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Wang B, Nan ZA, Li Q, Liu J, Lu ZX, Wang W, Zhuo Z, Li GL, Huang YG. Trapping an Ester Hydrate Intermediate in a π-Stacked Macrocycle with Multiple Hydrogen Bonds. Molecules 2023; 28:5705. [PMID: 37570674 PMCID: PMC10420806 DOI: 10.3390/molecules28155705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Ester hydrates, as the intermediates of the esterification between acid and alcohol, are very short-lived and challenging to be trapped. Therefore, the crystal structures of ester hydrates have rarely been characterized. Herein, we present that the mono-deprotonated ester hydrates [CH3OSO2(OH)2]-, serving as the template for the self-assembly of a π-stacked boat-shaped macrocycle (CH3OSO2(OH)2)0.67(CH3OSO3)1.33@{[ClLCoII]6}·Cl4·13CH3OH·9H2O (1) (L = tris(2-benzimidazolylmethyl) amine), can be trapped in the host by multiple NH···O hydrogen bonds. In the solution of CoCl2, L, and H2SO4 in MeOH, HSO4- reacts with MeOH, producing [CH3OSO3]- via the ester hydrate intermediate of [CH3OSO3(OH)2]-. Both the product and the intermediate serve as the template directing the self-assembly of the π-stacked macrocycle, in which the short-lived ester hydrate is firmly trapped and stabilized, as revealed by single-crystal analysis.
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Affiliation(s)
- Bin Wang
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Ang Nan
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qing Li
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jin Liu
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zi-Xiu Lu
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wei Wang
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhu Zhuo
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guo-Ling Li
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
| | - You-Gui Huang
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China; (B.W.); (Z.-A.N.); (Q.L.); (J.L.); (Z.-X.L.); (W.W.); (Z.Z.); (G.-L.L.)
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institutes, Chinese Academy of Sciences, Xiamen 361021, China
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2
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Niu Y, Chen Z, Jiang Z, Yang Y, Liu G, Cheng X, Jiang Z, Zhang G, Tong L, Tang B. Detection of Cysteine Sulfenic Acid on E. coli Proteins with a Biotin-Benzoboroxole Probe. ACS Chem Biol 2023; 18:1351-1359. [PMID: 37260364 DOI: 10.1021/acschembio.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
S-sulfenylation of cysteine residues on proteins can effectively change protein structures and accordingly regulate their functions in vivo. Investigation of S-sulfenylation in different biological environments is thus vital for a systematic understanding of cellular redox regulation. In this work, a functional probe, biotin-benzoboroxole (Bio-ben), was designed for the detection of cysteine sulfenic acid (Cys-SOH). The performance of Bio-ben was characterized by small-molecule sulfenic acid, protein models, and proteome tests via mass spectra and western blotting. The results showed that Bio-ben was validated for cysteine sulfenic acid on proteins with good capture efficiency even at low concentrations. Compared with commonly used probes such as dimedone, the current probe has significantly shortened labeling time and exhibited comparable sensitivity. The proposed method provides a new approach for exploring S-sulfenylation in the oxidative modification of proteins and is helpful for related biological and clinical applications.
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Affiliation(s)
- Yaxin Niu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhongyao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guangzhao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Xiufen Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhenhao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guanglu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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3
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Schwan AL, Nicol EA, Durant AG. Proximal interactions can direct selective sulfenate alkylation chemistry. PHOSPHORUS SULFUR 2023. [DOI: 10.1080/10426507.2023.2172409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Adrian L. Schwan
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada
| | - Eric A. Nicol
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada
| | - Andrew G. Durant
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada
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4
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Riddell AB, Smith MRA, Schwan AL. The generation and reactions of sulfenate anions. An update. J Sulphur Chem 2022. [DOI: 10.1080/17415993.2022.2077086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Adam B. Riddell
- Department of Chemistry, University of Guelph, Guelph, Canada
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5
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Durant AG, Nicol EA, McInnes BM, Schwan AL. A DFT examination of the role of proximal boron functionalities in the S-alkylation of sulfenic acid anions. Org Biomol Chem 2021; 20:649-657. [PMID: 34942637 DOI: 10.1039/d1ob02083h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sulfenic acid anions represent an emerging nucleophile for the preparation of sulfoxides. Their S-functionalization chemistry can often be influenced by a nearby group that interacts with the component atoms of the sulfenate through non-bonding interactions. This study uses DFT methods to assess the importance of proximal boron-containing functional groups to direct S-alkylation chemistry of selected sulfenate anions. Several structural variations were modelled at the B3LYP/6-311++G(d,p) level, with the boron species positioned 3 to 5 carbons away from the alkylation site. Transition state free energies of S-alkylation transition states were located with and without sulfenate oxygen precomplexing to the nearby boron atom. The outcomes suggest that an ortho-substituted boronate ester on benzyl bromide can direct and accelerate an alkylation reaction principally due to a reduction of the entropic barrier. It was also determined that an intermolecular precomplex imparts too much stabilization to the sulfenate, thereby reducing its reactivity. The modelling suggests a possible aryl migration of the boronate/sulfenate complex is not competitive with S-alkylation.
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Affiliation(s)
- Andrew G Durant
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2 W1.
| | - Eric A Nicol
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2 W1.
| | - Brandon M McInnes
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2 W1.
| | - Adrian L Schwan
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2 W1.
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6
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Benkovic SJ. From Bioorganic Models to Cells. Annu Rev Biochem 2021; 90:57-76. [PMID: 34153218 DOI: 10.1146/annurev-biochem-062320-062929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
I endeavor to share how various choices-some deliberate, some unconscious-and the unmistakable influence of many others shaped my scientific pursuits. I am fascinated by how two long-term, major streams of my research, DNA replication and purine biosynthesis, have merged with unexpected interconnections. If I have imparted to many of the talented individuals who have passed through my lab a degree of my passion for uncloaking the mysteries hidden in scientific research and an understanding of the honesty and rigor it demands and its impact on the world community, then my mentorship has been successful.
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Affiliation(s)
- Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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7
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A critical evaluation of probes for cysteine sulfenic acid. Curr Opin Chem Biol 2020; 60:55-65. [PMID: 32866852 DOI: 10.1016/j.cbpa.2020.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022]
Abstract
Cysteine oxidation is important in cellular redox regulation, signaling, and biocatalysis. To understand the biological relevance of cysteine oxidation, it is desirable to identify the proteins involved, the site of the oxidized cysteine, and the relevant oxidation states. Because the thiol of cysteine can be converted to a wide range of oxidation states, mapping these oxidative modifications is challenging. The dynamic and reversible nature of many cysteine oxidation states compounds the difficulty in such proteomic analyses. In this review, we examine methods to detect cysteine sulfenic acid - a particularly challenging functional group to analyze because of its reactive nature. We focus on the selectivity of recently reported probes and discuss some challenges and opportunities in this field.
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8
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Alcock LJ, Langini M, Stühler K, Remke M, Perkins MV, Bernardes GJL, Chalker JM. Proteome‐Wide Survey of Cysteine Oxidation by Using a Norbornene Probe. Chembiochem 2020; 21:1329-1334. [DOI: 10.1002/cbic.201900729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Lisa J. Alcock
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
- Flinders University Institute for Nanoscale Science and Technology Sturt Road Bedford Park South Australia 5042 Australia
| | - Maike Langini
- Molecular Proteomics Laboratory (MPL) Biomedical Research Center (BMFZ) Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Division of Pediatric Neuro-Oncogenomics German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner site University Hospital Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology Medical Faculty Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Neuropathology Medical Faculty Heinrich Heine University Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory (MPL) Biomedical Research Center (BMFZ) Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Molecular Medicine University Hospital Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner site University Hospital Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology Medical Faculty Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Neuropathology Medical Faculty Heinrich Heine University Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
| | - Michael V. Perkins
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
| | - Gonçalo J. L. Bernardes
- University of Cambridge Department of Chemistry Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Justin M. Chalker
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
- Flinders University Institute for Nanoscale Science and Technology Sturt Road Bedford Park South Australia 5042 Australia
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9
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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10
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Scinto SL, Ekanayake O, Seneviratne U, Pigga JE, Boyd SJ, Taylor MT, Liu J, Am Ende CW, Rozovsky S, Fox JM. Dual-Reactivity trans-Cyclooctenol Probes for Sulfenylation in Live Cells Enable Temporal Control via Bioorthogonal Quenching. J Am Chem Soc 2019; 141:10932-10937. [PMID: 31246462 DOI: 10.1021/jacs.9b01164] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sulfenylation (RSH → RSOH) is a post-translational protein modification associated with cellular mechanisms for signal transduction and the regulation of reactive oxygen species. Protein sulfenic acids are challenging to identify and study due to their electrophilic and transient nature. Described here are sulfenic acid modifying trans-cycloocten-5-ol (SAM-TCO) probes for labeling sulfenic acid functionality in live cells. These probes enable a new mode of capturing sulfenic acids via transannular thioetherification, whereas "ordinary" trans-cyclooctenes react only slowly with sulfenic acids. SAM-TCOs combine with sulfenic acid forms of a model peptide and proteins to form stable adducts. Analogously, SAM-TCO with the selenenic acid form of a model protein leads to a selenoetherification product. Control experiments illustrate the need for the transannulation process coupled with the activated trans-cycloalkene functionality. Bioorthogonal quenching of excess unreacted SAM-TCOs with tetrazines in live cells provides both temporal control and a means of preventing artifacts caused by cellular-lysis. A SAM-TCO biotin conjugate was used to label protein sulfenic acids in live cells, and subsequent quenching by tetrazine prevented further labeling even under harshly oxidizing conditions. A cell-based proteomic study validates the ability of SAM-TCO probes to identify and quantify known sulfenic acid redox proteins as well as targets not captured by dimedone-based probes.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Oshini Ekanayake
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Uthpala Seneviratne
- Pfizer Worldwide Research and Development , Cambridge , Massachusetts 02139 , United States
| | - Jessica E Pigga
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Samantha J Boyd
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Michael T Taylor
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jun Liu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development , Groton , Connecticut 06340 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Joseph M Fox
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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11
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De Armas MI, Esteves R, Viera N, Reyes AM, Mastrogiovanni M, Alegria TGP, Netto LES, Tórtora V, Radi R, Trujillo M. Rapid peroxynitrite reduction by human peroxiredoxin 3: Implications for the fate of oxidants in mitochondria. Free Radic Biol Med 2019; 130:369-378. [PMID: 30391677 DOI: 10.1016/j.freeradbiomed.2018.10.451] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Mitochondria are main sites of peroxynitrite formation. While at low concentrations mitochondrial peroxynitrite has been associated with redox signaling actions, increased levels can disrupt mitochondrial homeostasis and lead to pathology. Peroxiredoxin 3 is exclusively located in mitochondria, where it has been previously shown to play a major role in hydrogen peroxide reduction. In turn, reduction of peroxynitrite by peroxiredoxin 3 has been inferred from its protective actions against tyrosine nitration and neurotoxicity in animal models, but was not experimentally addressed so far. Herein, we demonstrate the human peroxiredoxin 3 reduces peroxynitrite with a rate constant of 1 × 107 M-1 s-1 at pH 7.8 and 25 °C. Reaction with hydroperoxides caused biphasic changes in the intrinsic fluorescence of peroxiredoxin 3: the first phase corresponded to the peroxidatic cysteine oxidation to sulfenic acid. Peroxynitrite in excess led to peroxiredoxin 3 hyperoxidation and tyrosine nitration, oxidative post-translational modifications that had been previously identified in vivo. A significant fraction of the oxidant is expected to react with CO2 and generate secondary radicals, which participate in further oxidation and nitration reactions, particularly under metabolic conditions of active oxidative decarboxylations or increased hydroperoxide formation. Our results indicate that both peroxiredoxin 3 and 5 should be regarded as main targets for peroxynitrite in mitochondria.
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Affiliation(s)
- María Inés De Armas
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Romina Esteves
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Nicolás Viera
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Aníbal M Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Thiago G P Alegria
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Verónica Tórtora
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay.
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12
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Tom CTMB, Crellin JE, Motiwala HF, Stone MB, Davda D, Walker W, Kuo YH, Hernandez JL, Labby KJ, Gomez-Rodriguez L, Jenkins PM, Veatch SL, Martin BR. Chemoselective ratiometric imaging of protein S-sulfenylation. Chem Commun (Camb) 2018; 53:7385-7388. [PMID: 28613292 DOI: 10.1039/c7cc02285a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we report a ratiometric fluorescent probe for chemoselective conjugation to sulfenic acids in living cells. Our approach couples an α-fluoro-substituted dimedone to an aminonaphthalene fluorophore (F-DiNap), which upon sulfenic acid conjugation is locked as the 1,3-diketone, changing the fluorophore excitation. F-DiNap reacts with S-sulfenylated proteins at equivalent rates to current probes, but the α-fluorine substitution blocks side-reactions with biological aldehydes.
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Affiliation(s)
- Christopher T M B Tom
- Department of Chemistry and Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI, USA.
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13
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14
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Alcock LJ, Perkins MV, Chalker JM. Chemical methods for mapping cysteine oxidation. Chem Soc Rev 2018; 47:231-268. [DOI: 10.1039/c7cs00607a] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.
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Affiliation(s)
- Lisa J. Alcock
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Michael V. Perkins
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Justin M. Chalker
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
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15
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Abstract
Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner. Reactive cysteines have been targeted by high-throughput screening and fragment-based ligand discovery efforts. New cysteine-reactive electrophiles and compound libraries have been synthesized to enable inhibitor discovery broadly and to minimize nonspecific toxicity and off-target activity of compounds. With the recent blockbuster success of several covalent inhibitors, and the development of new chemical proteomic strategies to broadly identify reactive, ligandable and posttranslationally modified cysteines, cysteine profiling is poised to enable the development of new potent and selective chemical probes and even, in some cases, new drugs.
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16
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Long MJC, Poganik JR, Ghosh S, Aye Y. Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology. ACS Chem Biol 2017; 12:586-600. [PMID: 28068059 DOI: 10.1021/acschembio.6b01148] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.
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Affiliation(s)
- Marcus J. C. Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jesse R. Poganik
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Souradyuti Ghosh
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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17
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Gupta V, Paritala H, Carroll KS. Reactivity, Selectivity, and Stability in Sulfenic Acid Detection: A Comparative Study of Nucleophilic and Electrophilic Probes. Bioconjug Chem 2016; 27:1411-8. [PMID: 27123991 DOI: 10.1021/acs.bioconjchem.6b00181] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The comparative reaction efficiencies of currently used nucleophilic and electrophilic probes toward cysteine sulfenic acid have been thoroughly evaluated in two different settings-(i) a small molecule dipeptide based model and (ii) a recombinant protein model. We further evaluated the stability of corresponding thioether and sulfoxide adducts under reducing conditions which are commonly encountered during proteomic protocols and in cell analysis. Powered by the development of new cyclic and linear C-nucleophiles, the unsurpassed efficiency in the capture of sulfenic acid under competitive conditions is achieved and thus holds great promise as highly potent tools for activity-based sulfenome profiling.
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Affiliation(s)
- Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Hanumantharao Paritala
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
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18
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Gupta V, Carroll KS. Profiling the Reactivity of Cyclic C-Nucleophiles towards Electrophilic Sulfur in Cysteine Sulfenic Acid. Chem Sci 2016; 7:400-415. [PMID: 26819701 PMCID: PMC4724439 DOI: 10.1039/c5sc02569a] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Oxidation of a protein cysteine thiol to sulfenic acid, termed S-sulfenylation, is a reversible post-translational modification that plays a crucial role in regulating protein function and is correlated with disease states. The majority of reaction-based small molecule and immunochemical probes used for detecting sulfenic acids are based on the 5,5-dimethyl-1,3-cyclohexanedione (dimedone) scaffold, which is selective, but suffers from low reactivity. In addition, mechanistic details and features that diminish or enhance nucleophile reactivity remain largely unknown. A significant hurdle to resolving the aforementioned issues has been the chemically unstable nature of small-molecule sulfenic acid models. Herein, we report a facile mass spectrometry-based assay and repurposed dipeptide-based model to screen a library of cyclic C-nucleophiles for reactivity with sulfenic acid under aqueous conditions. Observed rate constants for ~100 cyclic C-nucleophiles were obtained and, from this collection, we have identified novel compounds with more than 200-fold enhanced reactivity, as compared to dimedone. The increase in reactivity and retention of selectivity of these C-nucleophiles were validated in secondary assays, including a protein model for sulfenic acid. Together, this work represents a significant step toward developing new chemical reporters for detecting protein S-sulfenylation with superior kinetic resolution. The enhanced rates and varied composition of the C-nucleophiles should enable more comprehensive analyses of the sulfenome and serve as the foundation for reversible or irreversible nucleophilic covalent inhibitors that target oxidized cysteine residues in therapeutically important proteins.
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Affiliation(s)
- Vinayak Gupta
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , USA .
| | - Kate S. Carroll
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , USA .
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19
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Brewer TF, Garcia FJ, Onak CS, Carroll KS, Chang CJ. Chemical approaches to discovery and study of sources and targets of hydrogen peroxide redox signaling through NADPH oxidase proteins. Annu Rev Biochem 2015; 84:765-90. [PMID: 26034893 DOI: 10.1146/annurev-biochem-060614-034018] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen peroxide (H2O2) is a prime member of the reactive oxygen species (ROS) family of molecules produced during normal cell function and in response to various stimuli, but if left unchecked, it can inflict oxidative damage on all types of biological macromolecules and lead to cell death. In this context, a major source of H2O2 for redox signaling purposes is the NADPH oxidase (Nox) family of enzymes, which were classically studied for their roles in phagocytic immune response but have now been found to exist in virtually all mammalian cell types in various isoforms with distinct tissue and subcellular localizations. Downstream of this tightly regulated ROS generation, site-specific, reversible covalent modification of proteins, particularly oxidation of cysteine thiols to sulfenic acids, represents a prominent posttranslational modification akin to phosphorylation as an emerging molecular mechanism for transforming an oxidant signal into a dynamic biological response. We review two complementary types of chemical tools that enable (a) specific detection of H2O2 generated at its sources and (b) mapping of sulfenic acid posttranslational modification targets that mediate its signaling functions, which can be used to study this important chemical signal in biological systems.
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20
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Synthesis and evaluation of functionalized aminobenzoboroxoles as potential anti -cancer agents. J Organomet Chem 2015. [DOI: 10.1016/j.jorganchem.2015.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Devarie-Baez NO, Silva Lopez EI, Furdui CM. Biological chemistry and functionality of protein sulfenic acids and related thiol modifications. Free Radic Res 2015; 50:172-94. [PMID: 26340608 DOI: 10.3109/10715762.2015.1090571] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selective modification of proteins at cysteine residues by reactive oxygen, nitrogen or sulfur species formed under physiological and pathological states is emerging as a critical regulator of protein activity impacting cellular function. This review focuses primarily on protein sulfenylation (-SOH), a metastable reversible modification connecting reduced cysteine thiols to many products of cysteine oxidation. An overview is first provided on the chemistry principles underlining synthesis, stability and reactivity of sulfenic acids in model compounds and proteins, followed by a brief description of analytical methods currently employed to characterize these oxidative species. The following chapters present a selection of redox-regulated proteins for which the -SOH formation was experimentally confirmed and linked to protein function. These chapters are organized based on the participation of these proteins in the regulation of signaling, metabolism and epigenetics. The last chapter discusses the therapeutic implications of altered redox microenvironment and protein oxidation in disease.
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Affiliation(s)
- Nelmi O Devarie-Baez
- a Department of Internal Medicine, Section on Molecular Medicine , Wake Forest School of Medicine , Winston-Salem , NC , USA
| | - Elsa I Silva Lopez
- a Department of Internal Medicine, Section on Molecular Medicine , Wake Forest School of Medicine , Winston-Salem , NC , USA
| | - Cristina M Furdui
- a Department of Internal Medicine, Section on Molecular Medicine , Wake Forest School of Medicine , Winston-Salem , NC , USA
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22
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Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502731] [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]
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23
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Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew Chem Int Ed Engl 2015; 54:10763-7. [DOI: 10.1002/anie.201502731] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/26/2015] [Indexed: 11/07/2022]
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24
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Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate. Sci Rep 2015; 5:11870. [PMID: 26149121 PMCID: PMC4493562 DOI: 10.1038/srep11870] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/09/2015] [Indexed: 12/29/2022] Open
Abstract
Ergothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond formation reaction and a PLP-mediated C-S lyase (EgtE) reaction results in a net sulfur transfer from cysteine to histidine side-chain. This demonstrates a new sulfur transfer strategy in the biosynthesis of sulfur-containing natural products. Due to difficulties associated with the overexpression of Mycobacterium smegmatis EgtE protein, the proposed EgtE functionality remained to be verified biochemically. In this study, we have successfully overexpressed and purified M. smegmatis EgtE enzyme and evaluated its activities under different in vitro conditions: C-S lyase reaction using either thioether or sulfoxide as a substrate in the presence or absence of reductants. Results from our biochemical characterizations support the assignment of sulfoxide 4 as the native EgtE substrate and the involvement of a sulfenic acid intermediate in the ergothioneine C-S lyase reaction.
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25
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Adamczyk-Woźniak A, Borys KM, Sporzyński A. Recent Developments in the Chemistry and Biological Applications of Benzoxaboroles. Chem Rev 2015; 115:5224-47. [DOI: 10.1021/cr500642d] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Krzysztof M. Borys
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Andrzej Sporzyński
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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26
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Boronat S, García-Santamarina S, Hidalgo E. Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation. Free Radic Res 2015; 49:494-510. [PMID: 25782062 DOI: 10.3109/10715762.2015.1009053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.
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Affiliation(s)
- S Boronat
- Departament de Ciències Experimentals i de la Salut, Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , C/Dr. Aiguader 88, E-08003 Barcelona , Spain
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27
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Baez NOD, Reisz JA, Furdui CM. Mass spectrometry in studies of protein thiol chemistry and signaling: opportunities and caveats. Free Radic Biol Med 2015; 80:191-211. [PMID: 25261734 PMCID: PMC4355329 DOI: 10.1016/j.freeradbiomed.2014.09.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has become a powerful and widely utilized tool in the investigation of protein thiol chemistry, biochemistry, and biology. Very early biochemical studies of metabolic enzymes have brought to light the broad spectrum of reactivity profiles that distinguish cysteine thiols with functions in catalysis and protein stability from other cysteine residues in proteins. The development of MS methods for the analysis of proteins using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) coupled with the emergence of high-resolution mass analyzers has been instrumental in advancing studies of thiol modifications, both in single proteins and within the cellular context. This article reviews MS instrumentation and methods of analysis employed in investigations of thiols and their reactivity toward a range of small biomolecules. A selected number of studies are detailed to highlight the advantages brought about by the MS technologies along with the caveats associated with these analyses.
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Affiliation(s)
- Nelmi O Devarie Baez
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Julie A Reisz
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
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28
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Affiliation(s)
- Gizem Keceli
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - John P. Toscano
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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29
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Liu CT, Tomsho JW, Benkovic SJ. The unique chemistry of benzoxaboroles: current and emerging applications in biotechnology and therapeutic treatments. Bioorg Med Chem 2014; 22:4462-73. [PMID: 24864040 DOI: 10.1016/j.bmc.2014.04.065] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/21/2014] [Accepted: 04/30/2014] [Indexed: 12/25/2022]
Abstract
Benzoxaboroles have garnered much attention in recent years due to their diverse applications in bio-sensing technology, material science, and therapeutic intervention. Part of the reason arises from the benzoxaboroles' unique chemical properties, especially in comparison to their acyclic boronic acid counterparts. Furthermore, the low bio-toxicity combined with the high target specificity associated with benzoxaboroles make them very attractive as therapeutic agents. Herein, we provide an updated summary on the current knowledge of the fundamental chemical reactivity of benzoxaboroles, followed by highlighting their major applications reported to date.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, United States
| | - John W Tomsho
- Department of Chemistry & Biochemistry, University of the Sciences, 600 S. 43rd Street, Philadelphia, PA 19104-4495, United States.
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, United States.
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30
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Martinez S, Wu R, Sanishvili R, Liu D, Holz R. The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile. J Am Chem Soc 2014; 136:1186-9. [PMID: 24383915 PMCID: PMC3968781 DOI: 10.1021/ja410462j] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Indexed: 01/10/2023]
Abstract
Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of the nucleophile remains a mystery. Boronic acids have been shown to be potent inhibitors of numerous hydrolytic enzymes due to the open shell of boron, which allows it to expand from a trigonal planar (sp(2)) form to a tetrahedral form (sp(3)). Therefore, we examined the inhibition of the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) by boronic acids via kinetics and X-ray crystallography. Both 1-butaneboronic acid (BuBA) and phenylboronic acid (PBA) function as potent competitive inhibitors of PtNHase. X-ray crystal structures for BuBA and PBA complexed to PtNHase were solved and refined at 1.5, 1.6, and 1.2 Å resolution. The resulting PtNHase-boronic acid complexes represent a "snapshot" of reaction intermediates and implicate the cysteine-sulfenic acid ligand as the catalytic nucleophile, a heretofore unknown role for the αCys(113)-OH sulfenic acid ligand. Based on these data, a new mechanism of action for the hydration of nitriles by NHase is presented.
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Affiliation(s)
- Salette Martinez
- Department
of Chemistry, Marquette
University, Milwaukee, Wisconsin 53201, United States
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rui Wu
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Ruslan Sanishvili
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Dali Liu
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Richard Holz
- Department
of Chemistry, Marquette
University, Milwaukee, Wisconsin 53201, United States
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31
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Sene S, Berthomieu D, Donnadieu B, Richeter S, Vezzani J, Granier D, Bégu S, Mutin H, Gervais C, Laurencin D. A combined experimental-computational study of benzoxaborole crystal structures. CrystEngComm 2014. [DOI: 10.1039/c4ce00313f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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