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Pehlivan Ö, Waliczek M, Kijewska M, Stefanowicz P. Selenium in Peptide Chemistry. Molecules 2023; 28:molecules28073198. [PMID: 37049961 PMCID: PMC10096412 DOI: 10.3390/molecules28073198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/02/2023] [Indexed: 04/07/2023] Open
Abstract
In recent years, researchers have been exploring the potential of incorporating selenium into peptides, as this element possesses unique properties that can enhance the reactivity of these compounds. Selenium is a non-metallic element that has a similar electronic configuration to sulfur. However, due to its larger atomic size and lower electronegativity, it is more nucleophilic than sulfur. This property makes selenium more reactive toward electrophiles. One of the most significant differences between selenium and sulfur is the dissociation of the Se-H bond. The Se-H bond is more easily dissociated than the S-H bond, leading to higher acidity of selenocysteine (Sec) compared to cysteine (Cys). This difference in acidity can be exploited to selectively modify the reactivity of peptides containing Sec. Furthermore, Se-H bonds in selenium-containing peptides are more susceptible to oxidation than their sulfur analogs. This property can be used to selectively modify the peptides by introducing new functional groups, such as disulfide bonds, which are important for protein folding and stability. These unique properties of selenium-containing peptides have found numerous applications in the field of chemical biology. For instance, selenium-containing peptides have been used in native chemical ligation (NCL). In addition, the reactivity of Sec can be harnessed to create cyclic and stapled peptides. Other chemical modifications, such as oxidation, reduction, and photochemical reactions, have also been applied to selenium-containing peptides to create novel molecules with unique biological properties.
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Affiliation(s)
- Özge Pehlivan
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Monika Kijewska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Saebi A, Brown JS, Marando VM, Hartrampf N, Chumbler NM, Hanna S, Poskus M, Loas A, Kiessling LL, Hung DT, Pentelute BL. Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2. ACS Chem Biol 2023; 18:518-527. [PMID: 36821521 PMCID: PMC10460144 DOI: 10.1021/acschembio.2c00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The impermeable outer membrane of Pseudomonas aeruginosa is bypassed by antibacterial proteins known as S-type pyocins. Because of their properties, pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections. Their production and modification, however, remain challenging. To address this limitation, we employed automated fast-flow peptide synthesis for the rapid production of a pyocin S2 import domain. The N-terminal domain sequence (PyS2NTD) was synthesized in under 10 h and purified to yield milligram quantities of the desired product. To our knowledge, the 214 amino acid sequence of PyS2NTD is among the longest peptides produced from a "single-shot" synthesis, i.e., made in a single stepwise route without the use of ligation techniques. Biophysical characterization of the PyS2NTD with circular dichroism was consistent with the literature reports. Fluorescently labeled PyS2NTD binds to P. aeruginosa expressing the cognate ferripyoverdine receptor and is taken up into the periplasm. This selective uptake was validated with confocal and super resolution microscopy, flow cytometry, and fluorescence recovery after photobleaching. These modified, synthetic S-type pyocin domains can be used to probe import mechanisms of P. aeruginosa and leveraged to develop selective antimicrobial agents that bypass the outer membrane.
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Affiliation(s)
- Azin Saebi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph S Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicole M Chumbler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mackenzie Poskus
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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Total chemical synthesis of a biologically active and homogeneous analog of Human Growth Hormone [Nle 14,125,170 ,Glu 29,91 ,Gln 74 ,Asn 107 ,Asp 109 ]hGH-NH 2 by sequential native chemical ligation. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bacchi M, Jullian M, Sirigu S, Fould B, Huet T, Bruyand L, Antoine M, Vuillard L, Ronga L, Chavas LMG, Nosjean O, Ferry G, Puget K, Boutin JA. Total chemical synthesis, refolding, and crystallographic structure of fully active immunophilin calstabin 2 (FKBP12.6). Protein Sci 2016; 25:2225-2242. [PMID: 27670942 DOI: 10.1002/pro.3051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 01/05/2023]
Abstract
Synthetic biology (or chemical biology) is a growing field to which the chemical synthesis of proteins, particularly enzymes, makes a fundamental contribution. However, the chemical synthesis of catalytically active proteins (enzymes) remains poorly documented because it is difficult to obtain enough material for biochemical experiments. We chose calstabin, a 107-amino-acid proline isomerase, as a model. We synthesized the enzyme using the native chemical ligation approach and obtained several tens of milligrams. The polypeptide was refolded properly, and we characterized its biophysical properties, measured its catalytic activity, and then crystallized it in order to obtain its tridimensional structure after X-ray diffraction. The refolded enzyme was compared to the recombinant, wild-type enzyme. In addition, as a first step of validating the whole process, we incorporated exotic amino acids into the N-terminus. Surprisingly, none of the changes altered the catalytic activities of the corresponding mutants. Using this body of techniques, avenues are now open to further obtain enzymes modified with exotic amino acids in a way that is only barely accessible by molecular biology, obtaining detailed information on the structure-function relationship of enzymes reachable by complete chemical synthesis.
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Affiliation(s)
- Marine Bacchi
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Magali Jullian
- Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France
| | - Serena Sirigu
- PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France
| | - Benjamin Fould
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Tiphaine Huet
- PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France
| | - Lisa Bruyand
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Mathias Antoine
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Laurent Vuillard
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Luisa Ronga
- Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France
| | - Leonard M G Chavas
- PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Karine Puget
- Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
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Bondalapati S, Jbara M, Brik A. Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins. Nat Chem 2016; 8:407-18. [DOI: 10.1038/nchem.2476] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 02/04/2016] [Indexed: 12/18/2022]
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Meledin R, Mali SM, Brik A. Pushing the Boundaries of Chemical Protein Synthesis: The Case of Ubiquitin Chains and Polyubiquitinated Peptides and Proteins. CHEM REC 2015; 16:509-19. [DOI: 10.1002/tcr.201500209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Roman Meledin
- Schulich Department of Chemistry; Israel Institute of Technology - Technion; Haifa Israel
| | - Sachitanand M. Mali
- Schulich Department of Chemistry; Israel Institute of Technology - Technion; Haifa Israel
| | - Ashraf Brik
- Schulich Department of Chemistry; Israel Institute of Technology - Technion; Haifa Israel
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Seenaiah M, Jbara M, Mali SM, Brik A. Convergent Versus Sequential Protein Synthesis: The Case of Ubiquitinated and Glycosylated H2B. Angew Chem Int Ed Engl 2015; 54:12374-8. [DOI: 10.1002/anie.201503309] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/13/2015] [Indexed: 11/11/2022]
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Seenaiah M, Jbara M, Mali SM, Brik A. Convergent Versus Sequential Protein Synthesis: The Case of Ubiquitinated and Glycosylated H2B. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503309] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Synthesis and folding of a mirror-image enzyme reveals ambidextrous chaperone activity. Proc Natl Acad Sci U S A 2014; 111:11679-84. [PMID: 25071217 DOI: 10.1073/pnas.1410900111] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mirror-image proteins (composed of D-amino acids) are promising therapeutic agents and drug discovery tools, but as synthesis of larger D-proteins becomes feasible, a major anticipated challenge is the folding of these proteins into their active conformations. In vivo, many large and/or complex proteins require chaperones like GroEL/ES to prevent misfolding and produce functional protein. The ability of chaperones to fold D-proteins is unknown. Here we examine the ability of GroEL/ES to fold a synthetic d-protein. We report the total chemical synthesis of a 312-residue GroEL/ES-dependent protein, DapA, in both L- and D-chiralities, the longest fully synthetic proteins yet reported. Impressively, GroEL/ES folds both L- and D-DapA. This work extends the limits of chemical protein synthesis, reveals ambidextrous GroEL/ES folding activity, and provides a valuable tool to fold d-proteins for drug development and mirror-image synthetic biology applications.
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Abstract
The chemical synthesis of peptides or small proteins is often an important step in many research projects and has stimulated the development of numerous chemical methodologies. The aim of this review is to give a substantial overview of the solid phase methods developed for the production or purification of polypeptides. The solid phase peptide synthesis (SPPS) technique has facilitated considerably the access to short peptides (<50 amino acids). However, its limitations for producing large homogeneous peptides have stimulated the development of solid phase covalent or non-covalent capture purification methods. The power of the native chemical ligation (NCL) reaction for protein synthesis in aqueous solution has also been adapted to the solid phase by the combination of novel linker technologies, cysteine protection strategies and thioester or N,S-acyl shift thioester surrogate chemistries. This review details pioneering studies and the most recent publications related to the solid phase chemical synthesis of large peptides and proteins.
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Raibaut L, Adihou H, Desmet R, Delmas AF, Aucagne V, Melnyk O. Highly efficient solid phase synthesis of large polypeptides by iterative ligations of bis(2-sulfanylethyl)amido (SEA) peptide segments. Chem Sci 2013. [DOI: 10.1039/c3sc51824h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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