101
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Moroz YS, Binder W, Nygren P, Caputo GA, Korendovych IV. Painting proteins blue: β-(1-azulenyl)-L-alanine as a probe for studying protein-protein interactions. Chem Commun (Camb) 2013; 49:490-2. [PMID: 23207368 PMCID: PMC3547328 DOI: 10.1039/c2cc37550h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrated that β-(1-azulenyl)-L-alanine, a fluorescent pseudoisosteric analog of tryptophan, exhibits weak environmental dependence and thus allows for using weak intrinsic quenchers, such as methionines, to monitor protein-protein interactions while not perturbing them.
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Affiliation(s)
- Yurii S. Moroz
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Wolfgang Binder
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
- Department of Chemistry, Technical University of Graz, Graz, Austria
| | - Patrik Nygren
- Department of Hematology and Oncology, University of Pennsylvania Medical School, Philadelphia, PA 19014, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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102
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Acevedo-Rocha CG, Geiermann AS, Budisa N, Merkel L. Design of protein congeners containing β-cyclopropylalanine. MOLECULAR BIOSYSTEMS 2013; 8:2719-23. [PMID: 22833107 DOI: 10.1039/c2mb25193k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The non-canonical amino acid (ncAA) analogue of methionine (Met), β-cyclopropylalanine (Cpa), was successfully incorporated into recombinant proteins expressed in Escherichia coli in a residue-specific manner. Proteins substituted in this way are congeners because they derive from the same gene sequence as the parent protein but contain a fraction of ncAAs. We have expressed congeners using parent and mutant gene sequences of various proteins (lipase, annexin A5, enhanced green fluorescent protein, and barstar) and found that Cpa incorporation is highly dependent on the protein sequence composition. These results indicate that the global amino acid composition of proteins might be a crucial parameter that influences the outcome of unnatural translation. In addition, we could also demonstrate that the chemical nature of the second residue could be essential for successful ncAA incorporation.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany.
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103
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Acevedo-Rocha CG, Hoesl MG, Nehring S, Royter M, Wolschner C, Wiltschi B, Antranikian G, Budisa N. Non-canonical amino acids as a useful synthetic biological tool for lipase-catalysed reactions in hostile environments. Catal Sci Technol 2013. [DOI: 10.1039/c3cy20712a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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104
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Cvetesic N, Akmacic I, Gruic-Sovulj I. Lack of discrimination against non-proteinogenic amino acid norvaline by elongation factor Tu from Escherichia coli.. CROAT CHEM ACTA 2013; 86:73-82. [PMID: 23750044 DOI: 10.5562/cca2173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The GTP-bound form of elongation factor Tu (EF-Tu) brings aminoacylated tRNAs (aa-tRNA) to the A-site of the ribosome. EF-Tu binds all cognate elongator aa-tRNAs with highly similar affinities, and its weaker or tighter binding of misacylated tRNAs may discourage their participation in translation. Norvaline (Nva) is a non-proteinogenic amino acid that is activated and transferred to tRNALeu by leucyl-tRNA synthetase (LeuRS). No notable accumulation of Nva-tRNALeu has been observed in vitro, because of the efficient post-transfer hydrolytic editing activity of LeuRS. However, incorporation of norvaline into proteins in place of leucine does occur under certain conditions in vivo. Here we show that EF-Tu binds Nva-tRNALeu and Leu-tRNALeu with similar affinities, and that Nva-tRNALeu and Leu-tRNALeu dissociate from EF-Tu at comparable rates. The inability of EF-Tu to discriminate against norvaline may have driven evolution of highly efficient LeuRS editing as the main quality control mechanism against misincorporation of norvaline into proteins.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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105
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Evans AC, Meinert C, Bredehöft JH, Giri C, Jones NC, Hoffmann SV, Meierhenrich UJ. Anisotropy Spectra for Enantiomeric Differentiation of Biomolecular Building Blocks. Top Curr Chem (Cham) 2013; 341:271-99. [DOI: 10.1007/128_2013_442] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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106
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107
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Genetically encoded libraries of nonstandard peptides. J Nucleic Acids 2012; 2012:713510. [PMID: 23097693 PMCID: PMC3477784 DOI: 10.1155/2012/713510] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/12/2012] [Indexed: 11/17/2022] Open
Abstract
The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
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108
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Soundrarajan N, Sokalingam S, Raghunathan G, Budisa N, Paik HJ, Yoo TH, Lee SG. Conjugation of proteins by installing BIO-orthogonally reactive groups at their N-termini. PLoS One 2012; 7:e46741. [PMID: 23056430 PMCID: PMC3466299 DOI: 10.1371/journal.pone.0046741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/04/2012] [Indexed: 01/25/2023] Open
Abstract
N-terminal site-specific modification of a protein has many advantages over methods targeting internal positions, but it is not easy to install reactive groups onto a protein in an N-terminal specific manner. We here report a strategy to incorporate amino acid analogues specifically in the N-terminus of a protein in vivo and demonstrate it by preparing green fluorescent protein (GFP) having bio-orthogonally reactive groups at its N-terminus. In the first step, GFP was engineered to be a foldable, internal methionine-free sequence via the semi-rational mutagenesis of five internal methionine residues and the introduction of mutations for GFP folding enhancement. In the second step, the N-terminus of the engineered protein was modified in vivo with bio-orthogonally functional groups by reassigning functional methionine surrogates such as L-homopropargylglycine and L-azidohomoalanine into the first methionine codon of the engineered internal methionine-free GFP. The N-terminal specific incorporation of unnatural amino acids was confirmed by ESI-MS analysis and the incorporation did not affect significantly the specific activity, refolding rate and folding robustness of the protein. The two proteins which have alkyne or azide groups at their N-termini were conjugated each other by bio-orthogonal Cu(I)-catalyzed click chemistry. The strategy used in this study is expected to facilitate bio-conjugation applications of proteins such as N-terminal specific glycosylation, labeling of fluorescent dyes, and immobilization on solid surfaces.
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Affiliation(s)
| | - Sriram Sokalingam
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Govindan Raghunathan
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Franklinstrasse, Berlin, Germany
| | - Hyun-Jong Paik
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Sun-Gu Lee
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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109
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Pei L, Bar‐Yam S, Byers‐Corbin J, Casagrande R, Eichler F, Lin A, Österreicher M, Regardh PC, Turlington RD, Oye KA, Torgersen H, Guan Z, Wei W, Schmidt M. Regulatory Frameworks for Synthetic Biology. Synth Biol (Oxf) 2012. [DOI: 10.1002/9783527659296.ch5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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110
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111
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Zhang S, Chan KH, Prud'homme RK, Link AJ. Synthesis and evaluation of clickable block copolymers for targeted nanoparticle drug delivery. Mol Pharm 2012; 9:2228-36. [PMID: 22734614 DOI: 10.1021/mp3000748] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymeric nanoparticles with multifunctional capabilities, including surface functionalization, hold great promise to address challenges in targeted drug delivery. Here, we describe a concise, robust synthesis of a heterofunctional polyethylene glycol (PEG), HO-PEG-azide. This macromer was used to synthesize polylactide (PLA)-PEG-azide, a functional diblock copolymer. Rapid precipitation of this copolymer with a hydrophobic cargo resulted in the generation of monodisperse nanoparticles with azides in the surface corona. To demonstrate conjugation to these nanoparticles, a regioselectively modified alkyne-folate was employed as a model small molecule ligand, and the artificial protein A1 with an alkyne moiety introduced by unnatural amino acid substitution was selected as a model macromolecular ligand. Using the copper-catalyzed azide-alkyne ligation reaction, both ligands exhibited good conjugation efficiency even when low concentrations of ligands were used.
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Affiliation(s)
- Siyan Zhang
- Departments of †Chemical and Biological Engineering and ‡Molecular Biology, Princeton University , Princeton, New Jersey 08540, United States
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112
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Schmidt MJ, Summerer D. A Need for Speed: Genetic Encoding of Rapid Cycloaddition Chemistries for Protein Labelling in Living Cells. Chembiochem 2012; 13:1553-7. [DOI: 10.1002/cbic.201200321] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Indexed: 01/08/2023]
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113
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Shozen N, Watanabe T, Hohsaka T. Amber codon-mediated expanded saturation mutagenesis of proteins using a cell-free translation system. J Biosci Bioeng 2012; 113:704-9. [DOI: 10.1016/j.jbiosc.2012.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/27/2012] [Accepted: 01/27/2012] [Indexed: 11/28/2022]
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114
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Larregola M, Moore S, Budisa N. Congeneric bio-adhesive mussel foot proteins designed by modified prolines revealed a chiral bias in unnatural translation. Biochem Biophys Res Commun 2012; 421:646-50. [PMID: 22542516 DOI: 10.1016/j.bbrc.2012.04.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/05/2012] [Indexed: 12/14/2022]
Abstract
Chiral bias in the unnatural translation and 'sticky' mussel proteins. The residue-specific in vivo incorporation of hydroxylated amino acids as well as other synthetic analogs, such as fluoroprolines, emerges as the method of choice for recombinant synthesis of Pro-rich mussel adhesive protein congeners. Chemical diversifications introduced in this way provide a general route towards bio-adhesive congeners endowed with properties not developed by natural evolution. Most importantly, we have found that the co-translational incorporation of (4R)-, and (4S)-hyroxylated and fluorinated analogs into mussel proteins presented a chiral bias: the expressed protein was only detectable in samples incubated with analogs with (4R)-substituents. Possible relationship of these stereochemical preferences for (4R)-stereoisomers in the translation to intracellular tRNA concentrations, ribosomal editing and proofreading or structural effects such as preorganization remains to be addressed in future studies. These studies will generally provide a mechanistic framework for the flexibility of the translational machinery and establish the boundaries of the unnatural translation.
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Affiliation(s)
- Maud Larregola
- Department of Chemistry, Biocatalysis Group, Berlin Institute of Technology/TU Berlin, Franklinstraße 29, D-10587 Berlin, Germany
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115
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Eger S, Scheffner M, Marx A, Rubini M. Formation of ubiquitin dimers via azide-alkyne click reaction. Methods Mol Biol 2012; 832:589-596. [PMID: 22350914 DOI: 10.1007/978-1-61779-474-2_41] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The conjugation of poly-ubiquitin chains is a widespread post-translational modification of proteins that plays a role in many different cellular processes. Notably, the biological function of the attached ubiquitin chain depends on which lysine residue is used for chain formation. Here, we report a method for the modular synthesis of site-specifically linked ubiquitin dimers, which is based on click reaction between two artificial amino acids. In this way, it is possible to synthesize all seven naturally occurring ubiquitin connectivities, thus giving access to all ubiquitin dimers. Furthermore, this method can be generally applied to link ubiquitin to any substrate protein or even to link any two proteins site specifically.
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Affiliation(s)
- Silvia Eger
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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116
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Merkel L, Budisa N. Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes. Org Biomol Chem 2012; 10:7241-61. [DOI: 10.1039/c2ob06922a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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117
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Majkut P, Böhrsch V, Serwa R, Gerrits M, Hackenberger CPR. Site-specific modification of proteins by the staudinger-phosphite reaction. Methods Mol Biol 2012; 794:241-249. [PMID: 21956567 DOI: 10.1007/978-1-61779-331-8_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Chemoselective reactions are important tools for the modification of peptides and proteins. Thereby the modification is desired to be site specific and bioorthogonal. Here we describe the site-specific modification of azido-proteins via a Staudinger-type phosphite ligation. The reaction was carried out in aqueous system on proteins containing p-azido-phenylalanine in a single position introduced by the amber codon technique. A selective introduction of branched polyethylene scaffolds can be achieved with the application of the methodology reported herein.
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Affiliation(s)
- Paul Majkut
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
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118
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Abstract
Techniques to manipulate cellular gene expression such that amino acid analogs not encoded by the genetic code are incorporated into a polypeptide chain have recently gained increasing interest. The so-called noncanonical amino acids often have unusual properties that can be translated into target proteins by reprogrammed ribosomal protein synthesis. Residue-specific substitution of a specific canonical amino acid by its analogs provokes global effects in the resulting protein congeners that include improved stability or catalytic activity, reduced redox sensitivity, as well as altered spectral properties. Thus, the approach holds great promise for the engineering of synthetic proteins.This contribution describes a protocol for the incorporation of a noncanonical amino acid into a target protein expressed in an appropriate amino acid auxotrophic E. coli strain.
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119
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Tianero MDB, Donia MS, Young TS, Schultz PG, Schmidt EW. Ribosomal route to small-molecule diversity. J Am Chem Soc 2011; 134:418-25. [PMID: 22107593 DOI: 10.1021/ja208278k] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cyanobactin ribosomal peptide (RP) natural product pathway was manipulated to incorporate multiple tandem mutations and non-proteinogenic amino acids, using eight heterologous components simultaneously expressed in Escherichia coli . These studies reveal the potential of RPs for the rational synthesis of complex, new small molecules over multiple-step biosynthetic pathways using simple genetic engineering.
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Affiliation(s)
- Ma Diarey B Tianero
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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120
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Oldach F, Al Toma R, Kuthning A, Caetano T, Mendo S, Budisa N, Süssmuth RD. Lantibiotika-Kongenere mit nicht-kanonischen Aminosäuren durch ribosomale In-vivo-Peptidsynthese. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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121
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Oldach F, Al Toma R, Kuthning A, Caetano T, Mendo S, Budisa N, Süssmuth RD. Congeneric lantibiotics from ribosomal in vivo peptide synthesis with noncanonical amino acids. Angew Chem Int Ed Engl 2011; 51:415-8. [PMID: 22128014 DOI: 10.1002/anie.201106154] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/20/2011] [Indexed: 11/10/2022]
Abstract
Expanded repetoire: Synthetic amino acids translated into propeptides dramatically increase the chemical diversity of the two-component lantibiotic lichenicidin. This opens new routes towards novel and unique peptide antibiotic sequences, which could display features important for medical applications.
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Affiliation(s)
- Florian Oldach
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
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122
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Beck-Sickinger AG, Budisa N. Genetically Encoded Photocrosslinkers as Molecular Probes To Study G-Protein-Coupled Receptors (GPCRs). Angew Chem Int Ed Engl 2011; 51:310-2. [DOI: 10.1002/anie.201107211] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Indexed: 11/12/2022]
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123
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Beck-Sickinger AG, Budisa N. Genetisch kodierte Photovernetzer als molekulare Sonden zur Untersuchung von G-Protein-gekoppelten Rezeptoren (GPCR). Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201107211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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124
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Zheng S, Kwon I. Manipulation of enzyme properties by noncanonical amino acid incorporation. Biotechnol J 2011; 7:47-60. [PMID: 22121038 DOI: 10.1002/biot.201100267] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/22/2011] [Accepted: 09/22/2011] [Indexed: 11/07/2022]
Abstract
Since wild-type enzymes do not always have the properties needed for various applications, enzymes are often engineered to obtain desirable properties through protein engineering techniques. In the past decade, complementary to the widely used rational protein design and directed evolution techniques, noncanonical amino acid incorporation (NCAAI) has become a new and effective protein engineering technique. Recently, NCAAI has been used to improve intrinsic functions of proteins, such as enzymes and fluorescent proteins, beyond the capacities obtained with natural amino acids. Herein, recent progress on improving enzyme properties through NCAAI in vivo is reviewed and the challenges of current approaches and future directions are also discussed. To date, both NCAAI methods-residue- and site-specific incorporation-have been primarily used to improve the catalytic turnover number and substrate binding affinity of enzymes. Numerous strategies used to minimize structural perturbation and stability loss of a target enzyme upon NCAAI are also explored. Considering the generality of NCAAI incorporation, we expect its application could be expanded to improve other enzyme properties, such as substrate specificity and solvent resistance in the near future.
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Affiliation(s)
- Shun Zheng
- Department of Chemical Engineering University of Virginia, Charlottesville, VA 22904, USA
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125
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Artner LM, Merkel L, Bohlke N, Beceren-Braun F, Weise C, Dernedde J, Budisa N, Hackenberger CPR. Site-selective modification of proteins for the synthesis of structurally defined multivalent scaffolds. Chem Commun (Camb) 2011; 48:522-4. [PMID: 22068135 DOI: 10.1039/c1cc16039g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of classical site-directed mutagenesis, genetic code engineering and bioorthogonal reactions delivered a chemically modified barstar protein with one or four carbohydrates installed at specific residues. These protein conjugates were employed in multivalent binding studies, which support the use of proteins as structurally defined scaffolds for the presentation of multivalent ligands.
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Affiliation(s)
- Lukas M Artner
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustr. 3, 14195 Berlin, Germany
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126
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Vallée MRJ, Majkut P, Wilkening I, Weise C, Müller G, Hackenberger CPR. Staudinger-Phosphonite Reactions for the Chemoselective Transformation of Azido-Containing Peptides and Proteins. Org Lett 2011; 13:5440-3. [DOI: 10.1021/ol2020175] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Robert J. Vallée
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Paul Majkut
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Ina Wilkening
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Christoph Weise
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Gregor Müller
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
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127
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Baker PJ, Montclare JK. Enhanced Refoldability and Thermoactivity of Fluorinated Phosphotriesterase. Chembiochem 2011; 12:1845-8. [DOI: 10.1002/cbic.201100221] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Indexed: 12/13/2022]
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128
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Acevedo-Rocha CG, Budisa N. On the road towards chemically modified organisms endowed with a genetic firewall. Angew Chem Int Ed Engl 2011; 50:6960-2. [PMID: 21710510 DOI: 10.1002/anie.201103010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Indexed: 01/06/2023]
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129
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Acevedo-Rocha CG, Budisa N. Auf dem Weg zu chemisch veränderten Organismen mit genetischer Firewall. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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130
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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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131
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Tokuda Y, Watanabe T, Horiike K, Shiraga K, Abe R, Muranaka N, Hohsaka T. Biosynthesis of proteins containing modified lysines and fluorescent labels using non-natural amino acid mutagenesis. J Biosci Bioeng 2011; 111:402-7. [DOI: 10.1016/j.jbiosc.2010.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 11/24/2010] [Accepted: 12/13/2010] [Indexed: 11/28/2022]
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132
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Nagasundarapandian S, Merkel L, Budisa N, Govindan R, Ayyadurai N, Sriram S, Yun H, Lee SG. Engineering protein sequence composition for folding robustness renders efficient noncanonical amino acid incorporations. Chembiochem 2011; 11:2521-4. [PMID: 21064080 DOI: 10.1002/cbic.201000380] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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133
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Hoesl MG, Budisa N. In Vivo Incorporation of Multiple Noncanonical Amino Acids into Proteins. Angew Chem Int Ed Engl 2011; 50:2896-902. [DOI: 10.1002/anie.201005680] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Indexed: 11/11/2022]
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134
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Hoesl MG, Budisa N. Paralleler In-vivo-Einbau von mehreren nichtkanonischen Aminosäuren in Proteine. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005680] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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135
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Minajigi A, Deng B, Francklyn CS. Fidelity escape by the unnatural amino acid β-hydroxynorvaline: an efficient substrate for Escherichia coli threonyl-tRNA synthetase with toxic effects on growth. Biochemistry 2011; 50:1101-9. [PMID: 21222438 DOI: 10.1021/bi101360a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In all living systems, the fidelity of translation is maintained in part by the editing mechanisms of aminoacyl-tRNA synthetases (ARSs). Some nonproteogenic amino acids, including β-hydroxynorvaline (HNV) are nevertheless efficiently aminoacylated and become incorporated into proteins. To investigate the basis of HNV's ability to function in protein synthesis, the utilization of HNV by Escherichia coli threonyl-tRNA synthetase (ThrRS) was investigated through both in vitro functional experiments and bacterial growth studies. The measured specificity constant (k(cat)/K(M)) for HNV was found to be only 20-30-fold less than that of cognate threonine. The rate of aminoacyl transfer (10.4 s(-1)) was 10-fold higher than the multiple turnover k(cat) value (1 s(-1)), indicating that, as for cognate threonine, amino acid activation is likely to be the rate-limiting step. Like noncognate serine, HNV enhances the ATPase function of the synthetic site, at a rate not increased by nonaminoacylatable (3'-dA76) tRNA. ThrRS also failed to exhibit posttransfer editing activity against HNV. In growing bacteria, the addition of HNV dramatically suppressed growth rates, which indicates either negative phenotypic consequences associated with its incorporation into protein or inhibition of an unidentified metabolic reaction. The inability of wild ThrRS to prevent utilization of HNV as a substrate illustrates that, for at least one ARS, the naturally occurring enzyme lacks the capability to effectively discriminate against nonproteogenic amino acids that are not encountered under normal physiological conditions. Other examples of "fidelity escape" in the ARSs may serve as useful starting points in the design of ARSs with specificity for unnatural amino acids.
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Affiliation(s)
- Anand Minajigi
- Cell and Molecular Biology Program, College of Medicine, Health Sciences Complex, University of Vermont, Burlington, Vermont 05405-0068, United States
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136
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Hoesl MG, Budisa N. Expanding and Engineering the Genetic Code in a Single Expression Experiment. Chembiochem 2011; 12:552-5. [DOI: 10.1002/cbic.201000586] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 12/31/2022]
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137
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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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138
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Huang X, Liu X, Luo Q, Liu J, Shen J. Artificial selenoenzymes: Designed and redesigned. Chem Soc Rev 2011; 40:1171-84. [DOI: 10.1039/c0cs00046a] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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139
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Hayashi A, Hino N, Kobayashi T, Arai R, Shirouzu M, Yokoyama S, Sakamoto K. Dissecting Cell Signaling Pathways with Genetically Encoded 3-Iodo-L-tyrosine. Chembiochem 2010; 12:387-9. [DOI: 10.1002/cbic.201000665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Indexed: 11/05/2022]
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140
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Schmidt M, Pei L. Synthetic toxicology: where engineering meets biology and toxicology. Toxicol Sci 2010; 120 Suppl 1:S204-24. [PMID: 21068213 DOI: 10.1093/toxsci/kfq339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely, DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools, and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic toxicology. We differentiate between cases where SB offers opportunities for toxicology and where SB poses challenges for toxicology. Among the opportunities, we identified the assistance of SB to construct novel toxicity testing platforms, define new toxicity-pathway assays, explore the potential of SB to improve in vivo biotransformation of toxins, present novel biosensors developed by SB for environmental toxicology, discuss cell-free protein synthesis of toxins, reflect on the contribution to toxic use reduction, and the democratization of toxicology through do-it-yourself biology. Among the identified challenges for toxicology, we identify synthetic toxins and novel xenobiotics, biosecurity and dual-use considerations, the potential bridging of toxic substances and infectious agents, and do-it-yourself toxin production.
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Affiliation(s)
- Markus Schmidt
- Organization for International Dialogue and Conflict Management, Biosafety Working Group, 1070 Vienna, Austria.
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141
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Engineering of an Orthogonal Aminoacyl-tRNA Synthetase for Efficient Incorporation of the Non-natural Amino Acid O-Methyl-L-tyrosine using Fluorescence-based Bacterial Cell Sorting. J Mol Biol 2010; 404:70-87. [DOI: 10.1016/j.jmb.2010.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 08/14/2010] [Accepted: 09/01/2010] [Indexed: 11/18/2022]
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142
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Holzberger B, Marx A. Replacing 32 Proline Residues by a Noncanonical Amino Acid Results in a Highly Active DNA Polymerase. J Am Chem Soc 2010; 132:15708-13. [DOI: 10.1021/ja106525y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bastian Holzberger
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraβe 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraβe 10, 78457 Konstanz, Germany
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143
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Hoesl MG, Acevedo-Rocha CG, Nehring S, Royter M, Wolschner C, Wiltschi B, Budisa N, Antranikian G. Lipase Congeners Designed by Genetic Code Engineering. ChemCatChem 2010. [DOI: 10.1002/cctc.201000253] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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144
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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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145
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Garbe D, Thiel IV, Mootz HD. Protein trans-splicing on an M13 bacteriophage: towards directed evolution of a semisynthetic split intein by phage display. J Pept Sci 2010; 16:575-81. [DOI: 10.1002/psc.1243] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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146
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Tlusty T. A colorful origin for the genetic code: Information theory, statistical mechanics and the emergence of molecular codes. Phys Life Rev 2010; 7:362-76. [DOI: 10.1016/j.plrev.2010.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 01/25/2010] [Accepted: 02/06/2010] [Indexed: 10/19/2022]
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147
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Weikart ND, Mootz HD. Generation of site-specific and enzymatically stable conjugates of recombinant proteins with ubiquitin-like modifiers by the Cu(I)-catalyzed azide-alkyne cycloaddition. Chembiochem 2010; 11:774-7. [PMID: 20209558 DOI: 10.1002/cbic.200900738] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nadine D Weikart
- Fakultät Chemie-Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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148
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Lepthien S, Merkel L, Budisa N. Doppelte und dreifache In-vivo-Funktionalisierung von Proteinen mit synthetischen Aminosäuren. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000439] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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149
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Lepthien S, Merkel L, Budisa N. In Vivo Double and Triple Labeling of Proteins Using Synthetic Amino Acids. Angew Chem Int Ed Engl 2010; 49:5446-50. [DOI: 10.1002/anie.201000439] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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150
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Merkel L, Schauer M, Antranikian G, Budisa N. Parallel Incorporation of Different Fluorinated Amino Acids: On the Way to “Teflon” Proteins. Chembiochem 2010; 11:1505-7. [DOI: 10.1002/cbic.201000295] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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