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Mu B, Zeng Y, Luo L, Wang K. Oxidative stress-mediated protein sulfenylation in human diseases: Past, present, and future. Redox Biol 2024; 76:103332. [PMID: 39217848 DOI: 10.1016/j.redox.2024.103332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024] Open
Abstract
Reactive Oxygen Species (ROS) refer to a variety of derivatives of molecular oxygen that play crucial roles in regulating a wide range of physiological and pathological processes. Excessive ROS levels can cause oxidative stress, leading to cellular damage and even cell demise. However, moderately elevated levels of ROS can mediate the oxidative post-translational modifications (oxPTMs) of redox-sensitive proteins, thereby affecting protein functions and regulating various cellular signaling pathways. Among the oxPTMs, ROS-induced reversible protein sulfenylation represents the initial form of cysteine oxidation for sensing redox signaling. In this review, we will summarize the discovery, chemical formation, and detection approaches of protein sulfenylation. In addition, we will highlight recent findings for the roles of protein sulfenylation in various diseases, including thrombotic disorders, diabetes, cardiovascular diseases, neurodegenerative diseases, and cancer.
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Affiliation(s)
- Baoquan Mu
- West China School of Basic Medical Sciences & Forensic Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Zeng
- West China School of Basic Medical Sciences & Forensic Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Luo
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, China.
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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2
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Cannon AE, Horn PJ. The Molecular Frequency, Conservation and Role of Reactive Cysteines in Plant Lipid Metabolism. PLANT & CELL PHYSIOLOGY 2024; 65:826-844. [PMID: 38113384 DOI: 10.1093/pcp/pcad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/21/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Cysteines (Cys) are chemically reactive amino acids containing sulfur that play diverse roles in plant biology. Recent proteomics investigations in Arabidopsis thaliana have revealed the presence of thiol post-translational modifications (PTMs) in several Cys residues. These PTMs are presumed to impact protein structure and function, yet mechanistic data regarding the specific Cys susceptible to modification and their biochemical relevance remain limited. To help address these limitations, we have conducted a wide-ranging analysis by integrating published datasets encompassing PTM proteomics (comparing S-sulfenylation, persulfidation, S-nitrosylation and S-acylation), genomics and protein structures, with a specific focus on proteins involved in plant lipid metabolism. The prevalence and distribution of modified Cys residues across all analyzed proteins is diverse and multifaceted. Nevertheless, by combining an evaluation of sequence conservation across 100+ plant genomes with AlphaFold-generated protein structures and physicochemical predictions, we have unveiled structural propensities associated with Cys modifications. Furthermore, we have identified discernible patterns in lipid biochemical pathways enriched with Cys PTMs, notably involving beta-oxidation, jasmonic acid biosynthesis, fatty acid biosynthesis and wax biosynthesis. These collective findings provide valuable insights for future investigations targeting the mechanistic foundations of Cys modifications and the regulation of modified proteins in lipid metabolism and other metabolic pathways.
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Affiliation(s)
- Ashley E Cannon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
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3
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Yang M, Silverstein RL. Targeting Cysteine Oxidation in Thrombotic Disorders. Antioxidants (Basel) 2024; 13:83. [PMID: 38247507 PMCID: PMC10812781 DOI: 10.3390/antiox13010083] [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: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Oxidative stress increases the risk for clinically significant thrombotic events, yet the mechanisms by which oxidants become prothrombotic are unclear. In this review, we provide an overview of cysteine reactivity and oxidation. We then highlight recent findings on cysteine oxidation events in oxidative stress-related thrombosis. Special emphasis is on the signaling pathway induced by a platelet membrane protein, CD36, in dyslipidemia, and by protein disulfide isomerase (PDI), a member of the thiol oxidoreductase family of proteins. Antioxidative and chemical biology approaches to target cysteine are discussed. Lastly, the knowledge gaps in the field are highlighted as they relate to understanding how oxidative cysteine modification might be targeted to limit thrombosis.
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Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Harvard Medical School, 3 Blackfan Circle, CLS-924, Boston, MA 02115, USA
| | - Roy L. Silverstein
- Department of Medicine, Medical College of Wisconsin, Hub 8745, 8701 W Watertown Plank Rd., Milwaukee, WI 53226, USA
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
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4
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Vaissier Welborn V. Understanding Cysteine Reactivity in Protein Environments with Electric Fields. J Phys Chem B 2023; 127:9936-9942. [PMID: 37962274 DOI: 10.1021/acs.jpcb.3c05749] [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: 11/15/2023]
Abstract
The role cysteine residues play in proteins is mediated by their protonation state, whereby the thiolate form of the side chain is highly reactive while the thiol form is more inert. However, the pKa of cysteine residues is hard to predict as it can differ widely from its reference value in solution, an effect that is accentuated by local effects in the heterogeneous protein environment. Here, we present a new approach to the prediction of cysteine reactivity based on electric field calculations at the thiol/thiolate group. We validated our approach by predicting the protonation state of cysteine residues in different protein environments (in the active site, at the protein surface, and buried within the protein interior), including Cys-25 in papaya protease omega, which was proven problematic for the more traditional constant pH molecular dynamics (MD) technique. We predict pKa shifts consistent with experimental observations, and the decomposition of the electric fields into contributions from molecular fragments provides a direct handle to rationalize local pH and pKa effects in proteins without introducing parameters other than those of the force field used for MD simulations.
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Affiliation(s)
- Valerie Vaissier Welborn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
- Macromolecules Innovation Institute (MII),Virginia Tech, Blacksburg, Virginia 24060, United States
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5
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Si M, Hu M, Yang M, Peng Z, Li D, Zhao Y. Characterization of oxidative stress-induced cgahp, a gene coding for alkyl hydroperoxide reductase, from industrial importance Corynebacterium glutamicum. Biotechnol Lett 2023; 45:1309-1326. [PMID: 37606753 PMCID: PMC10460364 DOI: 10.1007/s10529-023-03421-8] [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: 04/20/2023] [Accepted: 07/29/2023] [Indexed: 08/23/2023]
Abstract
Alkyl hydroperoxide reductase (Ahp), comprised of four different subunits AhpC, AhpD, AhpE, and AhpF, is a thiol-based antioxidative enzyme with the ability to protect bacteria against oxidative stress. Functionally, AhpC and AhpE considered as peroxidases directly detoxify peroxides, while AhpD and AhpF as oxidoreductases restore oxidized peroxidases to their reduced form. Corynebacterium glutamicum ncgl0877 encodes a putative Ahp with a unique Cys-Pro-Phe-Cys (C-P-G-C) active-site motif, similar with those of the thiol-disulfide oxidoreductases such as thioredoxin (Trx), mycoredoxin-1 (Mrx1) and AhpD. However, its physiological and biochemical functions remain unknown in C. glutamicum. Here, we report that NCgl0877, designated CgAhp, is involved in the protection against organic peroxide (OP) stress. The cgahp-deleted strain is notably more sensitive to OP stress. The cgahp expression is controlled by a MarR-type transcriptional repressor OasR (organic peroxide- and antibiotic-sensing regulator). The physiological role of CgAhp in resistance to OP stresses is corroborated by its induced expression under stresses. Although CgAhp has a weak peroxidase activity toward OP, it mainly supports the OP-scavenging activity of the thiol-dependent peroxidase preferentially linked to the dihydrolipoamide dehydrogenase (Lpd)/dihydrolipoamide succinyltransferase (SucB)/NADH system. The C-P-G-C motif of CgAhp is essential to maintain the reductase activity. In conclusion, our study identifies CgAhp, behaving like AhpD, as a key disulfide oxidoreductase involved in the oxidative stress tolerance and the functional electron donor for peroxidase.
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Affiliation(s)
- Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Mengdie Hu
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Mingfei Yang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Zhaoxin Peng
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Donghan Li
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Yuying Zhao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China.
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6
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Bodnar Y, Gellert M, Hossain FM, Lillig CH. Breakdown of Arabidopsis thaliana thioredoxins and glutaredoxins based on electrostatic similarity-Leads to common and unique interaction partners and functions. PLoS One 2023; 18:e0291272. [PMID: 37695767 PMCID: PMC10495010 DOI: 10.1371/journal.pone.0291272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
The reversible reduction and oxidation of protein thiols was first described as mechanism to control light/dark-dependent metabolic regulation in photosynthetic organisms. Today, it is recognized as an essential mechanism of regulation and signal transduction in all kingdoms of life. Proteins of the thioredoxin (Trx) family, Trxs and glutaredoxins (Grxs) in particular, catalyze thiol-disulfide exchange reactions and are vital players in the operation of thiol switches. Various Trx and Grx isoforms are present in all compartments of the cell. These proteins have a rather broad but at the same time distinct substrate specificity. Understanding the molecular basis of their target specificity is central to the understanding of physiological and pathological redox signaling. Electrostatic complementarity of the redoxins with their target proteins has been proposed as a major reason. Here, we analyzed the electrostatic similarity of all Arabidopsis thaliana Trxs, Grxs, and proteins containing such domains. Clustering of the redoxins based on this comparison suggests overlapping and also distant target specificities and thus functions of the different sub-classes including all Trx isoforms as well as the three classes of Grxs, i.e. CxxC-, CGFS-, and CC-type Grxs. Our analysis also provides a rationale for the tuned substrate specificities of both the ferredoxin- and NADPH-dependent Trx reductases.
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Affiliation(s)
- Yana Bodnar
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
- Institute for Physics, University of Greifswald, Greifswald, Germany
| | - Manuela Gellert
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Faruq Mohammed Hossain
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
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7
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Bodnar Y, Lillig CH. Cysteinyl and methionyl redox switches: Structural prerequisites and consequences. Redox Biol 2023; 65:102832. [PMID: 37536083 PMCID: PMC10412846 DOI: 10.1016/j.redox.2023.102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
Redox modifications of specific cysteinyl and methionyl residues regulate key enzymes and signal-transducing proteins in various pathways. Here, we analyzed the effect of redox modifications on protein structure screening the RCSB protein data bank for oxidative modifications of proteins, i.e. protein disulfides, mixed disulfides with glutathione, cysteinyl sulfenic acids, cysteinyl S-nitrosylation, and methionyl sulfoxide residues. When available, these structures were compared to the structures of the same proteins in the reduced state with respect to both pre-requirements for the oxidative modifications as well as the structural consequences of the modifications. In general, the conformational changes induced by the redox modification are small, i.e. within the range of normal fluctuations. Some redox modifications, disulfides in particular, induces alterations in the electrostatic properties of the proteins. Solvent accessibility does not seem to be a strict pre-requirement for the redox modification of a particular residue. We identified an enrichment of certain other amino acid residues in the vicinity of the susceptible residues, for disulfide and sulfenic acid modifications, for instance, histidyl and tyrosyl residues. These motifs, as well as the specific features of the susceptible sulfur-containing amino acids, may become helpful for the prediction of redox modifications.
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Affiliation(s)
- Yana Bodnar
- Institut for Physics, University of Greifswald, Germany; Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany.
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8
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Shilovsky GA, Dibrova DV. Regulation of Cell Proliferation and Nrf2-Mediated Antioxidant Defense: Conservation of Keap1 Cysteines and Nrf2 Binding Site in the Context of the Evolution of KLHL Family. Life (Basel) 2023; 13:life13041045. [PMID: 37109574 PMCID: PMC10146909 DOI: 10.3390/life13041045] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Keap1 (Kelch-like ECH-associated protein 1) is one of the major negative regulators of the transcription factor Nrf2 (nuclear factor erythroid-2-related factor 2), which induces the expression of numerous proteins defending the cell against different stress conditions. Keap1 is generally negatively regulated by post-translational modification (mostly via its cysteine residues) and interaction with other proteins that compete with Nrf2 for binding. Cysteine residues in Keap1 have different effects on protein regulation, as basic residues (Lys, Arg, and His) in close proximity to them increase cysteine modification potential. In this paper, we present an evolutionary analysis of residues involved in both mechanisms of Keap1 regulation in the broader context of the KLHL protein family in vertebrates. We identified the typical domain structure of the KLHL protein family in several proteins outside of this family (namely in KBTBD proteins 2, 3, 4, 6, 7, 8, 12 and 14). We found several cysteines that are flanked by basic residues (namely, C14, C38, C151, C226, C241, C273, C288, C297, C319, and C613) and, therefore, may be considered more susceptible to regulatory modification. The Nrf2 binding site is completely conserved in Keap1 in vertebrates but is absent or located in nonaligned DA and BC loops of the Kelch domain within the KLHL family. The development of specific substrate binding regions could be an evolutionary factor of diversification in the KLHL protein family.
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Affiliation(s)
- Gregory A Shilovsky
- Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Russian Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 127051 Moscow, Russia
| | - Daria V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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9
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Awoonor-Williams E, Golosov AA, Hornak V. Benchmarking In Silico Tools for Cysteine p Ka Prediction. J Chem Inf Model 2023; 63:2170-2180. [PMID: 36996330 DOI: 10.1021/acs.jcim.3c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Accurate estimation of the pKa's of cysteine residues in proteins could inform targeted approaches in hit discovery. The pKa of a targetable cysteine residue in a disease-related protein is an important physiochemical parameter in covalent drug discovery, as it influences the fraction of nucleophilic thiolate amenable to chemical protein modification. Traditional structure-based in silico tools are limited in their predictive accuracy of cysteine pKa's relative to other titratable residues. Additionally, there are limited comprehensive benchmark assessments for cysteine pKa predictive tools. This raises the need for extensive assessment and evaluation of methods for cysteine pKa prediction. Here, we report the performance of several computational pKa methods, including single-structure and ensemble-based approaches, on a diverse test set of experimental cysteine pKa's retrieved from the PKAD database. The dataset consisted of 16 wildtype and 10 mutant proteins with experimentally measured cysteine pKa values. Our results highlight that these methods are varied in their overall predictive accuracies. Among the test set of wildtype proteins evaluated, the best method (MOE) yielded a mean absolute error of 2.3 pK units, highlighting the need for improvement of existing pKa methods for accurate cysteine pKa estimation. Given the limited accuracy of these methods, further development is needed before these approaches can be routinely employed to drive design decisions in early drug discovery efforts.
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Affiliation(s)
- Ernest Awoonor-Williams
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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10
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Mueller NPF, Carloni P, Alfonso-Prieto M. Molecular determinants of acrylamide neurotoxicity through covalent docking. Front Pharmacol 2023; 14:1125871. [PMID: 36937867 PMCID: PMC10018202 DOI: 10.3389/fphar.2023.1125871] [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: 12/16/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Acrylamide (ACR) is formed during food processing by Maillard reaction between sugars and proteins at high temperatures. It is also used in many industries, from water waste treatment to manufacture of paper, fabrics, dyes and cosmetics. Unfortunately, cumulative exposure to acrylamide, either from diet or at the workplace, may result in neurotoxicity. Such adverse effects arise from covalent adducts formed between acrylamide and cysteine residues of several neuronal proteins via a Michael addition reaction. The molecular determinants of acrylamide reactivity and its impact on protein function are not completely understood. Here we have compiled a list of acrylamide protein targets reported so far in the literature in connection with neurotoxicity and performed a systematic covalent docking study. Our results indicate that acrylamide binding to cysteine is favored in the presence of nearby positively charged amino acids, such as lysines and arginines. For proteins with more than one reactive Cys, docking scores were able to discriminate between the primary ACR modification site and secondary sites modified only at high ACR concentrations. Therefore, docking scores emerge as a potential filter to predict Cys reactivity against acrylamide. Inspection of the ACR-protein complex structures provides insights into the putative functional consequences of ACR modification, especially for non-enzyme proteins. Based on our study, covalent docking is a promising computational tool to predict other potential protein targets mediating acrylamide neurotoxicity.
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Affiliation(s)
- Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Department of Physics, RWTH Aachen University, Aachen, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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11
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Pedron FN, Messias A, Zeida A, Roitberg AE, Estrin DA. Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. J Chem Inf Model 2023; 63:595-604. [PMID: 36630702 DOI: 10.1021/acs.jcim.2c01104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cysteine is a common amino acid with a thiol group that plays a pivotal role in a variety of scenarios in redox biochemistry. In contrast, selenocysteine, the 21st amino acid, is only present in 25 human proteins. Classical force-field parameters for cysteine and selenocysteine are still scarce. In this context, we present a methodology to obtain Lennard-Jones parameters for cysteine and selenocysteine in different physiologically relevant oxidation and protonation states. The new force field parameters obtained in this work are available at https://github.com/MALBECC/AMBER-parameters-database. The parameters were adjusted to reproduce water radial distribution functions obtained by density functional theory ab initio molecular dynamics. We validated the results by evaluating the impact of the choice of parameters on the structure and dynamics in classical molecular dynamics simulations of representative proteins containing catalytic cysteine/selenocysteine residues. There are significant changes in protein structure and dynamics depending on the parameters choice, specifically affecting the residues close to the catalytic sites.
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Affiliation(s)
- Federico N Pedron
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Ari Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, 11800 Montevideo, Uruguay
| | - Adrián E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
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12
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Harris JA, Liu R, Martins de Oliveira V, Vázquez-Montelongo EA, Henderson JA, Shen J. GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber. J Chem Theory Comput 2022; 18:7510-7527. [PMID: 36377980 PMCID: PMC10130738 DOI: 10.1021/acs.jctc.2c00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Constant pH molecular dynamics (MD) simulations sample protonation states on the fly according to the conformational environment and user specified pH conditions; however, the current accuracy is limited due to the use of implicit-solvent models or a hybrid solvent scheme. Here, we report the first GPU-accelerated implementation, parametrization, and validation of the all-atom continuous constant pH MD (CpHMD) method with particle-mesh Ewald (PME) electrostatics in the Amber22 pmemd.cuda engine. The titration parameters for Asp, Glu, His, Cys, and Lys were derived for the CHARMM c22 and Amber ff14sb and ff19sb force fields. We then evaluated the PME-CpHMD method using the asynchronous pH replica-exchange titration simulations with the c22 force field for six benchmark proteins, including BBL, hen egg white lysozyme (HEWL), staphylococcal nuclease (SNase), thioredoxin, ribonuclease A (RNaseA), and human muscle creatine kinase (HMCK). The root-mean-square deviation from the experimental pKa's of Asp, Glu, His, and Cys is 0.76 pH units, and the Pearson's correlation coefficient for the pKa shifts with respect to model values is 0.80. We demonstrated that a finite-size correction or much enlarged simulation box size can remove a systematic error of the calculated pKa's and improve agreement with experiment. Importantly, the simulations captured the relevant biology in several challenging cases, e.g., the titration order of the catalytic dyad Glu35/Asp52 in HEWL and the coupled residues Asp19/Asp21 in SNase, the large pKa upshift of the deeply buried catalytic Asp26 in thioredoxin, and the large pKa downshift of the deeply buried catalytic Cys283 in HMCK. We anticipate that PME-CpHMD will offer proper pH control to improve the accuracies of MD simulations and enable mechanistic studies of proton-coupled dynamical processes that are ubiquitous in biology but remain poorly understood due to the lack of experimental tools and limitation of current MD simulations.
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Affiliation(s)
- Julie A Harris
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States
| | - Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States
| | - Vinicius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States.,Lilly Biotechnology Center, San Diego, California92121, United States
| | | | - Jack A Henderson
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States
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13
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Smith N, Wilson MA. Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography. CRYSTALS 2022; 12:1671. [PMID: 36685087 PMCID: PMC9850494 DOI: 10.3390/cryst12111671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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15
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Lee CG, Lee C, Lee J, Nam JS, Kim B, Kwon T. Dual‐Modulated Release of a Cytotoxic Photosensitizer Using Photogenerated Reactive Oxygen Species and Glutathione. Angew Chem Int Ed Engl 2022; 61:e202210623. [DOI: 10.1002/anie.202210623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Chae Gyu Lee
- Department of Chemistry Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
- Center for Wave Energy Materials Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
| | - Chaiheon Lee
- Department of Chemistry Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
- Center for Wave Energy Materials Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
| | - Joonhee Lee
- Department of Chemistry Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
- Department of Chemistry Yonsei University Seoul 03722 Republic of Korea
| | - Jung Seung Nam
- Department of Chemistry Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
- Center for Wave Energy Materials Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
- Institute for Cancer Genetics Department of Genetics and Development Columbia University Irving Medical Center New York NY 10032 USA
- Herbert Irving Comprehensive Cancer Center Columbia University Irving Medical Center New York NY 10032 USA
| | - Byeong‐Su Kim
- Department of Chemistry Yonsei University Seoul 03722 Republic of Korea
| | - Tae‐Hyuk Kwon
- Department of Chemistry Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
- Center for Wave Energy Materials Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Republic of Korea
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16
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Mazmanian K, Chen T, Sargsyan K, Lim C. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1607. [PMID: 35600063 PMCID: PMC9111396 DOI: 10.1002/wcms.1607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS-CoV-2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi-targeting strategy against SARS-CoV-2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+-sites in several SARS-CoV-2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+-bound, can be targeted using the same Zn-ejector drug (disulfiram/ebselen), which enables the use of broad-spectrum anti-virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn-ejector drug combined with other broad-spectrum anti-viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisStructure and Mechanism > Computational Biochemistry and BiophysicsElectronic Structure Theory > Density Functional Theory.
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Affiliation(s)
| | - Ting Chen
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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17
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Dos Santos AM, Oliveira ARS, da Costa CHS, Kenny PW, Montanari CA, Varela JDJG, Lameira J. Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces. J Chem Inf Model 2022; 62:4083-4094. [PMID: 36044342 DOI: 10.1021/acs.jcim.2c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials to investigate the reaction mechanism for covalent inhibition of cathepsin K and assess the reversibility of inhibition. The computed free energy profiles suggest that a nucleophilic attack by the catalytic cysteine on the inhibitor warhead and proton transfer from the catalytic histidine occur in a concerted manner. The results indicate that the reaction is more strongly exergonic for the alkyne-based inhibitors, which bind irreversibly to cathepsin K, than for the nitrile-based inhibitor odanacatib, which binds reversibly. Gas-phase energies were also calculated for the addition of methanethiol to structural prototypes for a number of warheads of interest in cysteine protease inhibitor design in order to assess electrophilicity. The approaches presented in this study are particularly applicable to assessment of novel warheads, and computed transition state geometries can be incorporated into molecular models for covalent docking.
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Affiliation(s)
- Alberto M Dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil.,Laboratório de Química Quântica Computacional, Universidade Federal do Maranhão, 65080 401 São Luis, MA, Brazil
| | - Amanda Ruslana Santana Oliveira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil
| | - Clauber H S da Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil
| | - Peter W Kenny
- Medicinal and Biological Chemistry Group, Institute of Chemistry of Sao Carlos, University of Sao Paulo, Avenue Trabalhador Sancarlense 400, 13566-590 São Carlos, SP, Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, Institute of Chemistry of Sao Carlos, University of Sao Paulo, Avenue Trabalhador Sancarlense 400, 13566-590 São Carlos, SP, Brazil
| | - Jaldyr de Jesus G Varela
- Laboratório de Química Quântica Computacional, Universidade Federal do Maranhão, 65080 401 São Luis, MA, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil
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18
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Lee CG, Lee C, Lee J, Nam JS, Kim BS, Kwon TH. Dual‐Modulated Release of a Cytotoxic Photosensitizer Using Photogenerated Reactive Oxygen Species and Glutathione. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chae Gyu Lee
- Ulsan National Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Chaiheon Lee
- Ulsan National Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Joonhee Lee
- Ulsan National Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Jung Seung Nam
- Ulsan National Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Byeong-Su Kim
- Yonsei University Department of Chemistry KOREA, REPUBLIC OF
| | - Tae-Hyuk Kwon
- Ulsan National Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
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19
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Corpas FJ, González-Gordo S, Rodríguez-Ruiz M, Muñoz-Vargas MA, Palma JM. Thiol-based Oxidative Posttranslational Modifications (OxiPTMs) of Plant Proteins. PLANT & CELL PHYSIOLOGY 2022; 63:889-900. [PMID: 35323963 PMCID: PMC9282725 DOI: 10.1093/pcp/pcac036] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/12/2022] [Accepted: 03/21/2022] [Indexed: 06/01/2023]
Abstract
The thiol group of cysteine (Cys) residues, often present in the active center of the protein, is of particular importance to protein function, which is significantly determined by the redox state of a protein's environment. Our knowledge of different thiol-based oxidative posttranslational modifications (oxiPTMs), which compete for specific protein thiol groups, has increased over the last 10 years. The principal oxiPTMs include S-sulfenylation, S-glutathionylation, S-nitrosation, persulfidation, S-cyanylation and S-acylation. The role of each oxiPTM depends on the redox cellular state, which in turn depends on cellular homeostasis under either optimal or stressful conditions. Under such conditions, the metabolism of molecules such as glutathione, NADPH (reduced nicotinamide adenine dinucleotide phosphate), nitric oxide, hydrogen sulfide and hydrogen peroxide can be altered, exacerbated and, consequently, outside the cell's control. This review provides a broad overview of these oxiPTMs under physiological and unfavorable conditions, which can regulate the function of target proteins.
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Affiliation(s)
- Francisco J Corpas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/ Professor Albareda, 1, Granada 18008, Spain
| | - Salvador González-Gordo
- Department of Biochemistry, Cell and Molecular Biology of Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/ Professor Albareda, 1, Granada 18008, Spain
| | - Marta Rodríguez-Ruiz
- Department of Biochemistry, Cell and Molecular Biology of Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/ Professor Albareda, 1, Granada 18008, Spain
| | - María A Muñoz-Vargas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/ Professor Albareda, 1, Granada 18008, Spain
| | - José M Palma
- Department of Biochemistry, Cell and Molecular Biology of Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/ Professor Albareda, 1, Granada 18008, Spain
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20
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Tossounian MA, Baczynska M, Dalton W, Newell C, Ma Y, Das S, Semelak JA, Estrin DA, Filonenko V, Trujillo M, Peak-Chew SY, Skehel M, Fraternali F, Orengo C, Gout I. Profiling the Site of Protein CoAlation and Coenzyme A Stabilization Interactions. Antioxidants (Basel) 2022; 11:antiox11071362. [PMID: 35883853 PMCID: PMC9312308 DOI: 10.3390/antiox11071362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 11/30/2022] Open
Abstract
Coenzyme A (CoA) is a key cellular metabolite known for its diverse functions in metabolism and regulation of gene expression. CoA was recently shown to play an important antioxidant role under various cellular stress conditions by forming a disulfide bond with proteins, termed CoAlation. Using anti-CoA antibodies and liquid chromatography tandem mass spectrometry (LC-MS/MS) methodologies, CoAlated proteins were identified from various organisms/tissues/cell-lines under stress conditions. In this study, we integrated currently known CoAlated proteins into mammalian and bacterial datasets (CoAlomes), resulting in a total of 2093 CoAlated proteins (2862 CoAlation sites). Functional classification of these proteins showed that CoAlation is widespread among proteins involved in cellular metabolism, stress response and protein synthesis. Using 35 published CoAlated protein structures, we studied the stabilization interactions of each CoA segment (adenosine diphosphate (ADP) moiety and pantetheine tail) within the microenvironment of the modified cysteines. Alternating polar-non-polar residues, positively charged residues and hydrophobic interactions mainly stabilize the pantetheine tail, phosphate groups and the ADP moiety, respectively. A flexible nature of CoA is observed in examined structures, allowing it to adapt its conformation through interactions with residues surrounding the CoAlation site. Based on these findings, we propose three modes of CoA binding to proteins. Overall, this study summarizes currently available knowledge on CoAlated proteins, their functional distribution and CoA-protein stabilization interactions.
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Affiliation(s)
- Maria-Armineh Tossounian
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Maria Baczynska
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - William Dalton
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Charlie Newell
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Yilin Ma
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Sayoni Das
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Jonathan Alexis Semelak
- Departmento de Química Inorgánica Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; (J.A.S.); (D.A.E.)
| | - Dario Ariel Estrin
- Departmento de Química Inorgánica Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; (J.A.S.); (D.A.E.)
| | - Valeriy Filonenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine;
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay;
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Sew Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London WC2R 2LS, UK;
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine;
- Correspondence:
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21
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West JD. Experimental Approaches for Investigating Disulfide-Based Redox Relays in Cells. Chem Res Toxicol 2022; 35:1676-1689. [PMID: 35771680 DOI: 10.1021/acs.chemrestox.2c00123] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible oxidation of cysteine residues within proteins occurs naturally during normal cellular homeostasis and can increase during oxidative stress. Cysteine oxidation often leads to the formation of disulfide bonds, which can impact protein folding, stability, and function. Work in both prokaryotic and eukaryotic models over the past five decades has revealed several multiprotein systems that use thiol-dependent oxidoreductases to mediate disulfide bond reduction, formation, and/or rearrangement. Here, I provide an overview of how these systems operate to carry out disulfide exchange reactions in different cellular compartments, with a focus on their roles in maintaining redox homeostasis, transducing redox signals, and facilitating protein folding. Additionally, I review thiol-independent and thiol-dependent approaches for interrogating what proteins partner together in such disulfide-based redox relays. While the thiol-independent approaches rely either on predictive measures or standard procedures for monitoring protein-protein interactions, the thiol-dependent approaches include direct disulfide trapping methods as well as thiol-dependent chemical cross-linking. These strategies may prove useful in the systematic characterization of known and newly discovered disulfide relay mechanisms and redox switches involved in oxidant defense, protein folding, and cell signaling.
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Affiliation(s)
- James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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22
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Tajima S, Nakata E, Sakaguchi R, Saimura M, Mori Y, Morii T. A two-step screening to optimize the signal response of an auto-fluorescent protein-based biosensor. RSC Adv 2022; 12:15407-15419. [PMID: 35693243 PMCID: PMC9121230 DOI: 10.1039/d2ra02226e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/15/2022] [Indexed: 11/21/2022] Open
Abstract
Auto-fluorescent protein (AFP)-based biosensors transduce the structural change in their embedded recognition modules induced by recognition/reaction events to fluorescence signal changes of AFP. The lack of detailed structural information on the recognition module often makes it difficult to optimize AFP-based biosensors. To enhance the signal response derived from detecting the putative structural change in the nitric oxide (NO)-sensing segment of transient receptor potential canonical 5 (TRPC5) fused to enhanced green fluorescent protein (EGFP), EGFP-TRPC5, a facile two-step screening strategy, in silico first and in vitro second, was applied to variants of EGFP-TRPC5 deletion-mutated within the recognition module. In in silico screening, the structural changes of the recognition modules were evaluated as root-mean-square-deviation (RMSD) values, and 10 candidates were efficiently selected from 47 derivatives. Through in vitro screening, four mutants were identified that showed a larger change in signal response than the parent EGFP-TRPC5. One mutant in particular, 551-575, showed four times larger change upon reaction with NO and H2O2. Furthermore, mutant 551-575 also showed a signal response upon reaction with H2O2 in mammalian HEK293 cells, indicating that the mutant has the potential to be applied as a biosensor for cell measurement. Therefore, this two-step screening method effectively allows the selection of AFP-based biosensors with sufficiently enhanced signal responses for application in mammalian cells. A two-step screening procedure allows optimization of the optical response of an auto-fluorescent protein-based biosensor for nitric oxide without structural information.![]()
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Affiliation(s)
- Shunsuke Tajima
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Reiko Sakaguchi
- School of Medicine, University of Occupational and Environmental Health 1-1 Iseigaoka, Yahatanishi-ku Kitakyushu Fukuoka 807-8555 Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University Kyotodaigakukatsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
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23
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Fata F, Gencheva R, Cheng Q, Lullo R, Ardini M, Silvestri I, Gabriele F, Ippoliti R, Bulman CA, Sakanari JA, Williams DL, Arnér ESJ, Angelucci F. Biochemical and structural characterizations of thioredoxin reductase selenoproteins of the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus. Redox Biol 2022; 51:102278. [PMID: 35276442 PMCID: PMC8914392 DOI: 10.1016/j.redox.2022.102278] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 01/21/2023] Open
Abstract
Enzymes in the thiol redox systems of microbial pathogens are promising targets for drug development. In this study we characterized the thioredoxin reductase (TrxR) selenoproteins from Brugia malayi and Onchocerca volvulus, filarial nematode parasites and causative agents of lymphatic filariasis and onchocerciasis, respectively. The two filarial enzymes showed similar turnover numbers and affinities for different thioredoxin (Trx) proteins, but with a clear preference for the autologous Trx. Human TrxR1 (hTrxR1) had a high and similar specific activity versus the human and filarial Trxs, suggesting that, in vivo, hTrxR1 could possibly be the reducing agent of parasite Trxs once they are released into the host. Both filarial TrxRs were efficiently inhibited by auranofin and by a recently described inhibitor of human TrxR1 (TRi-1), but not as efficiently by the alternative compound TRi-2. The enzyme from B. malayi was structurally characterized also in complex with NADPH and auranofin, producing the first crystallographic structure of a nematode TrxR. The protein represents an unusual fusion of a mammalian-type TrxR protein architecture with an N-terminal glutaredoxin-like (Grx) domain lacking typical Grx motifs. Unlike thioredoxin glutathione reductases (TGRs) found in platyhelminths and mammals, which are also Grx-TrxR domain fusion proteins, the TrxRs from the filarial nematodes lacked glutathione disulfide reductase and Grx activities. The structural determinations revealed that the Grx domain of TrxR from B. malayi contains a cysteine (C22), conserved in TrxRs from clade IIIc nematodes, that directly interacts with the C-terminal cysteine-selenocysteine motif of the homo-dimeric subunit. Interestingly, despite this finding we found that altering C22 by mutation to serine did not affect enzyme catalysis. Thus, although the function of the Grx domain in these filarial TrxRs remains to be determined, the results obtained provide insights on key properties of this important family of selenoprotein flavoenzymes that are potential drug targets for treatment of filariasis.
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Affiliation(s)
- Francesca Fata
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Radosveta Gencheva
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Rachel Lullo
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Matteo Ardini
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Ilaria Silvestri
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Federica Gabriele
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Rodolfo Ippoliti
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Christina A Bulman
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Judy A Sakanari
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - David L Williams
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden; Department of Selenoprotein Research, National Institute of Oncology, 1122, Budapest, Hungary
| | - Francesco Angelucci
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy.
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24
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Horai S, Abiko Y, Unoki T, Shinkai Y, Akiyama M, Nakata K, Kunisue T, Kumagai Y. Concentrations of nucleophilic sulfur species in small Indian mongoose (Herpestes auropunctatus) in Okinawa, Japan. CHEMOSPHERE 2022; 295:133833. [PMID: 35120952 DOI: 10.1016/j.chemosphere.2022.133833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Reactive sulfur species (RSS), such as hydrogen per (poly)sulfide, cysteine per (poly)sulfide, glutathione per (poly)sulfide, and protein-bound per (poly)sulfides, can easily react with environmental electrophiles such as methylmercury (MeHg), because of their high nucleophilicity. These RSS are produced by enzymes such as cystathionine β-synthase (CBS) and cystathionine γ-lyase (CSE) and are found in mammalian organs. Organs of wildlife have not been analyzed for hydrogen sulfide, cysteine, glutathione, and RSS. In this study, low molecular weight nucleophilic sulfur substances, including RSS, were quantified by stable isotope dilution assay-based liquid chromatography-mass spectrometry using β-(4-hydroxyphenyl)ethyl iodoacetamide to capture the target chemicals in the small Indian mongoose which species possesses high mercury content as same as some marine mammals. Western blotting revealed that the mongoose organs (liver, kidney, cerebrum, and cerebellum) contained proteins that cross-reacted with anti-CBS and CSE antibodies. The expression patterns of these enzymes were similar to those in mice, indicating that mongoose organs contain CBS and CSE. Moreover, bis-methylmercury sulfide (MeHg)2S, which is a low toxic compound in comparison to MeHg, was found in the liver of this species. These results suggest that the small Indian mongoose produces RSS and monothiols associated with detoxification of electrophilic organomercury. The animals which have high mercury content in their bodies may have function of mercury detoxification involved not only Se but also RSS interactions.
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Affiliation(s)
- Sawako Horai
- Environmental Health Section, Department of Environment and Public Health, National Institute for Minamata Disease, 4058-18 Hama, Minamata, Kumamoto, 867-0008, Japan.
| | - Yumi Abiko
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Takamitsu Unoki
- Hygienic Chemistry Section, Department of Basic Medical Sciences, National Institute for Minamata Disease, 4058-18 Hama, Minamata, Kumamoto, 867-0008, Japan.
| | - Yasuhiro Shinkai
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Masahiro Akiyama
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Science, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan.
| | - Katsushi Nakata
- Nansei Environmental Laboratory Co., Ltd., 4-4 Agarizaki, Nishihara, Okinawa, 903-0105, Japan.
| | - Tatsuya Kunisue
- Center for Marine Environmental Studies, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Yoshito Kumagai
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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Qureshi MK, Gawroński P, Munir S, Jindal S, Kerchev P. Hydrogen peroxide-induced stress acclimation in plants. Cell Mol Life Sci 2022; 79:129. [PMID: 35141765 PMCID: PMC11073338 DOI: 10.1007/s00018-022-04156-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023]
Abstract
Among all reactive oxygen species (ROS), hydrogen peroxide (H2O2) takes a central role in regulating plant development and responses to the environment. The diverse role of H2O2 is achieved through its compartmentalized synthesis, temporal control exerted by the antioxidant machinery, and ability to oxidize specific residues of target proteins. Here, we examine the role of H2O2 in stress acclimation beyond the well-studied transcriptional reprogramming, modulation of plant hormonal networks and long-distance signalling waves by highlighting its global impact on the transcriptional regulation and translational machinery.
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Affiliation(s)
- Muhammad Kamran Qureshi
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Bosan road, Multan, 60800, Pakistan
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Sana Munir
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Bosan road, Multan, 60800, Pakistan
| | - Sunita Jindal
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic.
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26
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Michie MS, Xu B, Sudlow G, Springer LE, Pham CT, Achilefu S. Side-chain modification of collagen-targeting peptide prevents dye aggregation for improved molecular imaging of arthritic joints. J Photochem Photobiol A Chem 2022; 424:113624. [PMID: 36406204 PMCID: PMC9673490 DOI: 10.1016/j.jphotochem.2021.113624] [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] [Indexed: 02/03/2023]
Abstract
Near-infrared (NIR) dye-peptide conjugates are widely used for tissue-targeted molecular fluorescence imaging of pathophysiologic conditions. However, the significant contribution of both dye and peptide to the net mass of these bioconjugates implies that small changes in either component could alter their photophysical and biological properties. Here, we synthesized and conjugated a type I collagen targeted peptide, RRANAALKAGELYKCILY, to either a hydrophobic (LS1000) or hydrophilic (LS1006) NIR fluorescent dye. Spectroscopic analysis revealed rapid self-assembly of both LS1000 and LS1006 in aqueous media to form stable dimeric/H aggregates, regardless of the free dye's solubility in water. We discovered that replacing the cysteine residue in LS1000 and LS1006 with acetamidomethyl cysteine to afford LS1001 and LS1107, respectively, disrupted the peptide's self-assembly and activated the previously quenched dye's fluorescence in aqueous conditions. These results highlight the dominant role of the octadecapeptide, but not the dye molecules, in controlling the photophysical properties of these conjugates by likely sequestering or extruding the hydrophobic or hydrophilic dyes, respectively. Application of the compounds for imaging collagen-rich tissue in an animal model of inflammatory arthritis showed enhanced uptake of all four conjugates, which retained high collagen-binding affinity, in inflamed joints. Moreover, LS1001 and LS1107 improved the arthritic joint-to-background contrast, suggesting that reduced aggregation enhanced the clearance of these compounds from non-target tissues. Our results highlight a peptide-driven strategy to alter the aggregation states of molecular probes in aqueous solutions, irrespective of the water-solubilizing properties of the dye molecules. The interplay between the monomeric and aggregated forms of the conjugates using simple thiol-modifiers lends the peptide-driven approach to diverse applications, including the effective imaging of inflammatory arthritis joints.
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Affiliation(s)
- Megan S. Michie
- Optical Radiology Laboratory, Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baogang Xu
- Optical Radiology Laboratory, Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gail Sudlow
- Optical Radiology Laboratory, Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luke E. Springer
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christine T.N. Pham
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Samuel Achilefu
- Optical Radiology Laboratory, Department of Radiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
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27
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Chen K, Yu X, Zhang X, Li X, Liu Y, Si M, Su T. Involvement of a mycothiol-dependent reductase NCgl0018 in oxidative stress response of Corynebacterium glutamicum. J GEN APPL MICROBIOL 2021; 67:225-239. [PMID: 34483223 DOI: 10.2323/jgam.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Corynebacterium glutamicum is an important industrial strain for amino acids and a key model organism for human pathogens. The study of C. glutamicum oxidoreductases, such as mycoredoxin 1 (Mrx1), dithiol-disulfide isomerase DsbA, and DsbA-like Mrx1, is helpful for understanding the survival, pathogenic infection, and stress resistance of its homologous species. However, the action mode and enzymatic function of C. glutamicum NCgl0018 preserving the Cys-Pro-Phe-Cys motif, annotated as a putative DsbA, have remained enigmatic. Here, we report that the NCgl0018-deleted strain increased sensitivity to various oxidative stresses. The ncgl0018 expression was induced in the stress-responsive extracytoplasmic function-sigma (ECF-σ) factor SigH- and organic peroxide- and antibiotic-sensing regulator (OasR)-dependent manner by stress. NCgl0018 reduced S-mycothiolated mixed disulfides and intramolecular disulfides via a monothiol-disulfide mechanism preferentially linking the mycothiol/mycothione reductase/NADPH electron pathway. Site-directed mutagenesis confirmed Cys107 was the resolving Cys residue, while Cys104 was the nucleophilic cysteine that was oxidized to a sulfenic acid and then could form an intramolecular disulfide bond with Cys107 or a mixed disulfide with mycothiol under stress. Biochemical analyses indicated that NCgl0018 lacked oxidase properties like the classical DsbA. Further, enzymatic rates and substrate preferences of NCgl0018 were highly similar to those of DsbA-like Mrx1. Collectively, our study presented the first evidence that NCgl0018 protected against stresses by functioning as a novel DsbA-like Mrx1 but not DsbA and Mrx1.
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Affiliation(s)
- Keyan Chen
- College of Life Sciences, Qufu Normal University
| | - Xiaoyang Yu
- College of Life Sciences, Qufu Normal University
| | - Xinyu Zhang
- College of Life Sciences, Qufu Normal University
| | - Xiaona Li
- College of Life Sciences, Qufu Normal University
| | - Yang Liu
- College of Life Sciences, Qufu Normal University
| | - Meiru Si
- College of Life Sciences, Qufu Normal University
| | - Tao Su
- College of Life Sciences, Qufu Normal University
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Hydrogen Peroxide and Amyotrophic Lateral Sclerosis: From Biochemistry to Pathophysiology. Antioxidants (Basel) 2021; 11:antiox11010052. [PMID: 35052556 PMCID: PMC8773294 DOI: 10.3390/antiox11010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/18/2021] [Accepted: 12/24/2021] [Indexed: 11/19/2022] Open
Abstract
Free radicals are unstable chemical reactive species produced during Redox dyshomeostasis (RDH) inside living cells and are implicated in the pathogenesis of various neurodegenerative diseases. One of the most complicated and life-threatening motor neurodegenerative diseases (MND) is amyotrophic lateral sclerosis (ALS) because of the poor understanding of its pathophysiology and absence of an effective treatment for its cure. During the last 25 years, researchers around the globe have focused their interest on copper/zinc superoxide dismutase (Cu/Zn SOD, SOD1) protein after the landmark discovery of mutant SOD1 (mSOD1) gene as a risk factor for ALS. Substantial evidence suggests that toxic gain of function due to redox disturbance caused by reactive oxygen species (ROS) changes the biophysical properties of native SOD1 protein thus, instigating its fibrillization and misfolding. These abnormal misfolding aggregates or inclusions of SOD1 play a role in the pathogenesis of both forms of ALS, i.e., Sporadic ALS (sALS) and familial ALS (fALS). However, what leads to a decrease in the stability and misfolding of SOD1 is still in question and our scientific knowledge is scarce. A large number of studies have been conducted in this area to explore the biochemical mechanistic pathway of SOD1 aggregation. Several studies, over the past two decades, have shown that the SOD1-catalyzed biochemical reaction product hydrogen peroxide (H2O2) at a pathological concentration act as a substrate to trigger the misfolding trajectories and toxicity of SOD1 in the pathogenesis of ALS. These toxic aggregates of SOD1 also cause aberrant localization of TAR-DNA binding protein 43 (TDP-43), which is characteristic of neuronal cytoplasmic inclusions (NCI) found in ALS. Here in this review, we present the evidence implicating the pivotal role of H2O2 in modulating the toxicity of SOD1 in the pathophysiology of the incurable and highly complex disease ALS. Also, highlighting the role of H2O2 in ALS, we believe will encourage scientists to target pathological concentrations of H2O2 thereby halting the misfolding of SOD1.
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Bibli SI, Fleming I. Oxidative Post-Translational Modifications: A Focus on Cysteine S-Sulfhydration and the Regulation of Endothelial Fitness. Antioxid Redox Signal 2021; 35:1494-1514. [PMID: 34346251 DOI: 10.1089/ars.2021.0162] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Significance: Changes in the oxidative balance can affect cellular physiology and adaptation through redox signaling. The endothelial cells that line blood vessels are particularly sensitive to reactive oxygen species, which can alter cell function by a number of mechanisms, including the oxidative post-translational modification (oxPTM) of proteins on critical cysteine thiols. Such modifications can act as redox-switches to alter the function of targeted proteins. Recent Advances: Mapping the cysteine oxPTM proteome and characterizing the effects of individual oxPTMs to gain insight into consequences for cellular responses has proven challenging. A recent addition to the list of reversible oxPTMs that contributes to cellular redox homeostasis is persulfidation or S-sulfhydration. Critical Issues: It has been estimated that up to 25% of proteins are S-sulfhydrated, making this modification almost as abundant as phosphorylation. In the endothelium, persulfides are generated by the trans-sulfuration pathway that catabolizes cysteine and cystathionine to generate hydrogen sulfide (H2S) and H2S-related sulfane sulfur compounds (H2Sn). This pathway is of particular importance for the vascular system, as the enzyme cystathionine γ lyase (CSE) in endothelial cells accounts for a significant portion of total vascular H2S/H2Sn production. Future Directions: Impaired CSE activity in endothelial dysfunction has been linked with marked changes in the endothelial cell S-sulfhydrome and can contribute to the development of atherosclerosis and hypertension. It will be interesting to determine how changes in the S-sulfhydration of specific networks of proteins contribute to endothelial cell physiology and pathophysiology. Antioxid. Redox Signal. 35, 1494-1514.
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Affiliation(s)
- Sofia-Iris Bibli
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany.,German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany.,German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt am Main, Germany
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30
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Yang M, Flaumenhaft R. Oxidative Cysteine Modification of Thiol Isomerases in Thrombotic Disease: A Hypothesis. Antioxid Redox Signal 2021; 35:1134-1155. [PMID: 34121445 PMCID: PMC8817710 DOI: 10.1089/ars.2021.0108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Significance: Oxidative stress is a characteristic of many systemic diseases associated with thrombosis. Thiol isomerases are a family of oxidoreductases important in protein folding and are exquisitely sensitive to the redox environment. They are essential for thrombus formation and represent a previously unrecognized layer of control of the thrombotic process. Yet, the mechanisms by which thiol isomerases function in thrombus formation are unknown. Recent Advances: The oxidoreductase activity of thiol isomerases in thrombus formation is controlled by the redox environment via oxidative changes to active site cysteines. Specific alterations can now be detected owing to advances in the chemical biology of oxidative cysteine modifications. Critical Issues: Understanding of the role of thiol isomerases in thrombus formation has focused largely on identifying single disulfide bond modifications in isolated proteins (e.g., αIIbβ3, tissue factor, vitronectin, or glycoprotein Ibα [GPIbα]). An alternative approach is to conceptualize thiol isomerases as effectors in redox signaling pathways that control thrombotic potential by modifying substrate networks. Future Directions: Cysteine-based chemical biology will be employed to study thiol-dependent dynamics mediated by the redox state of thiol isomerases at the systems level. This approach could identify thiol isomerase-dependent modifications of the disulfide landscape that are prothrombotic.
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Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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31
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Parise A, Romeo I, Russo N, Marino T. The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study. Int J Mol Sci 2021; 22:9792. [PMID: 34575955 PMCID: PMC8467846 DOI: 10.3390/ijms22189792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
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32
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Liu Y, Li X, Luo J, Su T, Si M, Chen C. A novel mycothiol-dependent thiol-disulfide reductase in Corynebacterium glutamicum involving oxidative stress resistance. 3 Biotech 2021; 11:372. [PMID: 34290951 PMCID: PMC8280269 DOI: 10.1007/s13205-021-02896-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/12/2021] [Indexed: 11/30/2022] Open
Abstract
ncgl2478 gene from Corynebacterium glutamicum encodes a thiol–disulfide oxidoreductase enzyme annotated as dithiol–disulfide isomerase DsbA. It preserves a Cys–Pro–Phe–Cys active-site motif, which is presumed to be an exclusive characteristic of the novel DsbA–mycoredoxin 1 (Mrx1) cluster. However, the real mode of action, the nature of the electron donor pathway and biological functions of NCgl2478 in C. glutamicum have remained enigmatic so far. Herein, we report that NCgl2478 plays an important role in stress resistance. Deletion of the ncgl2478 gene increases the size of growth inhibition zones. The ncgl2478 expression is induced in the stress-responsive extra-cytoplasmic function-sigma (ECF-σ) factor SigH-dependent manner by stress. It receives electrons preferentially from the mycothiol (MSH)/mycothione reductase (Mtr)/NADPH pathway. Further, NCgl2478 reduces S-mycothiolated mixed disulfides and intramolecular disulfides via a monothiol–disulfide and a dithiol–disulfide exchange mechanism, respectively. NCgl2478 lacks oxidase activity; kinetic properties of its demycothiolation are different from those of Mrx1. Site-directed mutagenesis confirms Cys24 is the resolving Cys residue, while Cys21 is the nucleophilic cysteine that is oxidized to a sulfenic acid and then forms an intramolecular disulfide bond with Cys24 or a mixed disulfide with MSH under oxidative stress. In conclusion, our study presents the first evidence that NCgl2478 protects against various stresses by acting as an MSH-dependent thiol–disulfide reductase, belonging to a novel DsbA–Mrx1 cluster.
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Affiliation(s)
- Yang Liu
- College of Life Sciences, Qufu Normal University, Qufu, 273165 Shandong China
| | - Xiaona Li
- College of Life Sciences, Qufu Normal University, Qufu, 273165 Shandong China
| | - Jiaxin Luo
- College of Life Sciences, Qufu Normal University, Qufu, 273165 Shandong China
| | - Tao Su
- College of Life Sciences, Qufu Normal University, Qufu, 273165 Shandong China
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, 273165 Shandong China
| | - Can Chen
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001 Henan China
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33
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Kenari F, Molnár S, Perjési P. Reaction of Chalcones with Cellular Thiols. The Effect of the 4-Substitution of Chalcones and Protonation State of the Thiols on the Addition Process. Diastereoselective Thiol Addition. Molecules 2021; 26:molecules26144332. [PMID: 34299607 PMCID: PMC8308006 DOI: 10.3390/molecules26144332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 12/03/2022] Open
Abstract
Several biological effects of chalcones have been reported to be associated with their thiol reactivity. In vivo, the reactions can result in the formation of small-molecule or protein thiol adducts. Both types of reactions can play a role in the biological effects of this class of compounds. Progress of the reaction of 4-methyl- and 4-methoxychalcone with glutathione and N-acetylcysteine was studied by the HPLC-UV-VIS method. The reactions were conducted under three different pH conditions. HPLC-MS measurements confirmed the structure of the formed adducts. The chalcones reacted with both thiols under all incubation conditions. The initial rate and composition of the equilibrium mixtures depended on the ratio of the deprotonated form of the thiols. In the reaction of 4-methoxychalcone with N-acetylcysteine under strongly basic conditions, transformation of the kinetic adduct into the thermodynamically more stable one was observed. Addition of S-protonated N-acetylcysteine onto the polar double bonds of the chalcones showed different degrees of diastereoselectivity. Both chalcones showed a Michael-type addition reaction with the ionized and non-ionized forms of the investigated thiols. The initial reactivity of the chalcones and the equilibrium composition of the incubates showed a positive correlation with the degree of ionization of the thiols. Conversions showed systematic differences under each set of conditions. The observed differences can hint at the difference in reported biological actions of 4-methyl- and 4-methoxy-substituted chalcones.
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Affiliation(s)
- Fatemeh Kenari
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (S.M.)
| | - Szilárd Molnár
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (S.M.)
- Research Institute for Viticulture and Oenology, University of Pécs, H-7624 Pécs, Hungary
| | - Pál Perjési
- Institute of Pharmaceutical Chemistry, University of Pécs, H-7624 Pécs, Hungary; (F.K.); (S.M.)
- Correspondence: ; Tel.: +36-72-503-650
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34
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Le Moigne T, Gurrieri L, Crozet P, Marchand CH, Zaffagnini M, Sparla F, Lemaire SD, Henri J. Crystal structure of chloroplastic thioredoxin z defines a type-specific target recognition. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:434-447. [PMID: 33930214 DOI: 10.1111/tpj.15300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Thioredoxins (TRXs) are ubiquitous disulfide oxidoreductases structured according to a highly conserved fold. TRXs are involved in a myriad of different processes through a common chemical mechanism. Plant TRXs evolved into seven types with diverse subcellular localization and distinct protein target selectivity. Five TRX types coexist in the chloroplast, with yet scarcely described specificities. We solved the crystal structure of a chloroplastic z-type TRX, revealing a conserved TRX fold with an original electrostatic surface potential surrounding the redox site. This recognition surface is distinct from all other known TRX types from plant and non-plant sources and is exclusively conserved in plant z-type TRXs. We show that this electronegative surface endows thioredoxin z (TRXz) with a capacity to activate the photosynthetic Calvin-Benson cycle enzyme phosphoribulokinase. The distinct electronegative surface of TRXz thereby extends the repertoire of TRX-target recognitions.
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Affiliation(s)
- Théo Le Moigne
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Faculty of Sciences, Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin, 91190, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
| | - Libero Gurrieri
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Pierre Crozet
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
- Sorbonne Université, Polytech Sorbonne, Paris, 75005, France
| | - Christophe H Marchand
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
- Plateforme de Protéomique, Institut de Biologie Physico-Chimique, FR 550, CNRS, 13 Rue Pierre et Marie Curie, Paris, 75005, France
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Francesca Sparla
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Stéphane D Lemaire
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
| | - Julien Henri
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
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Perkins A, Tudorica DA, Teixeira RD, Schirmer T, Zumwalt L, Ogba OM, Cassidy CK, Stansfeld PJ, Guillemin K. A Bacterial Inflammation Sensor Regulates c-di-GMP Signaling, Adhesion, and Biofilm Formation. mBio 2021; 12:e0017321. [PMID: 34154415 PMCID: PMC8262984 DOI: 10.1128/mbio.00173-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteria that colonize animals must overcome, or coexist, with the reactive oxygen species products of inflammation, a front-line defense of innate immunity. Among these is the neutrophilic oxidant bleach, hypochlorous acid (HOCl), a potent antimicrobial that plays a primary role in killing bacteria through nonspecific oxidation of proteins, lipids, and DNA. Here, we report that in response to increasing HOCl levels, Escherichia coli regulates biofilm production via activation of the diguanylate cyclase DgcZ. We identify the mechanism of DgcZ sensing of HOCl to be direct oxidation of its regulatory chemoreceptor zinc-binding (CZB) domain. Dissection of CZB signal transduction reveals that oxidation of the conserved zinc-binding cysteine controls CZB Zn2+ occupancy, which in turn regulates the catalysis of c-di-GMP by the associated GGDEF domain. We find DgcZ-dependent biofilm formation and HOCl sensing to be regulated in vivo by the conserved zinc-coordinating cysteine. Additionally, point mutants that mimic oxidized CZB states increase total biofilm. A survey of bacterial genomes reveals that many pathogenic bacteria that manipulate host inflammation as part of their colonization strategy possess CZB-regulated diguanylate cyclases and chemoreceptors. Our findings suggest that CZB domains are zinc-sensitive regulators that allow host-associated bacteria to perceive host inflammation through reactivity with HOCl. IMPORTANCE Immune cells are well equipped to eliminate invading bacteria, and one of their primary tools is the synthesis of bleach, hypochlorous acid (HOCl), the same chemical used as a household disinfectant. In this work, we present findings showing that many host-associated bacteria possess a bleach-sensing protein that allows them to adapt to the presence of this chemical in their environment. We find that the bacterium Escherichia coli responds to bleach by hunkering down and producing a sticky matrix known as biofilm, which helps it aggregate and adhere to surfaces. This behavior may play an important role in pathogenicity for E. coli and other bacteria, as it allows the bacteria to detect and adapt to the weapons of the host immune system.
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Affiliation(s)
- Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Dan A. Tudorica
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | | | | | - Lindsay Zumwalt
- Department of Chemistry and Biochemistry Program, Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - O. Maduka Ogba
- Department of Chemistry and Biochemistry Program, Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - C. Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Phillip J. Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada
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Molecular Insight into the Regulation of Vimentin by Cysteine Modifications and Zinc Binding. Antioxidants (Basel) 2021; 10:antiox10071039. [PMID: 34203497 PMCID: PMC8300659 DOI: 10.3390/antiox10071039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/20/2021] [Accepted: 06/24/2021] [Indexed: 01/11/2023] Open
Abstract
The intermediate filament protein vimentin is involved in essential cellular processes, including cell division and stress responses, as well as in the pathophysiology of cancer, pathogen infection, and autoimmunity. The vimentin network undergoes marked reorganizations in response to oxidative stress, in which modifications of vimentin single cysteine residue, Cys328, play an important role, and is modulated by zinc availability. However, the molecular basis for this regulation is not fully understood. Here, we show that Cys328 displays a low pKa, supporting its reactivity, and is readily alkylated and oxidized in vitro. Moreover, combined oxidation and crosslinking assays and molecular dynamics simulations support that zinc ions interact with Cys328 in its thiolate form, whereas Glu329 and Asp331 stabilize zinc coordination. Vimentin oxidation can induce disulfide crosslinking, implying the close proximity of Cys328 from neighboring dimers in certain vimentin conformations, supported by our computational models. Notably, micromolar zinc concentrations prevent Cys328 alkylation, lipoxidation, and disulfide formation. Moreover, zinc selectively protects vimentin from crosslinking using short-spacer cysteine-reactive but not amine-reactive agents. These effects are not mimicked by magnesium, consistent with a lower number of magnesium ions hosted at the cysteine region, according to molecular dynamics simulations. Importantly, the region surrounding Cys328 is involved in interaction with several drugs targeting vimentin and is conserved in type III intermediate filaments, which include glial fibrillary acidic protein and desmin. Altogether, our results identify this region as a hot spot for zinc binding, which modulates Cys328 reactivity. Moreover, they provide a molecular standpoint for vimentin regulation through the interplay between cysteine modifications and zinc availability.
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Molecular Basis for the Interactions of Human Thioredoxins with Their Respective Reductases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6621292. [PMID: 34122725 PMCID: PMC8189816 DOI: 10.1155/2021/6621292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/20/2021] [Accepted: 05/20/2021] [Indexed: 12/03/2022]
Abstract
The mammalian cytosolic thioredoxin (Trx) system consists of Trx1 and its reductase, the NADPH-dependent seleno-enzyme TrxR1. These proteins function as electron donor for metabolic enzymes, for instance in DNA synthesis, and the redox regulation of numerous processes. In this work, we analysed the interactions between these two proteins. We proposed electrostatic complementarity as major force controlling the formation of encounter complexes between the proteins and thus the efficiency of the subsequent electron transfer reaction. If our hypothesis is valid, formation of the encounter complex should be independent of the redox reaction. In fact, we were able to confirm that also a redox inactive mutant of Trx1 lacking both active site cysteinyl residues (C32,35S) binds to TrxR1 in a similar manner and with similar kinetics as the wild-type protein. We have generated a number of mutants with alterations in electrostatic properties and characterised their interaction with TrxR1 in kinetic assays. For human Trx1 and TrxR1, complementary electrostatic surfaces within the area covered in the encounter complex appear to control the affinity of the reductase for its substrate Trx. Electrostatic compatibility was even observed in areas that do not form direct molecular interactions in the encounter complex, and our results suggest that the electrostatic complementarity in these areas influences the catalytic efficiency of the reduction. The human genome encodes ten cytosolic Trx-like or Trx domain-containing proteins. In agreement with our hypothesis, the proteins that have been characterised as TrxR1 substrates also show the highest similarity in their electrostatic properties.
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Li L, Chen N, Xia D, Xu S, Dai W, Tong Y, Wang L, Jiang Z, You Q, Xu X. Discovery of a covalent inhibitor of heat shock protein 90 with antitumor activity that blocks the co-chaperone binding via C-terminal modification. Cell Chem Biol 2021; 28:1446-1459.e6. [PMID: 33932325 DOI: 10.1016/j.chembiol.2021.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 01/24/2023]
Abstract
Heat shock protein (Hsp90), a critical molecular chaperone that regulates the maturation of a large number of oncogenic client proteins, plays an essential role in the growth of neoplastic cells. Herein, DDO-6600 is identified to covalent modification of Cys598 on Hsp90 from in silico study and is verified by a series of biological assays. We demonstrated that DDO-6600 covalently bound to Cys598 on the Hsp90 C terminus and exhibited antiproliferative activities against multiple tumor cells without inhibiting ATPase activity. Further studies showed that DDO-6600 disrupted the interaction between Hsp90 and Cdc37, which induced the degradation of kinase client proteins in multiple tumor cell lines, promoted apoptosis, and inhibited cell motility. Our findings offer mechanic insights into the covalent modification of Hsp90 and provide an alternative strategy for the development of Hsp90 covalent regulators or chemical probes to explore the therapeutical potential of Hsp90.
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Affiliation(s)
- Li Li
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Nannan Chen
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Dandan Xia
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Shicheng Xu
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wei Dai
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuanyuan Tong
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Qidong You
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiaoli Xu
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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Interactions of zinc- and redox-signaling pathways. Redox Biol 2021; 41:101916. [PMID: 33662875 PMCID: PMC7937829 DOI: 10.1016/j.redox.2021.101916] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Zinc and cellular oxidants such as reactive oxygen species (ROS) each participate in a multitude of physiological functions. There is considerable overlap between the affected events, including signal transduction. While there is no obvious direct connection between zinc and ROS, mainly because the bivalent cation zinc does not change its oxidation state in biological systems, these are linked by their interaction with sulfur, forming the remarkable triad of zinc, ROS, and protein thiols. First, zinc binds to reduced thiols and can be released upon oxidation. Thereby, redox signals are translated into changes in the free zinc concentration, which can act as zinc signals. Second, zinc affects oxidation of thiols in several ways, directly as well as indirectly. A protein incorporating many of these interactions is metallothionein (MT), which is rich in cysteine and capable of binding up to seven zinc ions in its fully reduced state. Zinc binding is diminished after (partial) oxidation, while thiols show increased reactivity in the absence of bound metal ions. Adding still more complexity, the MT promoter is controlled by zinc (via metal regulatory transcription factor 1 (MTF-1)) as well as redox (via nuclear factor erythroid 2-related factor 2 (NRF2)). Many signaling cascades that are important for cell proliferation or apoptosis contain protein thiols, acting as centers for crosstalk between zinc- and redox-signaling. A prominent example for shared molecular targets for zinc and ROS are active site cysteine thiols in protein tyrosine phosphatases (PTP), their activity being downregulated by oxidation as well as zinc binding. Because zinc binding also protects PTP thiols form irreversible oxidation, there is a multi-faceted reciprocal interaction, illustrating that zinc- and redox-signaling are intricately linked on multiple levels.
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Viedma-Poyatos Á, González-Jiménez P, Langlois O, Company-Marín I, Spickett CM, Pérez-Sala D. Protein Lipoxidation: Basic Concepts and Emerging Roles. Antioxidants (Basel) 2021; 10:295. [PMID: 33669164 PMCID: PMC7919664 DOI: 10.3390/antiox10020295] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
Protein lipoxidation is a non-enzymatic post-translational modification that consists of the covalent addition of reactive lipid species to proteins. This occurs under basal conditions but increases in situations associated with oxidative stress. Protein targets for lipoxidation include metabolic and signalling enzymes, cytoskeletal proteins, and transcription factors, among others. There is strong evidence for the involvement of protein lipoxidation in disease, including atherosclerosis, neurodegeneration, and cancer. Nevertheless, the involvement of lipoxidation in cellular regulatory mechanisms is less understood. Here we review basic aspects of protein lipoxidation and discuss several features that could support its role in cell signalling, including its selectivity, reversibility, and possibilities for regulation at the levels of the generation and/or detoxification of reactive lipids. Moreover, given the great structural variety of electrophilic lipid species, protein lipoxidation can contribute to the generation of multiple structurally and functionally diverse protein species. Finally, the nature of the lipoxidised proteins and residues provides a frameshift for a complex interplay with other post-translational modifications, including redox and redox-regulated modifications, such as oxidative modifications and phosphorylation, thus strengthening the importance of detailed knowledge of this process.
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Affiliation(s)
- Álvaro Viedma-Poyatos
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (C.S.I.C.), 28040 Madrid, Spain
| | - Patricia González-Jiménez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (C.S.I.C.), 28040 Madrid, Spain
| | - Ophélie Langlois
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Idoia Company-Marín
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Corinne M Spickett
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (C.S.I.C.), 28040 Madrid, Spain
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41
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Schipper S, Wu H, Furdui CM, Poole LB, Delahunty CM, Park R, Yates JR, Becker K, Przyborski JM. Identification of sulfenylation patterns in trophozoite stage Plasmodium falciparum using a non-dimedone based probe. Mol Biochem Parasitol 2021; 242:111362. [PMID: 33513391 DOI: 10.1016/j.molbiopara.2021.111362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Plasmodium falciparum causes the deadliest form of malaria. Adequate redox control is crucial for this protozoan parasite to overcome oxidative and nitrosative challenges, thus enabling its survival. Sulfenylation is an oxidative post-translational modification, which acts as a molecular on/off switch, regulating protein activity. To obtain a better understanding of which proteins are redox regulated in malaria parasites, we established an optimized affinity capture protocol coupled with mass spectrometry analysis for identification of in vivo sulfenylated proteins. The non-dimedone based probe BCN-Bio1 shows reaction rates over 100-times that of commonly used dimedone-based probes, allowing for a rapid trapping of sulfenylated proteins. Mass spectrometry analysis of BCN-Bio1 labeled proteins revealed the first insight into the Plasmodium falciparum trophozoite sulfenylome, identifying 102 proteins containing 152 sulfenylation sites. Comparison with Plasmodium proteins modified by S-glutathionylation and S-nitrosation showed a high overlap, suggesting a common core of proteins undergoing redox regulation by multiple mechanisms. Furthermore, parasite proteins which were identified as targets for sulfenylation were also identified as being sulfenylated in other organisms, especially proteins of the glycolytic cycle. This study suggests that a number of Plasmodium proteins are subject to redox regulation and it provides a basis for further investigations into the exact structural and biochemical basis of regulation, and a deeper understanding of cross-talk between post-translational modifications.
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Affiliation(s)
- Susanne Schipper
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Hanzhi Wu
- 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
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Claire M Delahunty
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robin Park
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Katja Becker
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Jude M Przyborski
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany.
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Zhang W, Zhu Y, Yu H, Liu X, Jiao B, Lu X. Libertellenone H, a Natural Pimarane Diterpenoid, Inhibits Thioredoxin System and Induces ROS-Mediated Apoptosis in Human Pancreatic Cancer Cells. Molecules 2021; 26:molecules26020315. [PMID: 33435380 PMCID: PMC7827531 DOI: 10.3390/molecules26020315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 01/22/2023] Open
Abstract
Libertellenone H (LH), a marine-derived pimarane diterpenoid isolated from arctic fungus Eutypella sp. D-1, has shown effective cytotoxicity on a range of cancer cells. The present study is to explore the anticancer effect of LH on human pancreatic cancer cells and to investigate the intracellular molecular target and underlying mechanism. As shown, LH exhibited anticancer activity in human pancreatic cancer cells by promoting cell apoptosis. Mechanistic studies suggested that LH-induced reactive oxygen species (ROS) accumulation was responsible for apoptosis as antioxidant N-acetylcysteine (NAC) and antioxidant enzyme superoxide dismutase (SOD) antagonized the inhibitory effect of LH. Zymologic testing demonstrated that LH inhibited Trx system but had little effect on the glutathione reductase and glutaredoxin. Mass spectrometry (MS) analysis revealed that the mechanism of action was based on the direct conjugation of LH to the Cys32/Cys35 residue of Trx1 and Sec498 of TrxR, leading to a decrease in the cellular level of glutathione (GSH) and activation of downstream ASK1/JNK signaling pathway. Taken together, our findings revealed LH was a marine derived inhibitor of Trx system and an anticancer candidate.
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Affiliation(s)
- Weirui Zhang
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Naval Medical University, Shanghai 200433, China; (W.Z.); (H.Y.); (X.L.)
| | - Yuping Zhu
- College of Basic Medical Sciences, Experimental Teacher Center, Naval Medical University, Shanghai 200433, China;
| | - Haobing Yu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Naval Medical University, Shanghai 200433, China; (W.Z.); (H.Y.); (X.L.)
| | - Xiaoyu Liu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Naval Medical University, Shanghai 200433, China; (W.Z.); (H.Y.); (X.L.)
| | - Binghua Jiao
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Naval Medical University, Shanghai 200433, China; (W.Z.); (H.Y.); (X.L.)
- Correspondence: (B.J.); (X.L.); Tel.: +86-21-81870970 (ext. 8001) (B.J.); +86-21-81870970 (ext. 8004) (X.L.)
| | - Xiaoling Lu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Naval Medical University, Shanghai 200433, China; (W.Z.); (H.Y.); (X.L.)
- Correspondence: (B.J.); (X.L.); Tel.: +86-21-81870970 (ext. 8001) (B.J.); +86-21-81870970 (ext. 8004) (X.L.)
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Mukherjee S. Cysteine modifications (oxPTM) and protein sulphenylation-mediated sulfenome expression in plants: evolutionary conserved signaling networks? PLANT SIGNALING & BEHAVIOR 2021; 16:1831792. [PMID: 33300450 PMCID: PMC7781837 DOI: 10.1080/15592324.2020.1831792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant resilience to oxidative stress possibly operates through the restoration of intracellular redox milieu and the activity of various posttranslationally modified proteins. Among various modes of redox regulation operative in plants cys oxPTMs are brought about by the activity of reactive oxygen species (ROS), reactive nitrogen species (RNS), and hydrogen peroxide. Cysteine oxPTMs are capable of transducing ROS-mediated long-distance hormone signaling (ABA, JA, SA) in plants. S-sulphenylation is an intermediary modification en route to other oxidative states of cysteine. In silico analysis have revealed evolutionary conservation of certain S-sulphenylated proteins across human and plants. Further analysis of protein sulphenylation in plants should be extended to the functional follow-up studies followed by site-specific characterization and case-by-case validation of protein activity. The repertoire of physiological methods (fluorescent conjugates (dimedone) and yeast AP-1 (YAP1)-based genetic probes) in the recent past has been successful in the detection of sulphenylated proteins and other cysteine-based modifications in plants. In view of a better understanding of the sulfur-based redoxome it is necessary to update our timely progress on the methodological advancements for the detection of cysteine-based oxPTM. This substantiative information can extend our investigations on plant-environment interaction thus improving crop manipulation strategies. The simulation-based computational approach has emerged as a new method to determine the directive mechanism of cysteine oxidation in plants. Thus, sulfenome analysis in various plant systems might reflect as a pinnacle of plant redox biology in the future.
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Affiliation(s)
- Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West, Bengal, India
- CONTACT Soumya Mukherjee Department of Botany, Jangipur College, University of Kalyani, West, Bengal742213, India
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Perinelli M, Tegoni M, Freisinger E. Different Behavior of the Histidine Residue toward Cadmium and Zinc in a Cadmium-Specific Metallothionein from an Aquatic Fungus. Inorg Chem 2020; 59:16988-16997. [DOI: 10.1021/acs.inorgchem.0c02171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monica Perinelli
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matteo Tegoni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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45
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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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46
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Capdevila DA, Walsh BJC, Zhang Y, Dietrich C, Gonzalez-Gutierrez G, Giedroc DP. Structural basis for persulfide-sensing specificity in a transcriptional regulator. Nat Chem Biol 2020; 17:65-70. [PMID: 33106663 DOI: 10.1038/s41589-020-00671-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/11/2020] [Indexed: 12/23/2022]
Abstract
Cysteine thiol-based transcriptional regulators orchestrate the coordinated regulation of redox homeostasis and other cellular processes by 'sensing' or detecting a specific redox-active molecule, which in turn activates the transcription of a specific detoxification pathway. The extent to which these sensors are truly specific in cells for a singular class of reactive small-molecule stressors, for example, reactive oxygen or sulfur species, is largely unknown. Here, we report structural and mechanistic insights into the thiol-based transcriptional repressor SqrR, which reacts exclusively with oxidized sulfur species such as persulfides, to yield a tetrasulfide bridge that inhibits DNA operator-promoter binding. Evaluation of crystallographic structures of SqrR in various derivatized states, coupled with the results of a mass spectrometry-based kinetic profiling strategy, suggest that persulfide selectivity is determined by structural frustration of the disulfide form. These findings led to the identification of an uncharacterized repressor from the bacterial pathogen Acinetobacter baumannii as a persulfide sensor.
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Affiliation(s)
- Daiana A Capdevila
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.,Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Brenna J C Walsh
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Yifan Zhang
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Christopher Dietrich
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Giovanni Gonzalez-Gutierrez
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - David P Giedroc
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.
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47
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Smith SL, Pitt AR, Spickett CM. Approaches to Investigating the Protein Interactome of PTEN. J Proteome Res 2020; 20:60-77. [PMID: 33074689 DOI: 10.1021/acs.jproteome.0c00570] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The tumor suppressor phosphatase and tensin homologue (PTEN) is a redox-sensitive dual specificity phosphatase with an essential role in the negative regulation of the PI3K-AKT signaling pathway, affecting metabolic and cell survival processes. PTEN is commonly mutated in cancer, and dysregulation in the metabolism of PIP3 is implicated in other diseases such as diabetes. PTEN interactors are responsible for some functional roles of PTEN beyond the negative regulation of the PI3K pathway and are thus of great importance in cell biology. Both high-data content proteomics-based approaches and low-data content PPI approaches have been used to investigate the interactome of PTEN and elucidate further functions of PTEN. While low-data content approaches rely on co-immunoprecipitation and Western blotting, and as such require previously generated hypotheses, high-data content approaches such as affinity pull-down proteomic assays or the yeast 2-hybrid system are hypothesis generating. This review provides an overview of the PTEN interactome, including redox effects, and critically appraises the methods and results of high-data content investigations into the global interactome of PTEN. The biological significance of findings from recent studies is discussed and illustrates the breadth of cellular functions of PTEN that can be discovered by these approaches.
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Affiliation(s)
- Sarah L Smith
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, U.K
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, U.K.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, U.K
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48
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Martins VS, Triboni ER, Bonilha JBS, Gonçalves LM, Mortara L, Carvalho LAC, Manda BR, Lacerda CD, Meotti FC, Politi MJ, Chaimovich H, Cuccovia IM. Micellar effects and analytical applications of nitro substitution in 4-Nitro- N-alkyl-1,8-naphthalimide by cysteine derivatives. Heliyon 2020; 6:e04938. [PMID: 32995623 PMCID: PMC7502353 DOI: 10.1016/j.heliyon.2020.e04938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/26/2020] [Accepted: 09/10/2020] [Indexed: 12/03/2022] Open
Abstract
The aromatic nucleophilic substitution reactions of the nitro group of 4-Nitro-N-alkyl-1,8-naphthalimides by thiolate anions produce fluorescent derivatives and their rates are strongly accelerated by micelles of hexadecyltrimethylammonium chloride even at low pH. Acceleration factors of this reactions can reach million-fold. As the products are oxidant-insensible, this reaction allows the determination of SH- containing compounds such as cysteine, glutathione or proteins even in oxidative conditions. Limits of detection are as low as 5 × 10−7 M, ten times lower than the limit for the classic 5,5′-dithiobis-(2-nitrobenzoic) acid method. Moreover, this reaction can be developed at pHs between 6.5 and 7.5 thereby diminishing the rate of spontaneous oxidation of the thiols. In addition, we demonstrated that 4-Nitro-N-alkyl-1,8-naphthalimides can be used to evidence SH groups in peptides, proteins and living cells.
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Affiliation(s)
- V S Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - E R Triboni
- Escola de Engenharia de Lorena da Universidade de São Paulo, Departamento de Engenharia Química (DEQUI), Lorena, SP, Brazil
| | - J B S Bonilha
- Faculdade de Filosofia Ciências e Letras da Universidade de São Paulo, FFCLRP, Ribeirão Preto, SP, Brazil
| | - L M Gonçalves
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - L Mortara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - L A C Carvalho
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - B R Manda
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - C D Lacerda
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - F C Meotti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - M J Politi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - H Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - I M Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
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49
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Pignataro M, Di Rocco G, Lancellotti L, Bernini F, Subramanian K, Castellini E, Bortolotti CA, Malferrari D, Moro D, Valdrè G, Borsari M, Del Monte F. Phosphorylated cofilin-2 is more prone to oxidative modifications on Cys39 and favors amyloid fibril formation. Redox Biol 2020; 37:101691. [PMID: 32863228 PMCID: PMC7472925 DOI: 10.1016/j.redox.2020.101691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/06/2020] [Accepted: 08/17/2020] [Indexed: 02/01/2023] Open
Abstract
Cofilins are small protein of the actin depolymerizing family. Actin polymerization/depolymerization is central to a number of critical cellular physiological tasks making cofilin a key protein for several physiological functions of the cell. Cofilin activity is mainly regulated by phosphorylation on serine residue 3 making this post-translational modification key to the regulation of myofilament integrity. In fact, in this form, the protein segregates in myocardial aggregates in human idiopathic dilated cardiomyopathy. Since myofilament network is an early target of oxidative stress we investigated the molecular changes induced by oxidation on cofilin isoforms and their interplay with the protein phosphorylation state to get insight on whether/how those changes may predispose to early protein aggregation. Using different and complementary approaches we characterized the aggregation properties of cofilin-2 and its phosphomimetic variant (S3D) in response to oxidative stress in silico, in vitro and on isolated cardiomyocytes. We found that the phosphorylated (inactive) form of cofilin-2 is mechanistically linked to the formation of an extended network of fibrillar structures induced by oxidative stress via the formation of a disulfide bond between Cys39 and Cys80. Such phosphorylation-dependent effect is likely controlled by changes in the hydrogen bonding network involving Cys39. We found that the sulfide ion inhibits the formation of such structures. This might represent the mechanism for the protective effect of the therapeutic agent Na2S on ischemic injury.
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Affiliation(s)
- Marcello Pignataro
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, USA
| | - Giulia Di Rocco
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Lidia Lancellotti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabrizio Bernini
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Elena Castellini
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Daniele Malferrari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniele Moro
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Valdrè
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Borsari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy.
| | - Federica Del Monte
- Gazes Cardiac Research Institute, Medical University of South Carolina, Charleston, USA; Department of Experimental, Diagnostic and Specialty Medicine (DIMES), School of Medicine, University of Bologna, Bologna, Italy.
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50
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Finelli MJ. Redox Post-translational Modifications of Protein Thiols in Brain Aging and Neurodegenerative Conditions-Focus on S-Nitrosation. Front Aging Neurosci 2020; 12:254. [PMID: 33088270 PMCID: PMC7497228 DOI: 10.3389/fnagi.2020.00254] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
Reactive oxygen species and reactive nitrogen species (RONS) are by-products of aerobic metabolism. RONS trigger a signaling cascade that can be transduced through oxidation-reduction (redox)-based post-translational modifications (redox PTMs) of protein thiols. This redox signaling is essential for normal cellular physiology and coordinately regulates the function of redox-sensitive proteins. It plays a particularly important role in the brain, which is a major producer of RONS. Aberrant redox PTMs of protein thiols can impair protein function and are associated with several diseases. This mini review article aims to evaluate the role of redox PTMs of protein thiols, in particular S-nitrosation, in brain aging, and in neurodegenerative diseases. It also discusses the potential of using redox-based therapeutic approaches for neurodegenerative conditions.
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Affiliation(s)
- Mattéa J Finelli
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
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