiasong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Minhao Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Lin Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jianye Zang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
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128
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Beatty KE, Fisk JD, Smart BP, Lu YY, Szychowski J, Hangauer MJ, Baskin JM, Bertozzi CR, Tirrell DA. Live-cell imaging of cellular proteins by a strain-promoted azide-alkyne cycloaddition. Chembiochem 2010; 11:2092-5. [PMID: 20836119 PMCID: PMC3069858 DOI: 10.1002/cbic.201000419] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Kimberly E. Beatty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125 (USA)
| | - John D. Fisk
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125 (USA)
| | - Brian P. Smart
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California–Berkeley B84 Hildebrand Hall 1460, Berkeley, CA 94720 (USA)
| | - Ying Ying Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125 (USA)
| | - Janek Szychowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125 (USA)
| | - Matthew J. Hangauer
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California–Berkeley B84 Hildebrand Hall 1460, Berkeley, CA 94720 (USA)
| | - Jeremy M. Baskin
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California–Berkeley B84 Hildebrand Hall 1460, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California–Berkeley B84 Hildebrand Hall 1460, Berkeley, CA 94720 (USA)
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125 (USA)
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129
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Song W, Wang Y, Yu Z, Vera CIR, Qu J, Lin Q. A metabolic alkene reporter for spatiotemporally controlled imaging of newly synthesized proteins in Mammalian cells. ACS Chem Biol 2010; 5:875-85. [PMID: 20666508 DOI: 10.1021/cb100193h] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nonsymmetrical spatial distribution of newly synthesized proteins in animal cells plays a central role in many cellular processes. Here, we report that a simple alkene tag, homoallylglycine (HAG), was co-translationally incorporated into a recombinant protein as well as endogenous, newly synthesized proteins in mammalian cells with high efficiency. In conjunction with a photoinduced tetrazole-alkene cycloaddition reaction ("photoclick chemistry"), this alkene tag further served as a bioorthogonal chemical reporter both for the selective protein functionalization in vitro and for a spatiotemporally controlled imaging of the newly synthesized proteins in live mammalian cells. This two-step metabolic alkene tagging-photocontrolled chemical functionalization approach may offer a potentially useful tool to study the role of spatiotemporally regulated protein synthesis in mammalian cells.
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Affiliation(s)
| | | | | | | | - Jun Qu
- Department of Pharmaceutical Sciences
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130
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Boutureira O, D'Hooge F, Fernández-González M, Bernardes GJL, Sánchez-Navarro M, Koeppe JR, Davis BG. Fluoroglycoproteins: ready chemical site-selective incorporation of fluorosugars into proteins. Chem Commun (Camb) 2010; 46:8142-4. [PMID: 20714547 DOI: 10.1039/c0cc01576h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tag-and-modify strategy allows the practical synthesis of homogenous fluorinated glyco-amino acids, peptides and proteins carrying a fluorine label in the sugar and allows access to first examples of directly radiolabelled ([(18)F]-glyco)proteins.
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Affiliation(s)
- Omar Boutureira
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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131
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Roosenburg S, Laverman P, Joosten L, Eek A, Oyen WJG, de Jong M, Rutjes FPJT, van Delft FL, Boerman OC. Stabilized (111)in-labeled sCCK8 analogues for targeting CCK2-receptor positive tumors: synthesis and evaluation. Bioconjug Chem 2010; 21:663-70. [PMID: 20302291 DOI: 10.1021/bc900465y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Radiolabeled cholecystokinin-8 (CCK8) peptide analogues can be used for peptide receptor radionuclide imaging and therapy for tumors expressing CCK2/gastrin receptors. Earlier findings indicated that sulfated CCK8 (sCCK8, Asp-Tyr(OSO(3)H)-Met-Gly-Trp-Met-Asp-Phe-NH(2)) may have better characteristics for peptide receptor radionuclide therapy (PRRT) than gastrin analogues. However, sCCK8 contains an easily hydrolyzable sulfated tyrosine residue and two methionine residues which are prone to oxidation. Here, we describe the synthesis of stabilized sCCK8 analogues, resistant to hydrolysis and oxidation. Hydrolytic stability was achieved by replacement of the Tyr(OSO(3)H) moiety by a robust isosteric sulfonate, Phe(p-CH(2)SO(3)H). Replacement of methionine by norleucine (Nle) or homopropargylglycine (HPG) avoided undesired oxidation side-reactions. The phenylalanine analogue Phe(p-CH(2)SO(3)H) of l-tyrosine, synthesized by a modification of known synthetic routes, was incorporated in three peptides: sCCK8[Phe(2)(p-CH(2)SO(3)H),Met(3,6)], sCCK8[Phe(2)(p-CH(2)SO(3)H),Nle(3,6)], and sCCK8[Phe(2)(p-CH(2)SO(3)H),HPG(3,6)]. All peptides were N-terminally conjugated with the macrocyclic chelator DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) and radiolabeled with In-111. In vitro binding assays on CCK2R-expressing HEK293 cells revealed that all three peptides showed specific binding and receptor-mediated internalization, with binding affinity values (IC(50)) in the nanomolar range. In vitro oxidation studies demonstrated that peptides with Nle or HPG indeed were resistant to oxidation. In vivo targeting studies in mice with AR42J tumors showed that tumor uptake was highest for (111)In-DOTA-sCCK8 and (111)In-DOTA-sCCK8[Phe(2)(p-CH(2)SO(3)H),Nle(3,6)] (4.78 +/- 0.64 and 4.54 +/- 1.15%ID/g, respectively, 2 h p.i.). The peptide with the methionine residues replaced by norleucine ((111)In-DOTA-sCCK8[Phe(2)(p-CH(2)SO(3)H), Nle(3,6)]) showed promising in vivo characteristics and will be further investigated for radionuclide imaging and therapy of CCK2R-expressing tumors.
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Affiliation(s)
- Susan Roosenburg
- Department of Nuclear Medicine, Radboud University Nijmegen Medical Center, The Netherlands
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132
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Sengupta D, Heilshorn SC. Protein-Engineered Biomaterials: Highly Tunable Tissue Engineering Scaffolds. TISSUE ENGINEERING PART B-REVIEWS 2010; 16:285-93. [DOI: 10.1089/ten.teb.2009.0591] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Debanti Sengupta
- Department of Chemistry, Stanford University, Stanford, California
| | - Sarah C. Heilshorn
- Department of Materials Science and Engineering, Stanford University, Stanford, California
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133
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Viswanathan K, Li G, Gross RA. Protease Catalyzed In Situ C-Terminal Modification of Oligoglutamate. Macromolecules 2010. [DOI: 10.1021/ma100562j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kodandaraman Viswanathan
- Department of Chemical and Biological Sciences, NSF I/UCRC for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic Institute of New York University, Six Metrotech Center, Brooklyn, New York 11201
| | - Geng Li
- Department of Chemical and Biological Sciences, NSF I/UCRC for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic Institute of New York University, Six Metrotech Center, Brooklyn, New York 11201
| | - Richard A. Gross
- Department of Chemical and Biological Sciences, NSF I/UCRC for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic Institute of New York University, Six Metrotech Center, Brooklyn, New York 11201
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134
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135
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Abdeljabbar DM, Klein TJ, Zhang S, Link AJ. A single genomic copy of an engineered methionyl-tRNA synthetase enables robust incorporation of azidonorleucine into recombinant proteins in E. coli. J Am Chem Soc 2010; 131:17078-9. [PMID: 19894713 DOI: 10.1021/ja907969m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Engineered aminoacyl-tRNA synthetases have been used to enable the incorporation of many unnatural amino acids into recombinant proteins in vivo. In the majority of these studies, the engineered synthetase is harbored on a plasmid while the host retains a wild-type copy of the synthetase in its genome. Herein, we construct a strain carrying a single genomic copy of a methionyl-tRNA synthetase (MetRS) gene, metG*, engineered to enable the incorporation of azidonorleucine (ANL) into proteins. The resulting strain, M15MA metG*, is capable of both supporting robust cell growth and enabling the production of >20 mg/L culture of a recombinant protein, murine dihydrofolate reductase, containing ANL. The extent of replacement of methionine with ANL in this protein is 90%. Using this strain, we also produce ANL-containing OmpC, an outer membrane protein, and demonstrate that the surface of cells displaying this protein can be covalently modified using copper-catalyzed azide-alkyne cycloaddition. Since this mutant MetRS has been introduced into the genome, as opposed to a plasmid, M15MA metG* is genetically stable.
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Affiliation(s)
- Diya M Abdeljabbar
- Department of Chemical Engineering, Princeton University, A207 Engineering Quadrangle, Princeton, New Jersey 08544, USA
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136
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Maheshwari R, Levenson EA, Kiick KL. Manipulation of electrostatic and saccharide linker interactions in the design of efficient glycopolypeptide-based cholera toxin inhibitors. Macromol Biosci 2010; 10:68-81. [PMID: 19780061 PMCID: PMC2893567 DOI: 10.1002/mabi.200900182] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multivalent, glycopolymer inhibitors designed for the treatment of disease and pathogen infection have shown improvements in binding correlated with general changes in glycopolymer architecture and composition. We have previously demonstrated that control of glycopolypeptide backbone extension and ligand spacing significantly impacts the inhibition of the cholera toxin B subunit pentamer (CT B(5)) by these polymers. In the studies reported here, we elucidate the role of backbone charge and linker length in modulating the inhibition event. Peptides of the sequence AXPXG (where X is a positive, neutral or negative amino acid), equipped with the alkyne functionality of propargyl glycine, were designed and synthesized via solid-phase peptide synthetic methods and glycosylated via Cu(I)-catalyzed alkyne-azide cycloaddition reactions. The capacity of the glycopeptides to inhibit the binding of the B(5) subunit of cholera toxin was evaluated. These studies indicated that glycopeptides with a negatively charged backbone show improved inhibition of the binding event relative to the other glycopeptides. In addition, variations in the length of the linker between the peptide and the saccharide ligand also affected the inhibition of CT by the glycopeptides. Our findings suggest that, apart from appropriate saccharide spacing and polypeptide chain extension, saccharide linker conformation and the systematic placement of charges on the polypeptide backbone are also significant variables that can be tuned to improve the inhibitory potencies of glycopolypeptide-based multivalent inhibitors.
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Affiliation(s)
- Ronak Maheshwari
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716 USA Fax: +1 (302) 831-4545
| | - Eric A. Levenson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716 USA
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716 USA Fax: +1 (302) 831-4545. Delaware Biotechnology Institute, 15 Innovation Way, Newark, Delaware 19711 USA
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137
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Voloshchuk N, Montclare JK. Incorporation of unnatural amino acids for synthetic biology. ACTA ACUST UNITED AC 2010; 6:65-80. [DOI: 10.1039/b909200p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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138
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Floyd N, Vijayakrishnan B, Koeppe JR, Davis BG. Thiyl glycosylation of olefinic proteins: S-linked glycoconjugate synthesis. Angew Chem Int Ed Engl 2009; 48:7798-802. [PMID: 19739166 DOI: 10.1002/anie.200903135] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nicola Floyd
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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139
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Ai HW, Shen W, Brustad E, Schultz P. Genetically Encoded Alkenes in Yeast. Angew Chem Int Ed Engl 2009; 49:935-7. [DOI: 10.1002/anie.200905590] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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140
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Floyd N, Vijayakrishnan B, Koeppe J, Davis B. Thiyl Glycosylation of Olefinic Proteins: S-Linked Glycoconjugate Synthesis. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903135] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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141
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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142
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Nessen MA, Kramer G, Back J, Baskin JM, Smeenk LEJ, de Koning LJ, van Maarseveen JH, de Jong L, Bertozzi CR, Hiemstra H, de Koster CG. Selective enrichment of azide-containing peptides from complex mixtures. J Proteome Res 2009; 8:3702-11. [PMID: 19402736 PMCID: PMC2761887 DOI: 10.1021/pr900257z] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A general method is described to sequester peptides containing azides from complex peptide mixtures, aimed at facilitating mass spectrometric analysis to study different aspects of proteome dynamics. The enrichment method is based on covalent capture of azide-containing peptides by the azide-reactive cyclooctyne (ARCO) resin and is demonstrated for two different applications. Enrichment of peptides derived from cytochrome c treated with the azide-containing cross-linker bis(succinimidyl)-3-azidomethyl glutarate (BAMG) shows several cross-link containing peptides. Sequestration of peptides derived from an Escherichia coli proteome, pulse labeled with the bio-orthogonal amino acid azidohomoalanine as substitute for methionine, allows identification of numerous newly synthesized proteins. Furthermore, the method is found to be very specific, as after enrichment over 87% of all peptides contain (modified) azidohomoalanine.
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Affiliation(s)
- Merel A. Nessen
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | - Gertjan Kramer
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | | | | | - Linde E. J. Smeenk
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | - Leo J. de Koning
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | - Jan H. van Maarseveen
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | - Luitzen de Jong
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | | | - Henk Hiemstra
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
| | - Chris G. de Koster
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands and Organic Synthesis, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018WS Amsterdam, The Netherlands
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143
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Chalker JM, Bernardes GJL, Lin YA, Davis BG. Chemical modification of proteins at cysteine: opportunities in chemistry and biology. Chem Asian J 2009; 4:630-40. [PMID: 19235822 DOI: 10.1002/asia.200800427] [Citation(s) in RCA: 469] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Chemical modification of proteins is a rapidly expanding area in chemical biology. Selective installation of biochemical probes has led to a better understanding of natural protein modification and macromolecular function. In other cases such chemical alterations have changed the protein function entirely. Additionally, tethering therapeutic cargo to proteins has proven invaluable in campaigns against disease. For controlled, selective access to such modified proteins, a unique chemical handle is required. Cysteine, with its unique reactivity, has long been used for such modifications. Cysteine has enjoyed widespread use in selective protein modification, yet new applications and even new reactions continue to emerge. This Focus Review highlights the enduring utility of cysteine in protein modification with special focus on recent innovations in chemistry and biology associated with such modifications.
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Affiliation(s)
- Justin M Chalker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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144
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Best MD. Click Chemistry and Bioorthogonal Reactions: Unprecedented Selectivity in the Labeling of Biological Molecules. Biochemistry 2009; 48:6571-84. [DOI: 10.1021/bi9007726] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Michael D. Best
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996
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145
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Miyake-Stoner SJ, Miller AM, Hammill JT, Peeler JC, Hess KR, Mehl RA, Brewer SH. Probing Protein Folding Using Site-Specifically Encoded Unnatural Amino Acids as FRET Donors with Tryptophan. Biochemistry 2009; 48:5953-62. [DOI: 10.1021/bi900426d] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Andrew M. Miller
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Jared T. Hammill
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Jennifer C. Peeler
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Kenneth R. Hess
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Ryan A. Mehl
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
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146
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147
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Xiao J, Tolbert TJ. Synthesis of Polymerizable Protein Monomers for Protein-Acrylamide Hydrogel Formation. Biomacromolecules 2009; 10:1939-46. [DOI: 10.1021/bm900339q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junpeng Xiao
- Interdisciplinary Biochemistry Graduate Program and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Thomas J. Tolbert
- Interdisciplinary Biochemistry Graduate Program and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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148
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