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Tseng HW, Moldenhauer M, Friedrich T, Maksimov EG, Budisa N. Probing the spectral signatures of orange carotenoid protein by orthogonal translation with aromatic non-canonical amino acids. Biochem Biophys Res Commun 2022; 607:96-102. [DOI: 10.1016/j.bbrc.2022.03.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/02/2022]
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2
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Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger. Commun Chem 2020; 3:69. [PMID: 36703460 PMCID: PMC9814790 DOI: 10.1038/s42004-020-0313-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/06/2020] [Indexed: 01/29/2023] Open
Abstract
The understanding of biomolecular recognition of posttranslationally modified histone proteins is centrally important to the histone code hypothesis. Despite extensive binding and structural studies on the readout of histones, the molecular language by which posttranslational modifications on histone proteins are read remains poorly understood. Here we report physical-organic chemistry studies on the recognition of the positively charged trimethyllysine by the electron-rich aromatic cage containing PHD3 finger of KDM5A. The aromatic character of two tryptophan residues that solely constitute the aromatic cage of KDM5A was fine-tuned by the incorporation of fluorine substituents. Our thermodynamic analyses reveal that the wild-type and fluorinated KDM5A PHD3 fingers associate equally well with trimethyllysine. This work demonstrates that the biomolecular recognition of trimethyllysine by fluorinated aromatic cages is associated with weaker cation-π interactions that are compensated by the energetically more favourable trimethyllysine-mediated release of high-energy water molecules that occupy the aromatic cage.
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3
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Moroder L, Musiol H. Amino acid chalcogen analogues as tools in peptide and protein research. J Pept Sci 2019; 26:e3232. [DOI: 10.1002/psc.3232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Luis Moroder
- Bioorganic ChemistryMax‐Planck Institute of Biochemistry Martinsried Germany
| | - Hans‐Jürgen Musiol
- Bioorganic ChemistryMax‐Planck Institute of Biochemistry Martinsried Germany
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4
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Boknevitz K, Italia JS, Li B, Chatterjee A, Liu SY. Synthesis and characterization of an unnatural boron and nitrogen-containing tryptophan analogue and its incorporation into proteins. Chem Sci 2019; 10:4994-4998. [PMID: 31183048 PMCID: PMC6524624 DOI: 10.1039/c8sc05167d] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
A boron and nitrogen containing unnatural analogue of tryptophan is synthesized and incorporated into proteins.
A boron and nitrogen containing unnatural analogue of tryptophan is synthesized through the functionalization of BN-indole. The spectroscopic properties of BN-tryptophan are reported with respect to the natural tryptophan, and the incorporation of BN-tryptophan into proteins expressed in E. coli using selective pressure incorporation is described. This work shows that a cellular system can recognize the unnatural, BN-containing tryptophan. More importantly, it presents the first example of an azaborine containing amino acid being incorporated into proteins.
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Affiliation(s)
- Katherine Boknevitz
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - James S Italia
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - Bo Li
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - Abhishek Chatterjee
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - Shih-Yuan Liu
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
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5
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Painting argyrins blue: Negishi cross-coupling for synthesis of deep-blue tryptophan analogue β-(1-azulenyl)-l alanine and its incorporation into argyrin C. Bioorg Med Chem 2018; 26:5259-5269. [PMID: 29729984 DOI: 10.1016/j.bmc.2018.03.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 01/22/2023]
Abstract
The argyrins are a family of non-ribosomal peptides that exhibits different biological activities through only small structural changes. Ideally, a biologically active molecule can be tracked and observed in a variety of biological and clinical settings in a non-invasive manner. As a step towards this goal, we report here a chemical synthesis of unnatural deep blue amino acid β-(1-azulenyl)-l alanine with different fluorescence and photophysical properties, which allows a spectral separation from the native tryptophan signal. This might be especially useful for cell localization studies and visualizing the targeted proteins. In particular, the synthesis of β-(1-azulenyl)-l alanine was achieved through a Negishi coupling which proved to be a powerful tool for the synthesis of unnatural tryptophan analogs. Upon β-(1-azulenyl)-l alanine incorporation into argyrin C, deep blue octapeptide variant was spectrally and structurally characterized.
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6
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Towards Biocontained Cell Factories: An Evolutionarily Adapted Escherichia coli Strain Produces a New-to-nature Bioactive Lantibiotic Containing Thienopyrrole-Alanine. Sci Rep 2016; 6:33447. [PMID: 27634138 PMCID: PMC5025777 DOI: 10.1038/srep33447] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/25/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic code engineering that enables reassignment of genetic codons to non-canonical amino acids (ncAAs) is a powerful strategy for enhancing ribosomally synthesized peptides and proteins with functions not commonly found in Nature. Here we report the expression of a ribosomally synthesized and post-translationally modified peptide (RiPP), the 32-mer lantibiotic lichenicidin with a canonical tryptophan (Trp) residue replaced by the ncAA L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) which does not sustain cell growth in the culture. We have demonstrated that cellular toxicity of [3,2]Tpa for the production of the new-to-nature bioactive congener of lichenicidin in the host Escherichia coli can be alleviated by using an evolutionarily adapted host strain MT21 which not only tolerates [3,2]Tpa but also uses it as a proteome-wide synthetic building block. This work underscores the feasibility of the biocontainment concept and establishes a general framework for design and large scale production of RiPPs with evolutionarily adapted host strains.
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7
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Acevedo-Rocha CG, Budisa N. Xenomicrobiology: a roadmap for genetic code engineering. Microb Biotechnol 2016; 9:666-76. [PMID: 27489097 PMCID: PMC4993186 DOI: 10.1111/1751-7915.12398] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/27/2022] Open
Abstract
Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high‐throughput and low‐cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non‐natural building blocks in living cells. In this context, genetic code engineering respectively enables the re‐design of genes/genomes and proteins/proteomes with non‐canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new‐to‐nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a ‘genetic firewall’ will also allow to study and understand the relation between code evolution and horizontal gene transfer.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Biosyntia ApS, 2970, Hørsholm, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Nediljko Budisa
- Department of Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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8
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Biswas AK, Das A, Ganguly B. Can fused-pyrrole rings act as better π-spacer units than fused-thiophene in dye-sensitized solar cells? A computational study. NEW J CHEM 2016. [DOI: 10.1039/c6nj02040b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fused-pyrrole rings can be potential π-spacers in dye-sensitized solar cells.
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Affiliation(s)
- Abul Kalam Biswas
- Analytical Discipline and Centralized Instrument Facility
- Academy of Scientific and Innovative Research CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
| | - Amitava Das
- Analytical Discipline and Centralized Instrument Facility
- Academy of Scientific and Innovative Research CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
| | - Bishwajit Ganguly
- Analytical Discipline and Centralized Instrument Facility
- Academy of Scientific and Innovative Research CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
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9
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Eisenreich W, Joshi M, Illarionov B, Kacprzak S, Lukaschek M, Kothe G, Budisa N, Fischer M, Bacher A, Weber S. Strategy for Enhancement of (13)C-Photo-CIDNP NMR Spectra by Exploiting Fractional (13)C-Labeling of Tryptophan. J Phys Chem B 2015; 119:13934-43. [PMID: 26244593 DOI: 10.1021/acs.jpcb.5b06668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photo-CIDNP effect has proven to be useful to strongly enhance NMR signals of photochemically active proteins simply by irradiation with light. The evolving characteristic patterns of enhanced absorptive and emissive NMR lines can be exploited to elucidate the photochemistry and photophysics of light-driven protein reactions. In particular, by the assignment of (13)C NMR resonances, redox-active amino acids may be identified and thereby electron-transfer pathways unraveled, in favorable cases, even with (13)C at natural abundance. If signal enhancement is weak, uniform (13)C isotope labeling is traditionally applied to increase the signal strength of protein (13)C NMR. However, this typically leads to cross relaxation, which transfers light-induced nuclear-spin polarization to adjacent (13)C nuclei, thereby preventing an unambiguous analysis of the photo-CIDNP effect. In this contribution, two isotope labeling strategies are presented; one leads to specific but ubiquitous (13)C labeling in tryptophan, and the other is based on fractional isotope labeling affording sets of isotopologs with low probability of next-neighbor isotope accumulation within individual tryptophan molecules. Consequently, cross relaxation is largely avoided while the signal enhancement by (13)C enrichment is preserved. This results in significantly simplified polarization patterns that are easier to analyze with respect to the generation of light-generated nuclear-spin polarization.
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Affiliation(s)
- Wolfgang Eisenreich
- Technische Universität München , Lehrstuhl für Biochemie, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Monika Joshi
- Technische Universität München , Lehrstuhl für Biochemie, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Boris Illarionov
- Universität Hamburg , Institut für Lebensmittelchemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Sylwia Kacprzak
- Albert-Ludwigs-Universität Freiburg , Institut für Physikalische Chemie, Albertstr. 21, 79104 Freiburg, Germany
| | - Michail Lukaschek
- Albert-Ludwigs-Universität Freiburg , Institut für Physikalische Chemie, Albertstr. 21, 79104 Freiburg, Germany
| | - Gerd Kothe
- Albert-Ludwigs-Universität Freiburg , Institut für Physikalische Chemie, Albertstr. 21, 79104 Freiburg, Germany
| | - Nediljko Budisa
- Technische Universität Berlin , Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Markus Fischer
- Universität Hamburg , Institut für Lebensmittelchemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Adelbert Bacher
- Technische Universität München , Lehrstuhl für Biochemie, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Stefan Weber
- Albert-Ludwigs-Universität Freiburg , Institut für Physikalische Chemie, Albertstr. 21, 79104 Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS) , Albertstr. 19, 79104 Freiburg, Germany
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10
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Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L, Aerni HR, Rappsilber J, Rinehart J, Leach D, Söll D, Budisa N. Chemical Evolution of a Bacterial Proteome. Angew Chem Int Ed Engl 2015; 54:10030-4. [PMID: 26136259 PMCID: PMC4782924 DOI: 10.1002/anie.201502868] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/09/2022]
Abstract
We have changed the amino acid set of the genetic code of Escherichia coli by evolving cultures capable of growing on the synthetic noncanonical amino acid L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) as a sole surrogate for the canonical amino acid L-tryptophan (Trp). A long-term cultivation experiment in defined synthetic media resulted in the evolution of cells capable of surviving Trp→[3,2]Tpa substitutions in their proteomes in response to the 20,899 TGG codons of the E. coli W3110 genome. These evolved bacteria with new-to-nature amino acid composition showed robust growth in the complete absence of Trp. Our experimental results illustrate an approach for the evolution of synthetic cells with alternative biochemical building blocks.
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Affiliation(s)
- Michael Georg Hoesl
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany)
| | - Stefan Oehm
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany)
| | - Patrick Durkin
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany)
| | - Elise Darmon
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh (UK)
| | - Lauri Peil
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, 4.17 Michael Swann Building, Edinburgh EH9 3BF (UK)
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516 (USA)
| | - Juri Rappsilber
- Institut für Biotechnolgie, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin (Germany)
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, 4.17 Michael Swann Building, Edinburgh EH9 3BF (UK)
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516 (USA)
| | - David Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh (UK)
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520 (USA)
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany).
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11
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Synthesis of fluorescent d-amino acids with 4-acetamidobiphenyl and 4-N,N-dimethylamino-1,8-naphthalimido containing side chains. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.06.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L, Aerni HR, Rappsilber J, Rinehart J, Leach D, Söll D, Budisa N. Chemische Evolution eines bakteriellen Proteoms. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 791] [Impact Index Per Article: 79.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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14
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Singh-Blom A, Hughes RA, Ellington AD. Residue-specific incorporation of unnatural amino acids into proteins in vitro and in vivo. Methods Mol Biol 2013; 978:93-114. [PMID: 23423891 DOI: 10.1007/978-1-62703-293-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The incorporation of noncanonical (unnatural) amino acids into proteins offers researchers the ability to augment the biochemical functionality of proteins for a myriad of applications including bioorthogonal conjugation, biophysical and structural studies, and the enhancement or de novo creation of novel enzymatic activities. The augmentation of a protein throughout its coding sequence by global residue-specific incorporation of unnatural amino acid analogs is an attractive technique for studying both the utility of individual chemistries available through unnatural amino acids and the general effects of unnatural amino acid substitution on protein structure and function. Herein we describe protocols to introduce unnatural amino acids into proteins using the Escherichia coli translation system either in vivo or in vitro. Special attention is paid to obtaining high levels of incorporation while maintaining high yields of protein expression.
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Affiliation(s)
- Amrita Singh-Blom
- Department of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX, USA
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15
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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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16
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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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17
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Merkel L, Hoesl MG, Albrecht M, Schmidt A, Budisa N. Blue Fluorescent Amino Acids as In Vivo Building Blocks for Proteins. Chembiochem 2010; 11:305-14. [DOI: 10.1002/cbic.200900651] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Unnatural benz-X-azolyl asparagine derivatives as novel fluorescent amino acids: synthesis and photophysical characterization. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.08.086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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de Graaf AJ, Kooijman M, Hennink WE, Mastrobattista E. Nonnatural Amino Acids for Site-Specific Protein Conjugation. Bioconjug Chem 2009; 20:1281-95. [DOI: 10.1021/bc800294a] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Albert J. de Graaf
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
| | - Marlous Kooijman
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
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20
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Costa SP, Batista RM, Raposo MMM. Synthesis and photophysical characterization of new fluorescent bis-amino acids bearing a heterocyclic bridge containing benzoxazole and thiophene. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.07.096] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Costa SP, Oliveira E, Lodeiro C, Raposo MMM. Heteroaromatic alanine derivatives bearing (oligo)thiophene units: synthesis and photophysical properties. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.06.109] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Strable E, Prasuhn DE, Udit AK, Brown S, Link AJ, Ngo JT, Lander G, Quispe J, Potter CS, Carragher B, Tirrell DA, Finn MG. Unnatural amino acid incorporation into virus-like particles. Bioconjug Chem 2008; 19:866-75. [PMID: 18318461 PMCID: PMC2713011 DOI: 10.1021/bc700390r] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Virus-like particles composed of hepatitis B virus (HBV) or bacteriophage Qbeta capsid proteins have been labeled with azide- or alkyne-containing unnatural amino acids by expression in a methionine auxotrophic strain of E. coli. The substitution does not affect the ability of the particles to self-assemble into icosahedral structures indistinguishable from native forms. The azide and alkyne groups were addressed by Cu(I)-catalyzed [3 + 2] cycloaddition: HBV particles were decomposed by the formation of more than 120 triazole linkages per capsid in a location-dependent manner, whereas Qbeta suffered no such instability. The marriage of these well-known techniques of sense-codon reassignment and bioorthogonal chemical coupling provides the capability to construct polyvalent particles displaying a wide variety of functional groups with near-perfect control of spacing.
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23
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Hartman MCT, Josephson K, Lin CW, Szostak JW. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2007; 2:e972. [PMID: 17912351 PMCID: PMC1989143 DOI: 10.1371/journal.pone.0000972] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 09/12/2007] [Indexed: 11/23/2022] Open
Abstract
Background The application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. The specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. We have previously shown that over 90 unnatural amino acids can be enzymatically loaded onto tRNA. Methodology/Principal Findings We have now used a competition assay to assess the efficiency of tRNA-aminoacylation of these analogs. We have also used a series of peptide translation assays to measure the efficiency with which these analogs are incorporated into peptides. The translation apparatus tolerates most side chain derivatives, a few α,α disubstituted, N-methyl and α-hydroxy derivatives, but no β-amino acids. We show that over 50 unnatural amino acids can be incorporated into peptides by ribosomal translation. Using a set of analogs that are efficiently charged and translated we were able to prepare individual peptides containing up to 13 different unnatural amino acids. Conclusions/Significance Our results demonstrate that a diverse array of unnatural building blocks can be translationally incorporated into peptides. These building blocks provide new opportunities for in vitro selections with highly modified drug-like peptides.
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Affiliation(s)
- Matthew C. T. Hartman
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kristopher Josephson
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Chi-Wang Lin
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Lepthien S, Wiltschi B, Bolic B, Budisa N. In vivo engineering of proteins with nitrogen-containing tryptophan analogs. Appl Microbiol Biotechnol 2007; 73:740-54. [PMID: 17269153 DOI: 10.1007/s00253-006-0665-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recently, it has become possible to reprogram the protein synthesis machinery such that numerous noncanonical amino acids can be translated into target sequences yielding tailor-made proteins. The canonical amino acid tryptophan (Trp) encoded by a single nucleotide triplet (UGG) is a particularly interesting target for protein engineering and design. Trp-residues can be substituted with a variety of analogs and surrogates generated biosynthetically or by organic chemistry. Among them, nitrogen-containing tryptophan analogs occupy a central position, as they have distinct chemical properties in comparison with aliphatic amines and imines. They resemble purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. These special properties of the analogs can be directly transmitted into related protein structures via in vivo ribosome-mediated translation. Proteins expressed in this way are further endowed with unique properties like new spectral, altered redox and titration features or might serve as useful biomaterials. We present and discuss current works and future developments in protein engineering with nitrogen-containing tryptophan analogs and related compounds as well as their relevance for academic and applicative research.
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Affiliation(s)
- Sandra Lepthien
- Molecular Biotechnology, Max-Planck-Institut für Biochemie, BioFuture Independent Research Group, Am Klopferspitz 18, 82152 Martinsreid, Germany
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25
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Link AJ, Tirrell DA. Reassignment of sense codons in vivo. Methods 2005; 36:291-8. [PMID: 16076455 DOI: 10.1016/j.ymeth.2005.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 04/28/2005] [Indexed: 11/28/2022] Open
Abstract
The genetic code maps one or more of the 61 sense codons onto a set of 20 canonical amino acids. Reassignment of sense codons to non-canonical amino acids in model organisms such as Escherichia coli has been achieved through manipulation of the cellular protein synthesis machinery. Specifically, control of amino acid pools, coupled with engineering of the aminoacyl-tRNA synthetase activity of the host, has enabled assignment of sense codons to a wide variety of non-canonical amino acids under conditions routinely used for expression of recombinant proteins. Codon reassignment is leading to important advances in protein engineering and bioorganic chemistry. Here we summarize some of those advances, and provide detailed protocols for codon reassignment.
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Affiliation(s)
- A James Link
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Hu S, Huang Y, Poss MA, Gentles RG. A novel route to the 5,6-dihydro-4-H-thieno[3,2-b]pyrrol-5-one ring system involving an intermediate substituted-thiophene synthesis. J Heterocycl Chem 2005. [DOI: 10.1002/jhet.5570420427] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Budisa N, Pal PP. Designing novel spectral classes of proteins with a tryptophan-expanded genetic code. Biol Chem 2005; 385:893-904. [PMID: 15551863 DOI: 10.1515/bc.2004.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fluorescence methods are now well-established and powerful tools to study biological macromolecules. The canonical amino acid tryptophan (Trp), encoded by a single UGG triplet, is the main reporter of intrinsic fluorescence properties of most natural proteins and peptides and is thus an attractive target for tailoring their spectral properties. Recent advances in research have provided substantial evidence that the natural protein translational machinery can be genetically reprogrammed to introduce a large number of non-coded (i.e. noncanonical) Trp analogues and surrogates into various proteins. Especially attractive targets for such an engineering approach are fluorescent proteins in which the chromophore is formed post-translationally from an amino acid sequence, like the green fluorescent protein from Aequorea victoria. With the currently available translationally active fluoro-, hydroxy-, amino-, halogen-, and chalcogen-containing Trp analogues and surrogates, the traditional methods for protein engineering and design can be supplemented or even fully replaced by these novel approaches. Future research will provide a further increase in the number of Trp-like amino acids that are available for redesign (by engineering of the genetic code) of native Trp residues and enable novel strategies to generate proteins with tailored spectral properties.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany.
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28
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Budisa N. Prolegomena zum experimentellen Engineering des genetischen Codes durch Erweiterung seines Aminosäurerepertoires. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200300646] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Budisa N. Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire. Angew Chem Int Ed Engl 2004; 43:6426-63. [PMID: 15578784 DOI: 10.1002/anie.200300646] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Junior Research Group "Moleculare Biotechnologie", Am Klopferspitz 18a, 82152 Martinsried bei München, Germany.
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Budisa N, Pipitone O, Siwanowicz I, Rubini M, Pal PP, Holak TA, Gelmi ML. Efforts towards the Design of ?Teflon? Proteins:In vivo Translation with Trifluorinated Leucine and Methionine Analogues. Chem Biodivers 2004; 1:1465-75. [PMID: 17191790 DOI: 10.1002/cbdv.200490107] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In vivo incorporation of monofluorinated noncanonical amino acids into recombinant proteins has been well-established for decades. Proteins fluorinated in this way proved to be useful tools for many practical applications. In contrast, trifluorinated amino acids have been incorporated in only a few peptides and relatively small proteins by using expression systems in living cells. A novel class of proteins with a fluorous core can be envisaged only if full replacement of the core-building hydrophobic and aliphatic amino acids such as leucine or methionine with the related analogues trifluoromethionine and trifluoroleucine would be feasible. However, our systematic efforts to introduce these amino acids in larger proteins (over 10 Da) that contain different structural motifs clearly show that only partial substitutions are possible. The reasons are high toxicity of these substances and difficulties to accommodate them into the compact cores of natural proteins without adverse effects on their structural integrity. Therefore, engineering of such three dimensional 'Teflon'-like structures would require, besides an expansion of the amino acid repertoire of the genetic code, a de novo protein design as well.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried
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Abstract
The genetic code is established by the aminoacylation of transfer RNA, reactions in which each amino acid is linked to its cognate tRNA that, in turn, harbors the nucleotide triplet (anticodon) specific to the amino acid. The accuracy of aminoacylation is essential for building and maintaining the universal tree of life. The ability to manipulate and expand the code holds promise for the development of new methods to create novel proteins and to understand the origins of life. Recent efforts to manipulate the genetic code have fulfilled much of this potential. These efforts have led to incorporation of nonnatural amino acids into proteins for a variety of applications and have demonstrated the plausibility of specific proposals for early evolution of the code.
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Affiliation(s)
- Tamara L Hendrickson
- Department of Chemistry, 1Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA.
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Budisa N, Pal PP, Alefelder S, Birle P, Krywcun T, Rubini M, Wenger W, Bae JH, Steiner T. Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code. Biol Chem 2004; 385:191-202. [PMID: 15101562 DOI: 10.1515/bc.2004.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The expanded genetic code in combination with site-directed mutagenesis was used to probe spectroscopic and structural roles of tryptophan (Trp) residues in Aequorea victoria green fluorescent proteins (avGFPs). Nine different halogen-, chalcogen-, and methyl-containing Trp isosteric analogues and surrogates were incorporated into avGFPs containing indole moieties in, and outside of, the chromophore, by the use of the selective pressure incorporation method. Such isosteric replacements introduced minimal local geometry changes in indole moieties, often to the level of single atomic exchange ('atomic mutation') and do not affect three-dimensional structures of avGFPs but induce changes in spectral properties. Our approach offers a new platform to re-evaluate issues like resonance transfer, mechanisms of chromophore formation and maturation, as well as the importance of local geometry and weak sulphur-aromatic interactions for avGFP spectral properties and structural stability. The library of novel tailor-made avGFP mutants and variants generated in this work has demonstrated not only the potentials of the expanded genetic code to study spectroscopic functions, but also a new approach to generate tailor-made proteins with interesting and useful spectral properties.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany.
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Broos J, Gabellieri E, Biemans-Oldehinkel E, Strambini GB. Efficient biosynthetic incorporation of tryptophan and indole analogs in an integral membrane protein. Protein Sci 2003; 12:1991-2000. [PMID: 12930998 PMCID: PMC2323996 DOI: 10.1110/ps.03142003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Biosynthetic incorporation of tryptophan (Trp) analogs such as 7-azatryptophan, 5-hydroxytryptophan, and fluorotryptophan into a protein can facilitate its structural analysis by spectroscopic techniques such as fluorescence, phosphorescence, nuclear magnetic resonance, and Fourier transform infrared. Until now, the approach has dealt primarily with soluble proteins. In this article, we demonstrate that four different Trp analogs can be very efficiently incorporated into a membrane protein as demonstrated for the mannitol transporter of Escherichia coli (EII(mtl)). EII(mtl) overexpression was under control of the lambdaP(R) promoter, and the E. coli Trp auxotroph M5219 was used as host. This strain constitutively expresses the heat labile repressor protein of the lambdaP(R) promoter. Together with the presence of the repressor gene on the EII(mtl) plasmid, this resulted in a tightly controlled promoter system, a prerequisite for high Trp analog incorporation. A new method for determining the analog incorporation efficiency is presented that is suitable for membrane proteins. The procedure involves fitting of the phosphorescence spectrum as a linear combination of the Trp and Trp analog contributions, taking into account the influence of the protein environment on the Trp analog spectrum. The data show that the analog content of EII(mtl) samples is very high (>95%). In addition, we report here that biosynthetic incorporation of Trp analogs can also be effected with less expensive indole analogs, which in vivo are converted to L-Trp analogs.
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Affiliation(s)
- Jaap Broos
- Department of Biochemistry and Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands.
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Bae JH, Rubini M, Jung G, Wiegand G, Seifert MHJ, Azim MK, Kim JS, Zumbusch A, Holak TA, Moroder L, Huber R, Budisa N. Expansion of the genetic code enables design of a novel "gold" class of green fluorescent proteins. J Mol Biol 2003; 328:1071-81. [PMID: 12729742 DOI: 10.1016/s0022-2836(03)00364-4] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Much effort has been dedicated to the design of significantly red shifted variants of the green fluorescent protein (GFP) from Aequoria victora (av). These approaches have been based on classical engineering with the 20 canonical amino acids. We report here an expansion of these efforts by incorporation of an amino substituted variant of tryptophan into the "cyan" GFP mutant, which turned it into a "gold" variant. This variant possesses a red shift in emission unprecedented for any avFP, similar to "red" FPs, but with enhanced stability and a very low aggregation tendency. An increasing number of non-natural amino acids are available for chromophore redesign (by engineering of the genetic code) and enable new general strategies to generate novel classes of tailor-made GFP proteins.
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Affiliation(s)
- Jae Hyun Bae
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany
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