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Kulkarni SS, Watson EE, Maxwell JWC, Niederacher G, Johansen‐Leete J, Huhmann S, Mukherjee S, Norman AR, Kriegesmann J, Becker CFW, Payne RJ. Expressed Protein Selenoester Ligation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202200163. [PMID: 38505698 PMCID: PMC10947028 DOI: 10.1002/ange.202200163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 03/21/2024]
Abstract
Herein, we describe the development and application of a novel expressed protein selenoester ligation (EPSL) methodology for the one-pot semi-synthesis of modified proteins. EPSL harnesses the rapid kinetics of ligation reactions between modified synthetic selenopeptides and protein aryl selenoesters (generated from expressed intein fusion precursors) followed by in situ chemoselective deselenization to afford target proteins at concentrations that preclude the use of traditional ligation methods. The utility of the EPSL technology is showcased through the efficient semi-synthesis of ubiquitinated polypeptides, lipidated analogues of the membrane-associated GTPase YPT6, and site-specifically phosphorylated variants of the oligomeric chaperone protein Hsp27 at high dilution.
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Affiliation(s)
- Sameer S. Kulkarni
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Emma E. Watson
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Joshua W. C. Maxwell
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Gerhard Niederacher
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Jason Johansen‐Leete
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Susanne Huhmann
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Somnath Mukherjee
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Alexander R. Norman
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Julia Kriegesmann
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Christian F. W. Becker
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Richard J. Payne
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
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2
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Kulkarni SS, Watson EE, Maxwell JWC, Niederacher G, Johansen‐Leete J, Huhmann S, Mukherjee S, Norman AR, Kriegesmann J, Becker CFW, Payne RJ. Expressed Protein Selenoester Ligation. Angew Chem Int Ed Engl 2022; 61:e202200163. [PMID: 35194928 PMCID: PMC9314092 DOI: 10.1002/anie.202200163] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 12/23/2022]
Abstract
Herein, we describe the development and application of a novel expressed protein selenoester ligation (EPSL) methodology for the one-pot semi-synthesis of modified proteins. EPSL harnesses the rapid kinetics of ligation reactions between modified synthetic selenopeptides and protein aryl selenoesters (generated from expressed intein fusion precursors) followed by in situ chemoselective deselenization to afford target proteins at concentrations that preclude the use of traditional ligation methods. The utility of the EPSL technology is showcased through the efficient semi-synthesis of ubiquitinated polypeptides, lipidated analogues of the membrane-associated GTPase YPT6, and site-specifically phosphorylated variants of the oligomeric chaperone protein Hsp27 at high dilution.
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Affiliation(s)
- Sameer S. Kulkarni
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Emma E. Watson
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Joshua W. C. Maxwell
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Gerhard Niederacher
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Jason Johansen‐Leete
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Susanne Huhmann
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Somnath Mukherjee
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Alexander R. Norman
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Julia Kriegesmann
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Christian F. W. Becker
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Richard J. Payne
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
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3
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McLean JT, Milbeo P, Lynch DM, McSweeney L, Scanlan EM. Radical‐Mediated Acyl Thiol‐Ene Reaction for Rapid Synthesis of Biomolecular Thioester Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua T. McLean
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Pierre Milbeo
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Dylan M. Lynch
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Lauren McSweeney
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
| | - Eoin M. Scanlan
- School of Chemistry Trinity College Dublin The University of Dublin College Green Dublin 2 Ireland
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Bhagawati M, Hoffmann S, Höffgen KS, Piehler J, Busch KB, Mootz HD. In Cellulo Protein Semi‐Synthesis from Endogenous and Exogenous Fragments Using the Ultra‐Fast Split Gp41‐1 Intein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maniraj Bhagawati
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Simon Hoffmann
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Katharina S. Höffgen
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics University of Osnabrück Barbarastrasse 11 49076 Osnabrück Germany
| | - Karin B. Busch
- Institute of Molecular Cell Biology University of Münster Schlossplatz 5 48149 Münster Germany
| | - Henning D. Mootz
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
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5
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Bhagawati M, Hoffmann S, Höffgen KS, Piehler J, Busch KB, Mootz HD. In Cellulo Protein Semi-Synthesis from Endogenous and Exogenous Fragments Using the Ultra-Fast Split Gp41-1 Intein. Angew Chem Int Ed Engl 2020; 59:21007-21015. [PMID: 32777124 PMCID: PMC7693240 DOI: 10.1002/anie.202006822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/15/2020] [Indexed: 12/19/2022]
Abstract
Protein semi-synthesis inside live cells from exogenous and endogenous parts offers unique possibilities for studying proteins in their native context. Split-intein-mediated protein trans-splicing is predestined for such endeavors and has seen some successes, but a much larger variety of established split inteins and associated protocols is urgently needed. We characterized the association and splicing parameters of the Gp41-1 split intein, which favorably revealed a nanomolar affinity between the intein fragments combined with the exceptionally fast splicing rate. Following bead-loading of a chemically modified intein fragment precursor into live mammalian cells, we fluorescently labeled target proteins on their N- and C-termini with short peptide tags, thus ensuring minimal perturbation of their structure and function. In combination with a nuclear-entrapment strategy to minimize cytosolic fluorescence background, we applied our technique for super-resolution imaging and single-particle tracking of the outer mitochondrial protein Tom20 in HeLa cells.
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Affiliation(s)
- Maniraj Bhagawati
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Simon Hoffmann
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Katharina S. Höffgen
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Jacob Piehler
- Department of Biology and Center for Cellular NanoanalyticsUniversity of OsnabrückBarbarastrasse 1149076OsnabrückGermany
| | - Karin B. Busch
- Institute of Molecular Cell BiologyUniversity of MünsterSchlossplatz 548149MünsterGermany
| | - Henning D. Mootz
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
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6
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Hoffmann S, Terhorst TME, Singh RK, Kümmel D, Pietrokovski S, Mootz HD. Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein. Chembiochem 2020; 22:364-373. [PMID: 32813312 PMCID: PMC7891396 DOI: 10.1002/cbic.202000509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Indexed: 12/31/2022]
Abstract
Split inteins are indispensable tools for protein engineering because their ligation and cleavage reactions enable unique modifications of the polypeptide backbone. Three different classes of inteins have been identified according to the nature of the covalent intermediates resulting from the acyl rearrangements in the multistep protein‐splicing pathway. Class 3 inteins employ a characteristic internal cysteine for a branched thioester intermediate. A bioinformatic database search of non‐redundant protein sequences revealed the absence of split variants in 1701 class 3 inteins. We have discovered the first reported split class 3 intein in a metagenomics data set and report its biochemical, mechanistic and structural analysis. The AceL NrdHF intein exhibits low sequence conservation with other inteins and marked deviations in residues at conserved key positions, including a variation of the typical class‐3 WCT triplet motif. Nevertheless, functional analysis confirmed the class 3 mechanism of the intein and revealed excellent splicing yields within a few minutes over a wide range of conditions and with barely detectable cleavage side reactions. A high‐resolution crystal structure of the AceL NrdHF precursor and a mutagenesis study explained the importance and roles of several residues at the key positions. Tolerated substitutions in the flanking extein residues and a high affinity between the split intein fragments further underline the intein's future potential as a ligation tool.
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Affiliation(s)
- Simon Hoffmann
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Tobias M E Terhorst
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Rohit K Singh
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
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7
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. A Challenging Pie to Splice: Drugging the Spliceosome. Angew Chem Int Ed Engl 2017; 56:12052-12063. [PMID: 28371109 PMCID: PMC6311392 DOI: 10.1002/anie.201701065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 02/05/2023]
Abstract
Since its discovery in 1977, the study of alternative RNA splicing has revealed a plethora of mechanisms that had never before been documented in nature. Understanding these transitions and their outcome at the level of the cell and organism has become one of the great frontiers of modern chemical biology. Until 2007, this field remained in the hands of RNA biologists. However, the recent identification of natural product and synthetic modulators of RNA splicing has opened new access to this field, allowing for the first time a chemical-based interrogation of RNA splicing processes. Simultaneously, we have begun to understand the vital importance of splicing in disease, which offers a new platform for molecular discovery and therapy. As with many natural systems, gaining clear mechanistic detail at the molecular level is key towards understanding the operation of any biological machine. This minireview presents recent lessons learned in this emerging field of RNA splicing chemistry and chemical biology.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - Warren C. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
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8
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. Das Spliceosom als Angriffspunkt für Pharmaka. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - Warren C. Chan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
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9
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Camarero JA, Kimura RH, Woo YH, Shekhtman A, Cantor J. Biosynthesis of a fully functional cyclotide inside living bacterial cells. Chembiochem 2016; 8:1363-6. [PMID: 17590879 DOI: 10.1002/cbic.200700183] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Julio A Camarero
- Lawrence Livermore National Laboratory, University of California, 7000 East Avenue, L-231, Livermore, CA 94550, USA.
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10
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Thiel IV, Volkmann G, Pietrokovski S, Mootz HD. An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Thiel IV, Volkmann G, Pietrokovski S, Mootz HD. An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling. Angew Chem Int Ed Engl 2014; 53:1306-10. [DOI: 10.1002/anie.201307969] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/06/2022]
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12
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Mihaylov TT, Parac-Vogt TN, Pierloot K. A Mechanistic Study of the Spontaneous Hydrolysis of Glycylserine as the Simplest Model for Protein Self-Cleavage. Chemistry 2013; 20:456-66. [DOI: 10.1002/chem.201303564] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Indexed: 11/05/2022]
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13
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Michel E, Skrisovska L, Wüthrich K, Allain FHT. Amino Acid-Selective Segmental Isotope Labeling of Multidomain Proteins for Structural Biology. Chembiochem 2013; 14:457-66. [DOI: 10.1002/cbic.201200732] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Indexed: 11/12/2022]
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14
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Kita Y, Nishii Y, Higuchi T, Mashima K. Zinc-Catalyzed Amide Cleavage and Esterification of β-Hydroxyethylamides. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201789] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Kita Y, Nishii Y, Higuchi T, Mashima K. Zinc-Catalyzed Amide Cleavage and Esterification of β-Hydroxyethylamides. Angew Chem Int Ed Engl 2012; 51:5723-6. [DOI: 10.1002/anie.201201789] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 11/05/2022]
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16
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Magens S, Plietker B. Fe-Catalyzed Thioesterification of Carboxylic Esters. Chemistry 2011; 17:8807-9. [DOI: 10.1002/chem.201101073] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Indexed: 11/08/2022]
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17
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Berrade L, Kwon Y, Camarero J. Photomodulation of protein trans-splicing through backbone photocaging of the DnaE split intein. Chembiochem 2010; 11:1368-72. [PMID: 20512791 PMCID: PMC2935465 DOI: 10.1002/cbic.201000157] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Indexed: 01/14/2023]
Abstract
A novel strategy to modulate the assembly and trans-splicing activity of the Ssp DnaE split-intein was achieved by introducing two photolabile protecting groups onto the backbone of the C-intein polypeptide. This modification was not only able to efficiently block the trans-splicing activity, but also reduce significantly the binding affinity constant between the C- and N-intein fragments. The original activity of the wild-type split intein could be fully recovered by brief exposure to UV light.
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Affiliation(s)
- Luis Berrade
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Youngeun Kwon
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biomedical Engineering, Dongguk University-Seoul, Pildong 3-ga, Seoul, Korea 100-713
| | - Julio Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
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Affiliation(s)
- Henning D Mootz
- Technische Universität Dortmund, Fakultät Chemie, Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.
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19
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Wang H, Nakata E, Hamachi I. Recent progress in strategies for the creation of protein-based fluorescent biosensors. Chembiochem 2010; 10:2560-77. [PMID: 19693761 DOI: 10.1002/cbic.200900249] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The creation of novel bioanalytical tools for the detection and monitoring of a range of important target substances and biological events in vivo and in vitro is a great challenge in chemical biology and biotechnology. Protein-based fluorescent biosensors--integrated devices that convert a molecular-recognition event to a fluorescent signal--have recently emerged as a powerful tool. As the recognition units various proteins that can specifically recognize and bind a variety of molecules of biological significance with high affinity are employed. For the transducer, fluorescent proteins, such as green fluorescent protein (GFP) or synthetic fluorophores, are mostly adopted. Recent progress in protein engineering and organic synthesis allows us to manipulate proteins genetically and/or chemically, and a library of such protein scaffolds has been significantly expanded by genome projects. In this review, we briefly describe the recent progress of protein-based fluorescent biosensors on the basis of their platform and construction strategy, which are primarily divided into the genetically encoded fluorescent biosensors and chemically constructed biosensors.
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Affiliation(s)
- Hangxiang Wang
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
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20
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Brenzel S, Cebi M, Reiß P, Koert U, Mootz HD. Expanding the Scope of ProteinTrans-Splicing to Fragment Ligation of an Integral Membrane Protein: Towards Modulation of Porin-Based Ion Channels by Chemical Modification. Chembiochem 2009; 10:983-6. [DOI: 10.1002/cbic.200900039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Wollschläger K, Gaus K, Körnig A, Eckel R, Wilking SD, McIntosh M, Majer Z, Becker A, Ros R, Anselmetti D, Sewald N. Single-molecule experiments to elucidate the minimal requirement for DNA recognition by transcription factor epitopes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:484-495. [PMID: 19199332 DOI: 10.1002/smll.200800945] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Interactions between proteins and DNA are essential for the regulation of cellular processes in all living organisms. In this context, it is of special interest to investigate the sequence-specific molecular recognition between transcription factors and their cognate DNA sequences. As a model system, peptide and protein epitopes of the DNA-binding domain (DBD) of the transcription factor PhoB from Escherichia coli are analyzed with respect to DNA binding at the single-molecule level. Peptides representing the amphiphilic recognition helix of the PhoB DBD (amino acids 190-209) are chemically synthesized and C-terminally modified with a linker for atomic force microscopy-dynamic force spectroscopy experiments (AFM-DFS). For comparison, the entire PhoB DBD is overexpressed in E. coli and purified using an intein-mediated protein purification method. To facilitate immobilization for AFM-DFS experiments, an additional cysteine residue is ligated to the protein. Quantitative AFM-DFS analysis proves the specificity of the interaction and yields force-related properties and kinetic data, such as thermal dissociation rate constants. An alanine scan for strategic residues in both peptide and protein sequences is performed to reveal the contributions of single amino acid residues to the molecular-recognition process. Additionally, DNA binding is substantiated by electrophoretic mobility-shift experiments. Structural differences of the peptides, proteins, and DNA upon complex formation are analyzed by circular dichroism spectroscopy. This combination of techniques eventually provides a concise picture of the contribution of epitopes or single amino acids in PhoB to DNA binding.
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Affiliation(s)
- Katrin Wollschläger
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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22
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Piontek C, Ring P, Harjes O, Heinlein C, Mezzato S, Lombana N, Pöhner C, Püttner M, Varón Silva D, Martin A, Schmid F, Unverzagt C. Semisynthesis of a Homogeneous Glycoprotein Enzyme: Ribonuclease C: Part 1. Angew Chem Int Ed Engl 2009; 48:1936-40. [DOI: 10.1002/anie.200804734] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Piontek C, Ring P, Harjes O, Heinlein C, Mezzato S, Lombana N, Pöhner C, Püttner M, Varón Silva D, Martin A, Schmid F, Unverzagt C. Semisynthese eines homogenen Glycoprotein-Enzyms: Ribonuclease C (Teil 1). Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804734] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Liebeskind L, Yang H, Li H. A Copper‐Catalyzed, pH‐Neutral Construction of High‐Enantiopurity Peptidyl Ketones from PeptidicS‐Acylthiosalicylamides in Air at Room Temperature. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804524] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lanny S. Liebeskind
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (USA), Fax: (+1) 404‐727‐6604
| | - Hao Yang
- Abbott Laboratories, GPRD, Process R&D, R450‐NCR13‐323A, 1401 Sheridan Road, North Chicago, IL 60064 (USA)
| | - Hao Li
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (USA), Fax: (+1) 404‐727‐6604
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Kurpiers T, Mootz HD. Site-specific chemical modification of proteins with a prelabelled cysteine tag using the artificially split Mxe GyrA intein. Chembiochem 2009; 9:2317-25. [PMID: 18756552 DOI: 10.1002/cbic.200800319] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The selective modification of proteins with a synthetic probe is of central interest for many aspects of protein chemistry. We have recently reported a new approach in which a short cysteine-containing tag (CysTag) fused to one part of a split intein is first modified with a sulfhydryl-reactive probe. In a second step, protein trans-splicing is used to link the labelled CysTag to a target protein that has been expressed in fusion with the complementary split intein fragment. Here, we present the generation and biochemical characterisation of the artificially split Mycobacterium xenopi GyrA intein. We show that this split intein is active without a renaturation step and that it provides a significant improvement for the CysTag protein-labelling approach in terms of product yields and target protein tolerance. Two proteins with multiple cysteine residues, human growth hormone and a multidomain nonribosomal peptide synthetase, were site-specifically modified with high yields. Our approach combines the benefits of the plethora of commercially available cysteine-reactive probes with a straightforward route for their site-specific incorporation even into complex and cysteine-rich proteins.
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Affiliation(s)
- Thomas Kurpiers
- Technische Universität Dortmund, Fakultät Chemie-Chemische Biologie, Otto-Hahn-Strasse 6, 44229 Dortmund, Germany
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26
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Liebeskind LS, Yang H, Li H. A copper-catalyzed, pH-neutral construction of high-enantiopurity peptidyl ketones from peptidic s-acylthiosalicylamides in air at room temperature. Angew Chem Int Ed Engl 2009; 48:1417-21. [PMID: 19145620 PMCID: PMC2790066 DOI: 10.1002/anie.200804524] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A copper-catalyzed transformation of peptidic thiol esters and boronic acids gives peptidyl ketones and takes place in DMF or DMF/H(2)O at room temperature in air (see scheme). This aerobic reaction only occurs at a thiol ester group capable of coordinating to Cu through its appendage on the sulfur center and is not hampered by racemization of the reactants or products.
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Affiliation(s)
- Lanny S Liebeskind
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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27
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Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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29
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Kurpiers T, Mootz HD. Regioselective cysteine bioconjugation by appending a labeled cystein tag to a protein by using protein splicing in trans. Angew Chem Int Ed Engl 2007; 46:5234-7. [PMID: 17538921 DOI: 10.1002/anie.200700719] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Thomas Kurpiers
- Universität Dortmund, Fachbereich Chemie - Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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30
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Kurpiers T, Mootz H. Regioselektive Cysteinbiokonjugation durch Anhängen eines modifizierten Cystein-tags an ein Protein mithilfe vontrans-Proteinspleißen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700719] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Ludwig C, Pfeiff M, Linne U, Mootz HD. Ligation of a synthetic peptide to the N terminus of a recombinant protein using semisynthetic protein trans-splicing. Angew Chem Int Ed Engl 2007; 45:5218-21. [PMID: 16823791 DOI: 10.1002/anie.200600570] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christina Ludwig
- Philipps-Universität Marburg, Fachbereich Chemie/Biochemie, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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32
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Kimura RH, Tran AT, Camarero JA. Biosynthesis of the cyclotide Kalata B1 by using protein splicing. Angew Chem Int Ed Engl 2007; 45:973-6. [PMID: 16381044 DOI: 10.1002/anie.200503882] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Richard H Kimura
- Chemical Biology and Nuclear Sciences Division, Lawrence Livermore National Laboratory, University of California, CA 94550, USA
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Kwon Y, Coleman MA, Camarero JA. Selective immobilization of proteins onto solid supports through split-intein-mediated protein trans-splicing. Angew Chem Int Ed Engl 2007; 45:1726-9. [PMID: 16470557 DOI: 10.1002/anie.200503475] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Youngeun Kwon
- Chemical Biology and Nuclear Science Division, Lawrence Livermore National Laboratory, University of California, 94550, USA
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34
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Walsh CT, Garneau-Tsodikova S, Gatto GJ. Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 2007; 44:7342-72. [PMID: 16267872 DOI: 10.1002/anie.200501023] [Citation(s) in RCA: 1079] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The diversity of distinct covalent forms of proteins (the proteome) greatly exceeds the number of proteins predicted by DNA coding capacities owing to directed posttranslational modifications. Enzymes dedicated to such protein modifications include 500 human protein kinases, 150 protein phosphatases, and 500 proteases. The major types of protein covalent modifications, such as phosphorylation, acetylation, glycosylation, methylation, and ubiquitylation, can be classified according to the type of amino acid side chain modified, the category of the modifying enzyme, and the extent of reversibility. Chemical events such as protein splicing, green fluorescent protein maturation, and proteasome autoactivations also represent posttranslational modifications. An understanding of the scope and pattern of the many posttranslational modifications in eukaryotic cells provides insight into the function and dynamics of proteome compositions.
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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35
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Macmillan D. Strategien zur Proteinsynthese vereinigen sich mit der nativen chemischen Ligation. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602945] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Macmillan D. Evolving Strategies for Protein Synthesis Converge on Native Chemical Ligation. Angew Chem Int Ed Engl 2006; 45:7668-72. [PMID: 17091510 DOI: 10.1002/anie.200602945] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Derek Macmillan
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H0AJ, UK.
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37
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Ludwig C, Pfeiff M, Linne U, Mootz HD. Ligation eines synthetischen Peptids an den N-Terminus eines rekombinanten Proteins durch semisynthetischestrans-Proteinspleißen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600570] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Kwon Y, Coleman MA, Camarero JA. Selective Immobilization of Proteins onto Solid Supports through Split-Intein-Mediated Protein Trans-Splicing. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503475] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Kimura RH, Tran AT, Camarero JA. Biosynthesis of the Cyclotide Kalata B1 by Using Protein Splicing. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503882] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Walsh CT, Garneau-Tsodikova S, Gatto GJ. Posttranslationale Proteinmodifikation: die Chemie der Proteomdiversifizierung. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501023] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Abstract
Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.
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Affiliation(s)
- Lei Wang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Johnsson N, Johnsson K. A fusion of disciplines: chemical approaches to exploit fusion proteins for functional genomics. Chembiochem 2003; 4:803-10. [PMID: 12964152 DOI: 10.1002/cbic.200200603] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nils Johnsson
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, 76021 Karlsruhe, Germany.
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45
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Sewing A, Hilvert D. Fmoc-Compatible Solid-Phase Peptide Synthesis of Long C-Terminal Peptide Thioesters The authors are grateful to the ETH-Zürich and Novartis Pharma AG for support of this work. Fmoc=9-fluorenylmethoxycarbonyl. Angew Chem Int Ed Engl 2001; 40:3395-3396. [PMID: 11592149 DOI: 10.1002/1521-3773(20010917)40:18<3395::aid-anie3395>3.0.co;2-g] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Axel Sewing
- Laboratorium für Organische Chemie Swiss Federal Institute of Technology (ETH) Universitätstrasse 16, 8092 Zurich (Switzerland)
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