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Zeppilli D, Madabeni A, Nogara PA, Rocha JBT, Orian L. Reactivity of Zinc Fingers in Oxidizing Environments: Insight from Molecular Models Through Activation Strain Analysis. Chempluschem 2024:e202400252. [PMID: 38842473 DOI: 10.1002/cplu.202400252] [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: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/07/2024]
Abstract
The reactivity of Zn2+ tetrahedral complexes with H2O2 was investigated in silico, as a first step in their disruption process. The substrates were chosen to represent the cores of three different zinc finger protein motifs, i. e., a Zn2+ ion coordinated to four cysteines (CCCC), to three cysteines and one histidine (CCCH), and to two cysteines and two histidines (CCHH). The cysteine and histidine ligands were further simplified to methyl thiolate and imidazole, respectively. H2O2 was chosen as an oxidizing agent due to its biological role as a metabolic product and species involved in signaling processes. The mechanism of oxidation of a coordinated cysteinate to sulfenate-κS and the trends for the different substrates were rationalized through activation strain analysis and energy decomposition analysis in the framework of scalar relativistic Density Functional Theory (DFT) calculations at ZORA-M06/TZ2P ae // ZORA-BLYP-D3(BJ)/TZ2P. CCCC is oxidized most easily, an outcome explained considering both electrostatic and orbital interactions. The isomerization to sulfenate-κO was attempted to assess whether this step may affect the ligand dissociation; however, it was found to introduce a kinetic barrier without improving the energetics of the dissociation. Lastly, ligand exchange with free thiolates and selenolates was investigated as a trigger for ligand dissociation, possibly leading to metal ejection; molecular docking simulations also support this hypothesis.
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Affiliation(s)
- Davide Zeppilli
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Andrea Madabeni
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Pablo A Nogara
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Av. Leonel de Moura Brizola, 2501, 96418-400, Bagé, RS, Brasil
| | - João B T Rocha
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
| | - Laura Orian
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
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Ye J, Bazzi S, Fritz T, Tittmann K, Mata RA, Uranga J. Mechanisms of Cysteine-Lysine Covalent Linkage-The Role of Reactive Oxygen Species and Competition with Disulfide Bonds. Angew Chem Int Ed Engl 2023; 62:e202304163. [PMID: 37294559 DOI: 10.1002/anie.202304163] [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: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Recently, a new naturally occurring covalent linkage was characterised, involving a cysteine and a lysine, bridged through an oxygen atom. The latter was dubbed as the NOS bond, reflecting the individual atoms involved in this uncommon bond which finds little parallel in lab chemistry. It is found to form under oxidising conditions and is reversible upon addition of reducing agents. Further studies have identified the bond in crystal structures across a variety of systems and organisms, potentially playing an important role in regulation, cellular defense and replication. Not only that, double NOS bonds have been identified and even found to be competitive in relation to the formation of disulfide bonds. This raises several questions about how this exotic bond comes to be, what are the intermediates involved in its formation and how it competes with other pathways of sulfide oxidation. With this objective in mind, we revisited our first proposed mechanism for the reaction with model electronic structure calculations, adding information about the reactivity with alternative reactive oxygen species and other potential competing products of oxidation. We present a network with more than 30 reactions which provides one of the most encompassing pictures for cysteine oxidation pathways to date.
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Affiliation(s)
- Jin Ye
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Tobias Fritz
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ricardo A Mata
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Jon Uranga
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
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3
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Corteselli EM, Sharafi M, Hondal R, MacPherson M, White S, Lam YW, Gold C, Manuel AM, van der Vliet A, Schneebeli ST, Anathy V, Li J, Janssen-Heininger YMW. Structural and functional fine mapping of cysteines in mammalian glutaredoxin reveal their differential oxidation susceptibility. Nat Commun 2023; 14:4550. [PMID: 37507364 PMCID: PMC10382592 DOI: 10.1038/s41467-023-39664-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Protein-S-glutathionylation is a post-translational modification involving the conjugation of glutathione to protein thiols, which can modulate the activity and structure of key cellular proteins. Glutaredoxins (GLRX) are oxidoreductases that regulate this process by performing deglutathionylation. However, GLRX has five cysteines that are potentially vulnerable to oxidative modification, which is associated with GLRX aggregation and loss of activity. To date, GLRX cysteines that are oxidatively modified and their relative susceptibilities remain unknown. We utilized molecular modeling approaches, activity assays using recombinant GLRX, coupled with site-directed mutagenesis of each cysteine both individually and in combination to address the oxidizibility of GLRX cysteines. These approaches reveal that C8 and C83 are targets for S-glutathionylation and oxidation by hydrogen peroxide in vitro. In silico modeling and experimental validation confirm a prominent role of C8 for dimer formation and aggregation. Lastly, combinatorial mutation of C8, C26, and C83 results in increased activity of GLRX and resistance to oxidative inactivation and aggregation. Results from these integrated computational and experimental studies provide insights into the relative oxidizability of GLRX's cysteines and have implications for the use of GLRX as a therapeutic in settings of dysregulated protein glutathionylation.
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Affiliation(s)
- Elizabeth M Corteselli
- Department of Pathology and Laboratory of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Mona Sharafi
- Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Robert Hondal
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Maximilian MacPherson
- Department of Pathology and Laboratory of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Sheryl White
- Neuroscience Cellular and Molecular Core, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Ying-Wai Lam
- Vermont Biomedical Research Network Proteomics Facility, University of Vermont, Burlington, VT, 05405, USA
| | - Clarissa Gold
- Vermont Biomedical Research Network Proteomics Facility, University of Vermont, Burlington, VT, 05405, USA
| | - Allison M Manuel
- Department of Pathology and Laboratory of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Albert van der Vliet
- Department of Pathology and Laboratory of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Severin T Schneebeli
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vikas Anathy
- Department of Pathology and Laboratory of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Yvonne M W Janssen-Heininger
- Department of Pathology and Laboratory of Medicine, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA.
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Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge. Antioxidants (Basel) 2022; 11:antiox11050885. [PMID: 35624747 PMCID: PMC9137623 DOI: 10.3390/antiox11050885] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 11/17/2022] Open
Abstract
Thiyl radicals are exceptionally interesting reactive sulfur species (RSS), but rather rarely considered in a biological or medical context. We here review the reactivity of protein thiyl radicals in aqueous and lipid phases and provide an overview of their most relevant reaction partners in biological systems. We deduce that polyunsaturated fatty acids (PUFAs) are their preferred reaction substrates in lipid phases, whereas protein side chains arguably prevail in aqueous phases. In both cellular compartments, a single, dominating thiyl radical-specific antioxidant does not seem to exist. This conclusion is rationalized by the high reaction rate constants of thiyl radicals with several highly concentrated substrates in the cell, precluding effective interception by antioxidants, especially in lipid bilayers. The intractable reactivity of thiyl radicals may account for a series of long-standing, but still startling biochemical observations surrounding the amino acid cysteine: (i) its global underrepresentation on protein surfaces, (ii) its selective avoidance in aerobic lipid bilayers, especially the inner mitochondrial membrane, (iii) the inverse correlation between cysteine usage and longevity in animals, (iv) the mitochondrial synthesis and translational incorporation of cysteine persulfide, and potentially (v) the ex post introduction of selenocysteine into the genetic code.
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He Q, Qu M, Xu C, Shi W, Hussain M, Jin G, Zhu H, Zeng LH, Wu X. The emerging roles of nitric oxide in ferroptosis and pyroptosis of tumor cells. Life Sci 2021; 290:120257. [PMID: 34952041 DOI: 10.1016/j.lfs.2021.120257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
Abstract
Tumor cells can develop resistance to cell death which is divided into necrosis and programmed cell death (PCD). PCD, including apoptosis, autophagy, ferroptosis, pyroptosis, and necroptosis. Ferroptosis and pyroptosis, two new forms of cell death, have gradually been of interest to researchers. Boosting ferroptosis and pyroptosis of tumor cells could be a potential cancer therapy. Nitric oxide (NO) is a ubiquitous, lipophilic, highly diffusible, free-radical signaling molecule that plays various roles in tumorigenesis. In addition, NO also has regulatory mechanisms through S-nitrosylation that do not depend on the classic NO/sGC/cGMP signaling. The current tumor treatment strategy for NO is to promote cell death through promoting S-nitrosylation-induced apoptosis while multiple drawbacks dampen this tumor therapy. However, numerous studies have suggested that suppression of NO is perceived to active ferroptosis and pyroptosis, which could be a better anti-tumor treatment. In this review, ferroptosis and pyroptosis are described in detail. We summarize that NO influences ferroptosis and pyroptosis and infer that S-nitrosylation mediates ferroptosis- and pyroptosis-related signaling pathways. It could be a potential cancer therapy different from NO-induced apoptosis of tumor cells. Finally, the information shows the drugs that manipulate endogenous production and exogenous delivery of NO to modulate the levels of S-nitrosylation.
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Affiliation(s)
- Qiangqiang He
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China
| | - Meiyu Qu
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China
| | - Chengyun Xu
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wei Shi
- Department of Biology and Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Musaddique Hussain
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guojian Jin
- Department of Internal Medicine, Shaoxing Central Hospital Anchang Branch, Shaoxing City 312080, China
| | - Haibin Zhu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
| | - Ling-Hui Zeng
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China.
| | - Ximei Wu
- Department of Pharmacology, Zhejiang University City College, Hangzhou 310015, China; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China.
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Catalano C, AL Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Curr Res Struct Biol 2021; 3:239-256. [PMID: 34693344 PMCID: PMC8517007 DOI: 10.1016/j.crstbi.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Atomic-resolution protein structural models are prerequisites for many downstream activities like structure-function studies or structure-based drug discovery. Unfortunately, this data is often unavailable for some of the most interesting and therapeutically important proteins. Thus, computational tools for building native-like structural models from less-than-ideal experimental data are needed. To this end, interaction homology exploits the character, strength and loci of the sets of interactions that define a structure. Each residue type has its own limited set of backbone angle-dependent interaction motifs, as defined by their environments. In this work, we characterize the interactions of serine, cysteine and S-bridged cysteine in terms of 3D hydropathic environment maps. As a result, we explore several intriguing questions. Are the environments different between the isosteric serine and cysteine residues? Do some environments promote the formation of cystine S-S bonds? With the increasing availability of structural data for water-insoluble membrane proteins, are there environmental differences for these residues between soluble and membrane proteins? The environments surrounding serine and cysteine residues are dramatically different: serine residues are about 50% solvent exposed, while cysteines are only 10% exposed; the latter are more involved in hydrophobic interactions although there are backbone angle-dependent differences. Our analysis suggests that one driving force for -S-S- bond formation is a rather substantial increase in burial and hydrophobic interactions in cystines. Serine and cysteine become less and more, respectively, solvent-exposed in membrane proteins. 3D hydropathic environment maps are an evolving structure analysis tool showing promise as elements in a new protein structure prediction paradigm.
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Affiliation(s)
- Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed H. AL Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
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7
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Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations. Antioxidants (Basel) 2021; 10:antiox10030499. [PMID: 33807006 PMCID: PMC8004825 DOI: 10.3390/antiox10030499] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications regulate the structure and function of proteins that can result in changes to the activity of different pathways. These include modifications altering the redox state of thiol groups on protein cysteine residues, which are sensitive to oxidative environments. While mass spectrometry has advanced the identification of protein thiol modifications and expanded our knowledge of redox-sensitive pathways, the quantitative aspect of this technique is critical for the field of redox proteomics. In this review, we describe how mass spectrometry-based redox proteomics has enabled researchers to accurately quantify the stoichiometry of reversible oxidative modifications on specific cysteine residues of proteins. We will describe advancements in the methodology that allow for the absolute quantitation of thiol modifications, as well as recent reports that have implemented this approach. We will also highlight the significance and application of such measurements and why they are informative for the field of redox biology.
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Euceda N, Jahnke J, Espinal A, Louis MF, Bashkin E, Roccanova P, Espaillat A, Fuentes GV, Nieto F, Gao R. Thioguanine restoration through type I photosensitization-superoxide oxidation-glutathione reduction cycles. Phys Chem Chem Phys 2021; 23:5069-5073. [PMID: 33655288 DOI: 10.1039/d1cp00101a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UVA-induced deleterious effect of thiopurine prodrugs including azathioprine, 6-mercaptopurine and 6-thioguanine (6-TG) increases the risk of cancer development due to the incorporation of 6-TG in patients' DNA. The catalytic mechanism by which thiobases act as a sustained oxidant producer has yet to be explored, especially through the Type I electron transfer pathway that produces superoxide radicals (O2˙-). Under Fenton-like conditions O2˙- radicals convert to extremely reactive hydroxyl radicals (˙OH), thus carrying even higher risk of biological damage than that induced by the well-studied type II reaction. By monitoring 6-TG/UVA-induced photochemistry in mass spectra and superoxide radicals (O2˙-) via nitro blue tetrazolium (NBT) reduction, this work provides two new findings: (1) in the presence of reduced glutathione (GSH), the production of O2˙-via the type I reaction is enhanced 10-fold. 6-TG thiyl radicals are identified as the primary intermediate formed in the reaction of 6-TG with O2˙-. The restoration of 6-TG and concurrent generation of O2˙- occur via a 3-step-cycle: 6-TG type I photosensitization, O2˙- oxidation and GSH reduction. (2) In the absence of GSH, 6-TG thiyl radicals undergo oxygen addition and sulfur dioxide removal to form carbon radicals (C6) which further convert to thioether by reacting with 6-TG molecules. These findings help explain not only thiol-regulation in a biological system but chemoprevention of cancer.
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Affiliation(s)
- Nelson Euceda
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Joyce Jahnke
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Aileen Espinal
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Monique F Louis
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Edan Bashkin
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Patricia Roccanova
- Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA
| | - Abraham Espaillat
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - German V Fuentes
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Fernando Nieto
- Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA
| | - Ruomei Gao
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
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Zhang X, Huang H, Li X, Wang J, Wei Y, Zhang H. Bioinspired chlorine-resistant tailoring for polyamide reverse osmosis membrane based on tandem oxidation of natural α-lipoic acid on the surface. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2020.118521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Hagras MA, Bellucci MA, Gobbo G, Marek RA, Trout BL. Computational Modeling of the Disulfide Cross-Linking Reaction. J Phys Chem B 2020; 124:9840-9851. [PMID: 33111518 DOI: 10.1021/acs.jpcb.0c07510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Disulfide cross-linking is one of the fundamental covalent bonds that exist prevalently in many biological molecules that is involved in versatile functional activities such as antibody stability, viral assembly, and protein folding. Additionally, it is a crucial factor in various industrial applications. Therefore, a fundamental understanding of its reaction mechanism would help gain insight into its different functional activities. Computational simulation of the disulfide cross-linking reaction with hydrogen peroxide (H2O2) was performed at the integrated quantum mechanical/molecular mechanical (QM/MM) level of theory in a water box under periodic boundary conditions. A benchmarking study for the barrier height of the disulfide formation step was performed on a model system between methanethiol and methane sulfenic acid to determine, for the QM system, the best-fit density functional theory (DFT) functional/basis set combination that produces comparable results to a higher-level theory of the coupled-cluster method. Computational results show that the disulfide cross-linking reaction with H2O2 reagent can proceed through a one-step or a two-step pathway for the high pKa cysteines or two different pathways for the low pKa cysteines to ultimately produce the sulfenic acid/sulfenate intermediate complex. Subsequently, those intermediates react with another neutral/anionic cysteine residue to form the cysteine product. In addition, the solvent-assisted proton-exchange/proton-transfer effects were examined on the energetic barriers for the different transition states, and the molecular contributions of the chemically involved water molecules were studied in detail.
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Affiliation(s)
- Muhammad A Hagras
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael A Bellucci
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,XtalPi Inc., 245 Main Street, 11th Floor, Cambridge Massachusetts 02142, United States
| | - Gianpaolo Gobbo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,XtalPi Inc., 245 Main Street, 11th Floor, Cambridge Massachusetts 02142, United States
| | - Ryan A Marek
- MMD, Merck & Co Inc., West Point, Pennsylvania 19486, United States
| | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Hu J, Tian J, Wang K, Deng J, Luo G. Reaction Pathway and Selectivity Control of Tetraethyl Thiuram Disulfide Synthesis with NaHCO 3 as a pH Regulator. ACS OMEGA 2020; 5:23736-23742. [PMID: 32984692 PMCID: PMC7513355 DOI: 10.1021/acsomega.0c02707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
The selectivity of a chemical reaction is related to the effective utilization of raw materials as well as the cleanliness and economy of the process. Herein, it has been first proposed to synthesize tetraethyl thiuram disulfide (TETD) with sodium bicarbonate as the pH regulator with a reaction selectivity of ∼100%. The existence of a reaction intermediate, a sodium salt of diethyl dithiocarbamoylsulfenic acid (NaEt2DTCS), has been proved by experiments and theoretical calculations. The results indicate that TETD can not only be generated from NaEt2DTCS oxidized by H2O2 directly, but also from the conjugation of NaEt2DTC and NaEt2DTCS generated in the first stage of oxidation meanwhile. Accordingly, an oxidation reaction pathway has been proposed. The reaction selectivity with NaHCO3 or CO2 as the pH regulator has been compared, and the selectivity control mechanism is discussed. At relatively higher pH values with NaHCO3 as the pH regulator, peroxidation could be almost avoided.
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12
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Dalla Tiezza M, Bickelhaupt FM, Flohé L, Maiorino M, Ursini F, Orian L. A dual attack on the peroxide bond. The common principle of peroxidatic cysteine or selenocysteine residues. Redox Biol 2020; 34:101540. [PMID: 32428845 PMCID: PMC7231847 DOI: 10.1016/j.redox.2020.101540] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 01/07/2023] Open
Abstract
The (seleno)cysteine residues in some protein families react with hydroperoxides with rate constants far beyond those of fully dissociated low molecular weight thiol or selenol compounds. In case of the glutathione peroxidases, we could demonstrate that high rate constants are achieved by a proton transfer from the chalcogenol to a residue of the active site [Orian et al. Free Radic. Biol. Med. 87 (2015)]. We extended this study to three more protein families (OxyR, GAPDH and Prx). According to DFT calculations, a proton transfer from the active site chalcogenol to a residue within the active site is a prerequisite for both, creating a chalcogenolate that attacks one oxygen of the hydroperoxide substrate and combining the delocalized proton with the remaining OH or OR, respectively, to create an ideal leaving group. The “parking postions” of the delocalized proton differ between the protein families. It is the ring nitrogen of tryptophan in GPx, a histidine in GAPDH and OxyR and a threonine in Prx. The basic principle, however, is common to all four families of proteins. We, thus, conclude that the principle outlined in this investigation offers a convincing explanation for how a cysteine residue can become peroxidatic. In some protein families, (seleno)cysteine residues react with hydroperoxides with very high rate constants. In GPx, DFT models of the oxidation of the catalytic site support a two-step mechanism for the H2O2 reduction. This mechanism is here found to operate in other thiol-based enzymes, i.e. OxyR, GAPDH and Prx.
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Affiliation(s)
- M Dalla Tiezza
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - F M Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, the Netherlands; Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - L Flohé
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, V.le G. Colombo 3, 35121, Padova, Italy; Departamento de Bioquímica, Universidad de la República, Avda. General Flores 2125, 11800, Montevideo, Uruguay
| | - M Maiorino
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, V.le G. Colombo 3, 35121, Padova, Italy
| | - F Ursini
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, V.le G. Colombo 3, 35121, Padova, Italy
| | - L Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy.
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13
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Hendinejad N, Timerghazin QK. Biological control of S-nitrosothiol reactivity: potential role of sigma-hole interactions. Phys Chem Chem Phys 2020; 22:6595-6605. [PMID: 32159182 DOI: 10.1039/c9cp06377c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
S-Nitrosothiols (RSNOs) are ubiquitous biomolecules whose chemistry is tightly controlled in vivo, although the specific molecular mechanisms behind this biological control remain unknown. In this work, we demonstrate, using high-level ab initio and DFT calculations, the ability of RSNOs to participate in intermolecular interactions with electron pair donors/Lewis bases (LBs) via a σ-hole, a region of positive electrostatic potential on the molecular surface at the extension of the N-S bond. Importantly, σ-hole binding is able to modulate the properties of RSNOs by changing the balance between two chemically opposite (antagonistic) resonance components, R-S+[double bond, length as m-dash]N-O- (D) and R-S-/NO+ (I), which are, in addition to the main resonance structure R-S-N[double bond, length as m-dash]O, necessary to describe the unusual electronic structure of RSNOs. σ-Hole binding at the sulfur atom of RSNO promotes the resonance structure D and reduces the resonance structure I, thereby stabilizing the weak N-S bond and making the sulfur atom more electrophilic. On the other hand, increasing the D-character of RSNO by other means (e.g. via N- or O-coordination of a Lewis acid) in turn enhances the σ-hole bonding. Our calculations suggest that in the protein environment a combination of σ-hole bonding of a negatively charged amino acid sidechain at the sulfur atom and N- or O-coordination of a positively charged amino acid sidechain is expected to have a profound effect on the RSNO electronic structure and reactivity.
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Affiliation(s)
- Niloufar Hendinejad
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, Wisconsin 53201-1881, USA.
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14
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Olivieri FA, Burastero O, Drusin SI, Defelipe LA, Wetzler DE, Turjanski A, Marti M. Conformational and Reaction Dynamic Coupling in Histidine Kinases: Insights from Hybrid QM/MM Simulations. J Chem Inf Model 2020; 60:833-842. [PMID: 31923359 DOI: 10.1021/acs.jcim.9b00806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histidine kinases (HK) of bacterial two-component systems represent a hallmark of allosterism in proteins, being able to detect a signal through the sensor domain and transmit this information through the protein matrix to the kinase domain which, once active, autophosphorylates a specific histidine residue. Inactive-to-active transition results in a large conformational change that moves the kinase on top of the histidine. In the present work, we use several molecular simulation techniques (Molecular Dynamics, Hybrid QM/MM, and constant pH molecular dynamics) to study the activation and autophosphorylation reactions in L. plantarum WalK, a cis-acting HK. In agreement with previous results, we show that the chemical step requires tight coupling with the conformational step in order to maintain the histidine phosphoacceptor in the correct tautomeric state, with a reactive δ-nitrogen. During the conformational transition, the kinase domain is never released and walks along the HK helix axis, breaking and forming several conserved residue-based contacts. The phosphate transfer reaction is concerted in the transition state region and is catalyzed through the stabilization of the negative developing charge of transferring phosphate along the reaction.
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Affiliation(s)
- Federico A Olivieri
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Osvaldo Burastero
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Salvador I Drusin
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Área Fı́sica, Departamento de Quı́mico-Fı́sica, Facultad de Ciencias Bioquı́micas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , S2002LRK Rosario , Santa Fe , Argentina
| | - Lucas A Defelipe
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,European Molecular Biology Laboratory Hamburg , Notkestrasse 85 , D-22607 Hamburg , Germany
| | - Diana E Wetzler
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Adrián Turjanski
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
| | - Marcelo Marti
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina.,Instituto de Quı́mica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Ciudad Universitaria , Intendente Guiraldes 2160 , C1428EGA Ciudad Autónoma de Buenos Aires , Argentina
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15
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Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
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Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
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16
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Mapes NJ, Rodriguez C, Chowriappa P, Dua S. Residue Adjacency Matrix Based Feature Engineering for Predicting Cysteine Reactivity in Proteins. Comput Struct Biotechnol J 2018; 17:90-100. [PMID: 30671196 PMCID: PMC6327741 DOI: 10.1016/j.csbj.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 01/31/2023] Open
Abstract
Free radicals that form from reactive species of nitrogen and oxygen can react dangerously with cellular components and are involved with the pathogenesis of diabetes, cancer, Parkinson's, and heart disease. Cysteine amino acids, due to their reactive nature, are prone to oxidation by these free radicals. Determining which cysteines oxidize within proteins is crucial to our understanding of these chronic diseases. Wet lab techniques, like differential alkylation, to determine which cysteines oxidize are often expensive and time-consuming. We utilize machine learning as a fast and inexpensive approach to identifying cysteines with oxidative capabilities. We created the original features RAMmod and RAMseq for use in classification. We also incorporated well-known features such as PROPKA, SASA, PSS, and PSSM. Our algorithm requires only the protein sequence to operate; however, we do use template matching by MODELLER to acquire 3D coordinates for additional feature extraction. There was a mean improvement of RAM over N6C by 22.04% MCC. It was statistically significant with a p-value of 0.015. RAM provided a significant increase over PSSM with a p-value of 0.040 and an average 70.09% improvement MCC.
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Affiliation(s)
| | | | - Pradeep Chowriappa
- Program of Computer Science, College of Engineering and Science, Louisiana Tech University, 305 Wisteria St., Ruston, LA 71272, United States
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17
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Olivito F, Costanzo P, Di Gioia ML, Nardi M, M O, Procopio A. Efficient synthesis of organic thioacetates in water. Org Biomol Chem 2018; 16:7753-7759. [PMID: 30299446 DOI: 10.1039/c8ob01896k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Thioacetates as precursors of thiols are interesting starting points for synthesizing other organosulfur compounds. Herein, we propose a simple, efficient and fast method to obtain organic thioacetates using water as a solvent. Taking into account the great attention that has been paid toward environmentally friendly synthetic procedures in the past decades, we prove the role and the strength of the thioacetate anion as a nucleophile for nucleophilic displacement reactions in an aqueous medium. The reactions were carried out under pH control, to prevent the decomposition of the mesylate starting materials, using potassium carbonate as a safe and mild base. A simple work up allows products to be obtained with excellent yield and acceptable purity.
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Affiliation(s)
- F Olivito
- Dipartimento di Scienze della Salute, Università Magna Græcia, Viale Europa, Germaneto, CZ, Italy. and Dipartimento di Chimica, Università della Calabria, Cubo 12C, Arcavacata di Rende, CS, Italy
| | - P Costanzo
- Dipartimento di Scienze della Salute, Università Magna Græcia, Viale Europa, Germaneto, CZ, Italy.
| | - M L Di Gioia
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Edificio Polifunzionale, Università della Calabria, 87030 Arcavacata di Rende, Cosenza, Italy
| | - M Nardi
- Dipartimento di Chimica, Università della Calabria, Cubo 12C, Arcavacata di Rende, CS, Italy and Dipartimento di Agraria, Università Telematica San Raffaele, Roma, Via di Val Cannuta, 247, 00166, Italy
| | - Oliverio M
- Dipartimento di Scienze della Salute, Università Magna Græcia, Viale Europa, Germaneto, CZ, Italy.
| | - A Procopio
- Dipartimento di Scienze della Salute, Università Magna Græcia, Viale Europa, Germaneto, CZ, Italy.
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18
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Engineering oxidative stability in human hemoglobin based on the Hb providence (βK82D) mutation and genetic cross-linking. Biochem J 2017; 474:4171-4192. [PMID: 29070524 DOI: 10.1042/bcj20170491] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/04/2017] [Accepted: 10/23/2017] [Indexed: 12/24/2022]
Abstract
Previous work suggested that hemoglobin (Hb) tetramer formation slows autoxidation and hemin loss and that the naturally occurring mutant, Hb Providence (HbProv; βK82D), is much more resistant to degradation by H2O2 We have examined systematically the effects of genetic cross-linking of Hb tetramers with and without the HbProv mutation on autoxidation, hemin loss, and reactions with H2O2, using native HbA and various wild-type recombinant Hbs as controls. Genetically cross-linked Hb Presbyterian (βN108K) was also examined as an example of a low oxygen affinity tetramer. Our conclusions are: (a) at low concentrations, all the cross-linked tetramers show smaller rates of autoxidation and hemin loss than HbA, which can dissociate into much less stable dimers and (b) the HbProv βK82D mutation confers more resistance to degradation by H2O2, by markedly inhibiting oxidation of the β93 cysteine side chain, particularly in cross-linked tetramers and even in the presence of the destabilizing Hb Presbyterian mutation. These results show that cross-linking and the βK82D mutation do enhance the resistance of Hb to oxidative degradation, a critical element in the design of a safe and effective oxygen therapeutic.
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19
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Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
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20
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Lauwers K, Breynaert E, Rombouts I, Delcour JA, Kirschhock CEA. Water electrolyte promoted oxidation of functional thiol groups. Food Chem 2016; 197 Pt B:1235-9. [PMID: 26675862 DOI: 10.1016/j.foodchem.2015.11.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
The formation of disulfide bonds is of the utmost importance for a wide range of food products with gluten or globular proteins as functional agents. Here, the impact of mineral electrolyte composition of aqueous solutions on thiol oxidation kinetics was studied, using glutathione (GSH) and cysteine (CYS) as model systems. Interestingly, the oxidation rate of both compounds into their corresponding disulfides was significantly higher in common tap water than in ultrapure water. The systematic study of different electrolyte components showed that especially CaCl2 improved the oxidation rate of GSH. However, this effect was not observed for CYS, which indicated a strong impact of the local chemical environment on thiol oxidation kinetics.
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Affiliation(s)
- K Lauwers
- KULeuven, Center for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, Celestijnenlaan 200f, B-3001 Leuven, Belgium
| | - E Breynaert
- KULeuven, Center for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, Celestijnenlaan 200f, B-3001 Leuven, Belgium.
| | - I Rombouts
- KULeuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - J A Delcour
- KULeuven, Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - C E A Kirschhock
- KULeuven, Center for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, Celestijnenlaan 200f, B-3001 Leuven, Belgium
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21
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Butler M, Michael Siu KW, Hopkinson AC. Transnitrosylation products of the dipeptide cysteinyl-cysteine: an examination by tandem mass spectrometry and density functional theory. Phys Chem Chem Phys 2016; 18:6047-52. [PMID: 26841083 DOI: 10.1039/c5cp08014b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation pathways of protonated mono- and di-nitrosylated derivatives from the dipeptide Cys-Cys obtained by electrospray were examined. Protonated mononitrosylated dipeptide upon loss of ˙NO formed a radical cation, which in turn shows two fragment ions, one from the loss of HS˙ and the other from a neutral loss giving a radical cation of formula C2H5NS˙(+). Protonated dinitrosylated dipeptide dissociated by losing both ˙NO molecules, forming a cyclic structure with a vicinal disulfide bridge whose major dissociation channel was the loss of CO. After CO loss, two pathways were observed (loss of NH3 and C2H3NS) which were preceded by proton exchange occurring between one β-carbon and the nitrogen atom. DFT calculations did not show significant differences in the energies involved for the loss of the NO radical from either of the cysteine residues of the protonated di-nitrosylated dipeptide. Upon loss of the first NO radical, the thiyl radical afforded the vicinal disulfide product with a small barrier through radical substitution of the remaining NO moiety. The calculated relative energy barriers for the different channels are in good agreement with experimental observations. Structures of the ions obtained after dissociation are suggested on the basis of the proposed mechanisms.
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Affiliation(s)
- Matias Butler
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3.
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3. and Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, Canada N9B 3P4
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3.
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22
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23
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Trujillo M, Alvarez B, Radi R. One- and two-electron oxidation of thiols: mechanisms, kinetics and biological fates. Free Radic Res 2015; 50:150-71. [PMID: 26329537 DOI: 10.3109/10715762.2015.1089988] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The oxidation of biothiols participates not only in the defense against oxidative damage but also in enzymatic catalytic mechanisms and signal transduction processes. Thiols are versatile reductants that react with oxidizing species by one- and two-electron mechanisms, leading to thiyl radicals and sulfenic acids, respectively. These intermediates, depending on the conditions, participate in further reactions that converge on different stable products. Through this review, we will describe the biologically relevant species that are able to perform these oxidations and we will analyze the mechanisms and kinetics of the one- and two-electron reactions. The processes undergone by typical low-molecular-weight thiols as well as the particularities of specific thiol proteins will be described, including the molecular determinants proposed to account for the extraordinary reactivities of peroxidatic thiols. Finally, the main fates of the thiyl radical and sulfenic acid intermediates will be summarized.
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Affiliation(s)
- Madia Trujillo
- a Departamento de Bioquímica , Facultad de Medicina, Universidad de la República , Montevideo , Uruguay .,b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and
| | - Beatriz Alvarez
- b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and.,c Laboratorio de Enzimología, Facultad de Ciencias , Universidad de la República , Montevideo , Uruguay
| | - Rafael Radi
- a Departamento de Bioquímica , Facultad de Medicina, Universidad de la República , Montevideo , Uruguay .,b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and
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24
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Khavani M, Izadyar M, Reza Housaindokht M. Quantum chemistry study on the mechanism of oxidation of cysteine to cystine using hydrogen peroxide. PHOSPHORUS SULFUR 2015. [DOI: 10.1080/10426507.2015.1019069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Mohammad Khavani
- Faculty of Sciences, Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Izadyar
- Faculty of Sciences, Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran
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25
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Dokainish HM, Gauld JW. Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B). ACS Catal 2015. [DOI: 10.1021/cs501707h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hisham M. Dokainish
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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26
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Flister M, Timerghazin QK. Structure, Stability, and Substituent Effects in Aromatic S-Nitrosothiols: The Crucial Effect of a Cascading Negative Hyperconjugation/Conjugation Interaction. J Phys Chem A 2014; 118:9914-24. [DOI: 10.1021/jp5079136] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Matthew Flister
- Department of Chemistry, Marquette University, P.O. Box
1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Qadir K. Timerghazin
- Department of Chemistry, Marquette University, P.O. Box
1881, Milwaukee, Wisconsin 53201-1881, United States
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