1
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Sastre S, Manta B, Semelak JA, Estrin D, Trujillo M, Radi R, Zeida A. Catalytic Mechanism of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A. Biochemistry 2024; 63:533-544. [PMID: 38286790 DOI: 10.1021/acs.biochem.3c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The oxidation of Met to methionine sulfoxide (MetSO) by oxidants such as hydrogen peroxide, hypochlorite, or peroxynitrite has profound effects on protein function. This modification can be reversed by methionine sulfoxide reductases (msr). In the context of pathogen infection, the reduction of oxidized proteins gains significance due to microbial oxidative damage generated by the immune system. For example, Mycobacterium tuberculosis (Mt) utilizes msrs (MtmsrA and MtmsrB) as part of the repair response to the host-induced oxidative stress. The absence of these enzymes makes Mycobacteria prone to increased susceptibility to cell death, pointing them out as potential therapeutic targets. This study provides a detailed characterization of the catalytic mechanism of MtmsrA using a comprehensive approach, including experimental techniques and theoretical methodologies. Confirming a ping-pong type enzymatic mechanism, we elucidate the catalytic parameters for sulfoxide and thioredoxin substrates (kcat/KM = 2656 ± 525 M-1 s-1 and 1.7 ± 0.8 × 106 M-1 s-1, respectively). Notably, the entropic nature of the activation process thermodynamics, representing ∼85% of the activation free energy at room temperature, is underscored. Furthermore, the current study questions the plausibility of a sulfurane intermediate, which may be a transition-state-like structure, suggesting the involvement of a conserved histidine residue as an acid-base catalyst in the MetSO reduction mechanism. This mechanistic insight not only advances our understanding of Mt antioxidant enzymes but also holds implications for future drug discovery and biotechnological applications.
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Affiliation(s)
- Santiago Sastre
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Departamento de Biofísica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Programa de Doctorado en Química, Facultad de Química, Universidad de la República, Gral Flores 2124, CP 11800 Montevideo, Uruguay
| | - Bruno Manta
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Cátedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Gral Las Heras 1925, CP 11600 Montevideo, Uruguay
| | - Jonathan A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Ciudad Universitaria, Intendente Güiraldes 2160, CP C1428EGA Buenos Aires, Argentina
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Ciudad Universitaria, Intendente Güiraldes 2160, CP C1428EGA Buenos Aires, Argentina
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
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Villar SF, Corrales-González L, Márquez de Los Santos B, Dalla Rizza J, Zeida A, Denicola A, Ferrer-Sueta G. Kinetic and structural assessment of the reduction of human 2-Cys peroxiredoxins by thioredoxins. FEBS J 2024; 291:778-794. [PMID: 37985387 DOI: 10.1111/febs.17006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/09/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
We have studied the reduction reactions of two cytosolic human peroxiredoxins (Prx) in their disulfide form by three thioredoxins (Trx; two human and one bacterial), with the aim of better understanding the rate and mechanism of those reactions, and their relevance in the context of the catalytic cycle of Prx. We have developed a new methodology based on stopped-flow and intrinsic fluorescence to study the bimolecular reactions, and found rate constants in the range of 105 -106 m-1 s-1 in all cases, showing that there is no marked kinetic preference for the expected Trx partner. By combining experimental findings and molecular dynamics studies, we found that the reactivity of the nucleophilic cysteine (CN ) in the Trx is greatly affected by the formation of the Prx-Trx complex. The protein-protein interaction forces the CN thiolate into an unfavorable hydrophobic microenvironment that reduces its hydration and results in a remarkable acceleration of the thiol-disulfide exchange reactions by more than three orders of magnitude and also produces a measurable shift in the pKa of the CN . This mechanism of activation of the thiol disulfide exchange may help understand the reduction of Prx by alternative reductants involved in redox signaling.
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Affiliation(s)
- Sebastián F Villar
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Laura Corrales-González
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Belén Márquez de Los Santos
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Joaquín Dalla Rizza
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
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3
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Chavarría C, Ivagnes R, Zeida A, Piñeyro MD, Souza JM. Revisiting the role of 3-nitrotyrosine residues in the formation of alpha-synuclein oligomers and fibrils. Arch Biochem Biophys 2024; 752:109858. [PMID: 38104957 DOI: 10.1016/j.abb.2023.109858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Nitration of tyrosine residues in alpha-synuclein (a-syn) has been detected in different synucleinopathies, including Parkinson's disease. The potential role of 3-nitrotyrosine formation in a-syn, as an oxidative post-translational modification, is still elusive. In this work, we generated well-characterized tyrosine nitrated a-syn monomers and studied their capability to form oligomers and fibrils. We constructed tyrosine to phenylalanine mutants, containing a single tyrosine residue, a-syn mutant Y(125/133/136)F and Y(39/125/133)F) and assessed the impact in a-syn biophysical properties. Nitrated wild-type a-syn and the Y-F mutants, with one 3-nitrotyrosine residue in either the protein's N-terminal or C-terminal region, showed inhibition of fibril formation but retained the capacity of oligomer formation. The inhibition of a-syn fibrillation occurs even when an important amount of unmodified a-syn is still present. We characterized oligomers from both nitrated and non-nitrated forms of the wild-type protein and the mutant forms obtained. Our results indicate that the formation of 3-nitrotyrosine in a-syn could induce an off-pathway oligomer formation which may have an important impact in the development of synucleinopathies.
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Affiliation(s)
- Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - Rodrigo Ivagnes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - María Dolores Piñeyro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - José M Souza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay.
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Semelak JA, Zeida A, Foglia NO, Estrin DA. Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands. J Chem Theory Comput 2023; 19:6273-6293. [PMID: 37647166 DOI: 10.1021/acs.jctc.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The determination of minimum free energy pathways (MFEP) is one of the most widely used strategies to study reactive processes. For chemical reactions in complex environments, the combination of quantum mechanics (QM) with a molecular mechanics (MM) representation is usually necessary in a hybrid QM/MM framework. However, even within the QM/MM approximation, the affordable sampling of the phase space is, in general, quite restricted. To reduce drastically the computational cost of the simulations, several methods such as umbrella sampling require performing a priori a selection of a reaction coordinate. The quality of the computed results, in an affordable computational time, is intimately related to the reaction coordinate election which is, in general, a nontrivial task. In this work, we provide an approach to model reactive processes in complex environments that does not require the a priori selection of a reaction coordinate. The proposed methodology combines QM/MM simulations with an extrapolation of the nudged elastic bands (NEB) method to the free energy surface (FENEB). We present and apply our own FENEB scheme to optimize MFEP in different reactive processes, using QM/MM frameworks at semiempirical and density functional theory levels. Our implementation is based on performing the FENEB optimization by uncoupling the optimization of the band in a perpendicular and tangential direction. In each step, a full optimization with the spring force is performed, which guarantees that the images remain evenly distributed. The robustness of the method and the influence of sampling on the quality of the optimized MFEP and its associated free energy barrier are studied. We show that the FENEB method provides a good estimation of the reaction barrier even with relatively short simulation times, supporting that its combination with QM/MM frameworks provides an adequate tool to study chemical processes in complex environments.
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Affiliation(s)
- Jonathan A Semelak
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Ari Zeida
- 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
| | - Nicolás O Foglia
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
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5
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Mansilla S, Tórtora V, Pignataro F, Sastre S, Castro I, Chiribao ML, Robello C, Zeida A, Santos J, Castro L. Redox sensitive human mitochondrial aconitase and its interaction with frataxin: In vitro and in silico studies confirm that it takes two to tango. Free Radic Biol Med 2023; 197:71-84. [PMID: 36738801 DOI: 10.1016/j.freeradbiomed.2023.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/11/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Mitochondrial aconitase (ACO2) has been postulated as a redox sensor in the tricarboxylic acid cycle. Its high sensitivity towards reactive oxygen and nitrogen species is due to its particularly labile [4Fe-4S]2+ prosthetic group which yields an inactive [3Fe-4S]+ cluster upon oxidation. Moreover, ACO2 was found as a main oxidant target during aging and in pathologies where mitochondrial dysfunction is implied. Herein, we report the expression and characterization of recombinant human ACO2 and its interaction with frataxin (FXN), a protein that participates in the de novo biosynthesis of Fe-S clusters. A high yield of pure ACO2 (≥99%, 22 ± 2 U/mg) was obtained and kinetic parameters for citrate, isocitrate, and cis-aconitate were determined. Superoxide, carbonate radical, peroxynitrite, and hydrogen peroxide reacted with ACO2 with second-order rate constants of 108, 108, 105, and 102 M-1 s-1, respectively. Temperature-induced unfolding assessed by tryptophan fluorescence of ACO2 resulted in apparent melting temperatures of 51.1 ± 0.5 and 43.6 ± 0.2 °C for [4Fe-4S]2+ and [3Fe-4S]+ states of ACO2, sustaining lower thermal stability upon cluster oxidation. Differences in protein dynamics produced by the Fe-S cluster redox state were addressed by molecular dynamics simulations. Reactivation of [3Fe-4S]+-ACO2 by FXN was verified by activation assays and direct iron-dependent interaction was confirmed by protein-protein interaction ELISA and fluorescence spectroscopic assays. Multimer modeling and protein-protein docking predicted an ACO2-FXN complex where the metal ion binding region of FXN approaches the [3Fe-4S]+ cluster, supporting that FXN is a partner for reactivation of ACO2 upon oxidative cluster inactivation.
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Affiliation(s)
- Santiago Mansilla
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Verónica Tórtora
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Educación Médica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Florencia Pignataro
- Instituto de Biociencias, Biotecnología y Biología traslacional, Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Sastre
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Biofísica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ignacio Castro
- Instituto de Biociencias, Biotecnología y Biología traslacional, Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ma Laura Chiribao
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Institut Pasteur de Montevideo, Uruguay
| | - Carlos Robello
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Institut Pasteur de Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología traslacional, Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Laura Castro
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Cardozo G, Mastrogiovanni M, Zeida A, Viera N, Radi R, Reyes AM, Trujillo M. Mitochondrial Peroxiredoxin 3 Is Rapidly Oxidized and Hyperoxidized by Fatty Acid Hydroperoxides. Antioxidants (Basel) 2023; 12:antiox12020408. [PMID: 36829967 PMCID: PMC9952270 DOI: 10.3390/antiox12020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Human peroxiredoxin 3 (HsPrx3) is a thiol-based peroxidase responsible for the reduction of most hydrogen peroxide and peroxynitrite formed in mitochondria. Mitochondrial disfunction can lead to membrane lipoperoxidation, resulting in the formation of lipid-bound fatty acid hydroperoxides (LFA-OOHs) which can be released to become free fatty acid hydroperoxides (fFA-OOHs). Herein, we report that HsPrx3 is oxidized and hyperoxidized by fFA-OOHs including those derived from arachidonic acid and eicosapentaenoic acid peroxidation at position 15 with remarkably high rate constants of oxidation (>3.5 × 107 M-1s-1) and hyperoxidation (~2 × 107 M-1s-1). The endoperoxide-hydroperoxide PGG2, an intermediate in prostanoid synthesis, oxidized HsPrx3 with a similar rate constant, but was less effective in causing hyperoxidation. Biophysical methodologies suggest that HsPrx3 can bind hydrophobic structures. Indeed, molecular dynamic simulations allowed the identification of a hydrophobic patch near the enzyme active site that can allocate the hydroperoxide group of fFA-OOHs in close proximity to the thiolate in the peroxidatic cysteine. Simulations performed using available and herein reported kinetic data indicate that HsPrx3 should be considered a main target for mitochondrial fFA-OOHs. Finally, kinetic simulation analysis support that mitochondrial fFA-OOHs formation fluxes in the range of nM/s are expected to contribute to HsPrx3 hyperoxidation, a modification that has been detected in vivo under physiological and pathological conditions.
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Affiliation(s)
- Giuliana Cardozo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Nicolás Viera
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Aníbal M. Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
- Correspondence: (A.M.R.); (M.T.)
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
- Correspondence: (A.M.R.); (M.T.)
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7
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Cuevasanta E, Benchoam D, Semelak JA, Möller MN, Zeida A, Trujillo M, Alvarez B, Estrin DA. Possible molecular basis of the biochemical effects of cysteine-derived persulfides. Front Mol Biosci 2022; 9:975988. [PMID: 36213129 PMCID: PMC9538486 DOI: 10.3389/fmolb.2022.975988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/15/2022] [Indexed: 12/03/2022] Open
Abstract
Persulfides (RSSH/RSS−) are species closely related to thiols (RSH/RS−) and hydrogen sulfide (H2S/HS−), and can be formed in biological systems in both low and high molecular weight cysteine-containing compounds. They are key intermediates in catabolic and biosynthetic processes, and have been proposed to participate in the transduction of hydrogen sulfide effects. Persulfides are acidic, more acidic than thiols, and the persulfide anions are expected to be the predominant species at neutral pH. The persulfide anion has high nucleophilicity, due in part to the alpha effect, i.e., the increased reactivity of a nucleophile when the neighboring atom has high electron density. In addition, persulfides have electrophilic character, a property that is absent in both thiols and hydrogen sulfide. In this article, the biochemistry of persulfides is described, and the possible ways in which the formation of a persulfide could impact on the properties of the biomolecule involved are discussed.
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Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Dayana Benchoam
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Jonathan A. Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
| | - Matías N. Möller
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
- *Correspondence: Darío A. Estrin,
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9
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Freeman SL, Skafar V, Kwon H, Fielding AJ, Moody PCE, Martínez A, Issoglio FM, Inchausti L, Smircich P, Zeida A, Piacenza L, Radi R, Raven EL. Crystal structure of Trypanosoma cruzi heme peroxidase and characterization of its substrate specificity and compound I intermediate. J Biol Chem 2022; 298:102204. [PMID: 35772495 PMCID: PMC9358470 DOI: 10.1016/j.jbc.2022.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022] Open
Abstract
The protozoan parasite Trypanosoma cruzi is the causative agent of American trypanosomiasis, otherwise known as Chagas disease. To survive in the host, the T. cruzi parasite needs antioxidant defense systems. One of these is a hybrid heme peroxidase, the T. cruzi ascorbate peroxidase-cytochrome c peroxidase enzyme (TcAPx-CcP). TcAPx-CcP has high sequence identity to members of the class I peroxidase family, notably ascorbate peroxidase (APX) and cytochrome c peroxidase (CcP), as well as a mitochondrial peroxidase from Leishmania major (LmP). The aim of this work was to solve the structure and examine the reactivity of the TcAPx-CcP enzyme. Low temperature electron paramagnetic resonance spectra support the formation of an exchange-coupled [Fe(IV)=O Trp233•+] compound I radical species, analogous to that used in CcP and LmP. We demonstrate that TcAPx-CcP is similar in overall structure to APX and CcP, but there are differences in the substrate-binding regions. Furthermore, the electron transfer pathway from cytochrome c to the heme in CcP and LmP is preserved in the TcAPx-CcP structure. Integration of steady state kinetic experiments, molecular dynamic simulations, and bioinformatic analyses indicates that TcAPx-CcP preferentially oxidizes cytochrome c but is still competent for oxidization of ascorbate. The results reveal that TcAPx-CcP is a credible cytochrome c peroxidase, which can also bind and use ascorbate in host cells, where concentrations are in the millimolar range. Thus, kinetically and functionally TcAPx-CcP can be considered a hybrid peroxidase.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Vera Skafar
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Hanna Kwon
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | - Alistair J Fielding
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moore University, Liverpool, United Kingdom
| | - Peter C E Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | - Alejandra Martínez
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico M Issoglio
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Lucas Inchausti
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay; Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay; Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Lucía Piacenza
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol, United Kingdom.
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10
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Affiliation(s)
- Lucìa Piacenza
- Departamento de Bioquímica, Facultad de Medicina; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
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11
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Shi Y, Zeida A, Edwards CE, Mallory ML, Sastre S, Machado MR, Pickles RJ, Fu L, Liu K, Yang J, Baric RS, Boucher RC, Radi R, Carroll KS. Thiol-based chemical probes exhibit antiviral activity against SARS-CoV-2 via allosteric disulfide disruption in the spike glycoprotein. Proc Natl Acad Sci U S A 2022; 119:e2120419119. [PMID: 35074895 PMCID: PMC8833197 DOI: 10.1073/pnas.2120419119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/13/2021] [Indexed: 01/07/2023] Open
Abstract
The development of small-molecules targeting different components of SARS-CoV-2 is a key strategy to complement antibody-based treatments and vaccination campaigns in managing the COVID-19 pandemic. Here, we show that two thiol-based chemical probes that act as reducing agents, P2119 and P2165, inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, the angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity to the reduction of key disulfides, specifically by disruption of the Cys379-Cys432 and Cys391-Cys525 pairs distal to the receptor binding motif in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol-reducing moiety pointed directly toward Cys432. These collective findings establish the vulnerability of human coronaviruses to thiol-based chemical probes and lay the groundwork for developing compounds of this class, as a strategy to inhibit the SARS-CoV-2 infection by shifting the spike glycoprotein redox scaffold.
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MESH Headings
- Allosteric Regulation
- Amino Alcohols/chemistry
- Amino Alcohols/pharmacology
- Angiotensin-Converting Enzyme 2/antagonists & inhibitors
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Antiviral Agents/chemistry
- Antiviral Agents/pharmacology
- Binding Sites
- COVID-19/virology
- Cell Line
- Disulfides/antagonists & inhibitors
- Disulfides/chemistry
- Disulfides/metabolism
- Dose-Response Relationship, Drug
- Humans
- Molecular Docking Simulation
- Nasal Mucosa/drug effects
- Nasal Mucosa/metabolism
- Nasal Mucosa/virology
- Oxidation-Reduction
- Phenyl Ethers/chemistry
- Phenyl Ethers/pharmacology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/antagonists & inhibitors
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Sulfhydryl Compounds/chemistry
- Sulfhydryl Compounds/pharmacology
- COVID-19 Drug Treatment
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Affiliation(s)
- Yunlong Shi
- Department of Chemistry, Scripps Research, Jupiter, FL 33458
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina and Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Santiago Sastre
- Departamento de Bioquímica, Facultad de Medicina and Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Matías R Machado
- Protein Engineering Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Raymond J Pickles
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina and Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay;
| | - Kate S Carroll
- Department of Chemistry, Scripps Research, Jupiter, FL 33458;
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12
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Scochera F, Zerbetto De Palma G, Canessa Fortuna A, Chevriau J, Toriano R, Soto G, Zeida A, Alleva K. PIP aquaporin pH sensing is regulated by the length and charge of the C-terminal region. FEBS J 2021; 289:246-261. [PMID: 34293244 DOI: 10.1111/febs.16134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/21/2021] [Indexed: 11/27/2022]
Abstract
Plant PIP aquaporins play a central role in controlling plant water status. The current structural model for PIP pH-gating states that the main pH sensor is located in loopD and that all the mobile cytosolic elements participate in a complex interaction network that ensures the closed structure. However, the precise participation of the last part of the C-terminal domain (CT) in PIP pH gating remains unknown. This last part has not been resolved in PIP crystal structures and is a key difference between PIP1 and PIP2 paralogues. Here, by a combined experimental and computational approach, we provide data about the role of CT in pH gating of Beta vulgaris PIP. We demonstrate that the length of CT and the positive charge located among its last residues modulate the pH at which the open/closed transition occurs. We also postulate a molecular-based mechanism for the differential pH sensing in PIP homo- or heterotetramers by performing atomistic molecular dynamics simulations (MDS) on complete models of PIP tetramers. Our findings show that the last part of CT can affect the environment of loopD pH sensors in the closed state. Results presented herein contribute to the understanding of how the characteristics of CT in PIP channels play a crucial role in determining the pH at which water transport through these channels is blocked, highlighting the relevance of the differentially conserved very last residues in PIP1 and PIP2 paralogues.
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Affiliation(s)
- Florencia Scochera
- Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Universidad de Buenos Aires, Argentina
| | - Gerardo Zerbetto De Palma
- Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Universidad de Buenos Aires, Argentina.,Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Facultad de Farmacia y Bioquímica, CONICET, Universidad de Buenos Aires, Argentina.,Instituto de Biotecnología, Universidad Nacional de Hurlingham, Villa Tesei, Argentina
| | - Agustina Canessa Fortuna
- Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Universidad de Buenos Aires, Argentina
| | - Jonathan Chevriau
- Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Facultad de Farmacia y Bioquímica, CONICET, Universidad de Buenos Aires, Argentina
| | - Roxana Toriano
- Facultad de Medicina, CONICET, Instituto de Fisiología y Biofísica "Bernardo Houssay" (IFIBIO "Houssay"), Universidad de Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina.,Instituto de Genética (INTA), Buenos Aires, Argentina
| | - Ari Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (Ceinbio), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Karina Alleva
- Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Universidad de Buenos Aires, Argentina.,Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Facultad de Farmacia y Bioquímica, CONICET, Universidad de Buenos Aires, Argentina
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13
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Demicheli V, Tomasina F, Sastre S, Zeida A, Tórtora V, Lima A, Batthyány C, Radi R. Cardiolipin interactions with cytochrome c increase tyrosine nitration yields and site-specificity. Arch Biochem Biophys 2021; 703:108824. [PMID: 33675813 DOI: 10.1016/j.abb.2021.108824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
The interaction between cytochrome c and cardiolipin is a relevant process in the mitochondrial redox homeostasis, playing roles in the mechanism of electron transfer to cytochrome c oxidase and also modulating cytochrome c conformation, reactivity and function. Peroxynitrite is a widespread nitrating agent formed in mitochondria under oxidative stress conditions, and can result in the formation of tyrosine nitrated cytochrome c. Some of the nitro-cytochrome c species undergo conformational changes at physiological pH and increase its peroxidase activity. In this work we evaluated the influence of cardiolipin on peroxynitrite-mediated cytochrome c nitration yields and site-specificity. Our results show that cardiolipin enhances cytochrome c nitration by peroxynitrite and targets it to heme-adjacent Tyr67. Cytochrome c nitration also modifies the affinity of protein with cardiolipin. Using a combination of experimental techniques and computer modeling, it is concluded that structural modifications in the Tyr67 region are responsible for the observed changes in protein-derived radical and tyrosine nitration levels, distribution of nitrated proteoforms and affinity to cardiolipin. Increased nitration of cytochrome c in presence of cardiolipin within mitochondria and the gain of peroxidatic activity could then impact events such as the onset of apoptosis and other processes related to the disruption of mitochondrial redox homeostasis.
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Affiliation(s)
- Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Florencia Tomasina
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Santiago Sastre
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Verónica Tórtora
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Analía Lima
- Institut Pasteur de Montevideo, Uruguay; Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Carlos Batthyány
- Institut Pasteur de Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.
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14
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Blaustein M, Piegari E, Martínez Calejman C, Vila A, Amante A, Manese MV, Zeida A, Abrami L, Veggetti M, Guertin DA, van der Goot FG, Corvi MM, Colman-Lerner A. Akt Is S-Palmitoylated: A New Layer of Regulation for Akt. Front Cell Dev Biol 2021; 9:626404. [PMID: 33659252 PMCID: PMC7917195 DOI: 10.3389/fcell.2021.626404] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
The protein kinase Akt/PKB participates in a great variety of processes, including translation, cell proliferation and survival, as well as malignant transformation and viral infection. In the last few years, novel Akt posttranslational modifications have been found. However, how these modification patterns affect Akt subcellular localization, target specificity and, in general, function is not thoroughly understood. Here, we postulate and experimentally demonstrate by acyl-biotin exchange (ABE) assay and 3H-palmitate metabolic labeling that Akt is S-palmitoylated, a modification related to protein sorting throughout subcellular membranes. Mutating cysteine 344 into serine blocked Akt S-palmitoylation and diminished its phosphorylation at two key sites, T308 and T450. Particularly, we show that palmitoylation-deficient Akt increases its recruitment to cytoplasmic structures that colocalize with lysosomes, a process stimulated during autophagy. Finally, we found that cysteine 344 in Akt1 is important for proper its function, since Akt1-C344S was unable to support adipocyte cell differentiation in vitro. These results add an unexpected new layer to the already complex Akt molecular code, improving our understanding of cell decision-making mechanisms such as cell survival, differentiation and death.
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Affiliation(s)
- Matías Blaustein
- Departamento de Fisiología, Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UBA, Buenos Aires, Argentina.,Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Estefanía Piegari
- Departamento de Fisiología, Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UBA, Buenos Aires, Argentina
| | - Camila Martínez Calejman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Antonella Vila
- Departamento de Fisiología, Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UBA, Buenos Aires, Argentina.,Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Analía Amante
- Departamento de Fisiología, Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UBA, Buenos Aires, Argentina.,Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Manese
- Laboratorio de bioquímica y biología celular de parásitos, Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) - CONICET, Chascomús, Argentina
| | - Ari Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laurence Abrami
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mariela Veggetti
- Departamento de Fisiología, Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UBA, Buenos Aires, Argentina
| | - David A Guertin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.,Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States.,Lei Weibo Institute for Rare Diseases, University of Massachusetts Medical School, Worcester, MA, United States
| | - F Gisou van der Goot
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - María Martha Corvi
- Laboratorio de bioquímica y biología celular de parásitos, Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) - CONICET, Chascomús, Argentina
| | - Alejandro Colman-Lerner
- Departamento de Fisiología, Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UBA, Buenos Aires, Argentina
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15
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Benchoam D, Semelak JA, Cuevasanta E, Mastrogiovanni M, Grassano JS, Ferrer-Sueta G, Zeida A, Trujillo M, Möller MN, Estrin DA, Alvarez B. Acidity and nucleophilic reactivity of glutathione persulfide. J Biol Chem 2020; 295:15466-15481. [PMID: 32873707 DOI: 10.1074/jbc.ra120.014728] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Persulfides (RSSH/RSS-) participate in sulfur trafficking and metabolic processes, and are proposed to mediate the signaling effects of hydrogen sulfide (H2S). Despite their growing relevance, their chemical properties are poorly understood. Herein, we studied experimentally and computationally the formation, acidity, and nucleophilicity of glutathione persulfide (GSSH/GSS-), the derivative of the abundant cellular thiol glutathione (GSH). We characterized the kinetics and equilibrium of GSSH formation from glutathione disulfide and H2S. A pKa of 5.45 for GSSH was determined, which is 3.49 units below that of GSH. The reactions of GSSH with the physiologically relevant electrophiles peroxynitrite and hydrogen peroxide, and with the probe monobromobimane, were studied and compared with those of thiols. These reactions occurred through SN2 mechanisms. At neutral pH, GSSH reacted faster than GSH because of increased availability of the anion and, depending on the electrophile, increased reactivity. In addition, GSS- presented higher nucleophilicity with respect to a thiolate with similar basicity. This can be interpreted in terms of the so-called α effect, i.e. the increased reactivity of a nucleophile when the atom adjacent to the nucleophilic atom has high electron density. The magnitude of the α effect correlated with the Brønsted nucleophilic factor, βnuc, for the reactions with thiolates and with the ability of the leaving group. Our study constitutes the first determination of the pKa of a biological persulfide and the first examination of the α effect in sulfur nucleophiles, and sheds light on the chemical basis of the biological properties of persulfides.
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Affiliation(s)
- Dayana Benchoam
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Jonathan A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Argentina
| | - Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Juan S Grassano
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Argentina
| | - Gerardo Ferrer-Sueta
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Matías N Möller
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Argentina.
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.
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16
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Valera MJ, Zeida A, Boido E, Beltran G, Torija MJ, Mas A, Radi R, Dellacassa E, Carrau F. Genetic and transcriptomic evidences suggest ARO10 genes are involved in benzenoid biosynthesis by yeast. Yeast 2020; 37:427-435. [PMID: 32638443 DOI: 10.1002/yea.3508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/09/2020] [Accepted: 07/03/2020] [Indexed: 12/27/2022] Open
Abstract
Benzenoids are compounds associated with floral and fruity flavours in flowers, fruits and leaves and present a role in hormonal signalling in plants. These molecules are produced by the phenyl ammonia lyase pathway. However, some yeasts can also synthesize them from aromatic amino acids using an alternative pathway that remains unknown. Hanseniaspora vineae can produce benzenoids at levels up to two orders of magnitude higher than Saccharomyces species, so it is a model microorganism for studying benzenoid biosynthesis pathways in yeast. According to their genomes, several enzymes have been proposed to be involved in a mandelate pathway similar to that described for some prokaryotic cells. Among them, the ARO10 gene product could present benzoylformate decarboxylase activity. This enzyme catalyses the decarboxylation of benzoylformate into benzaldehyde at the end of the mandelate pathway in benzyl alcohol formation. Two homologous genes of ARO10 were found in the two sequenced H. vineae strains. In this study, nine other H. vineae strains were analysed to detect the presence and per cent homology of ARO10 sequences by PCR using specific primers designed for this species. Also, the copy number of the genes was estimated by quantitative PCR. To verify the relation of ARO10 with the production of benzyl alcohol during fermentation, a deletion mutant in the ARO10 gene of Saccharomyces cerevisiae was used. The two HvARO10 paralogues were analysed and compared with other α-ketoacid decarboxylases at the sequence and structural level.
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Affiliation(s)
- Maria Jose Valera
- Facultad de Quimica, Food Science and Technology Department, Enology and Fermentation Biotechnology Area, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Boido
- Facultad de Quimica, Food Science and Technology Department, Enology and Fermentation Biotechnology Area, Universidad de la República, Montevideo, Uruguay
| | - Gemma Beltran
- Department of Biochemistry and Biotechnology, Biotecnología Enológica, Universitat Rovira i Virgili, Tarragona, Spain
| | - María Jesús Torija
- Department of Biochemistry and Biotechnology, Biotecnología Enológica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Albert Mas
- Department of Biochemistry and Biotechnology, Biotecnología Enológica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Rafael Radi
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Dellacassa
- Departamento de Química Orgánica, Laboratorio de Biotecnología de Aromas, Universidad de la República, Montevideo, Uruguay
| | - Francisco Carrau
- Facultad de Quimica, Food Science and Technology Department, Enology and Fermentation Biotechnology Area, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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17
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Domingos RM, Teixeira RD, Zeida A, Agudelo WA, Alegria TGP, da Silva Neto JF, Vieira PS, Murakami MT, Farah CS, Estrin DA, Netto LES. Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Renato M. Domingos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Raphael D. Teixeira
- Departamento de Biociências, Instituto de Quı́mica, Universidade de São Paulo, 05508-000 Sao Paulo, Brazil
| | - Ari Zeida
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - William A. Agudelo
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Thiago G. P. Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - José F. da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Biociências, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900 São Paulo, Brazil
| | - Plínio S. Vieira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
| | - Mario T. Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
| | - Chuck S. Farah
- Departamento de Biociências, Instituto de Quı́mica, Universidade de São Paulo, 05508-000 Sao Paulo, Brazil
| | - Dario A. Estrin
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Luis E. S. Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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18
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Vazquez DS, Zeida A, Agudelo WA, Montes MR, Ferrer-Sueta G, Santos J. Exploring the conformational transition between the fully folded and locally unfolded substates of Escherichia coli thiol peroxidase. Phys Chem Chem Phys 2020; 22:9518-9533. [DOI: 10.1039/d0cp00140f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Temporal acquisition of the fully folded conformational substate of the Escherichia coli thiol peroxidase by accelerated molecular dynamics simulations.
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Affiliation(s)
- Diego S. Vazquez
- Laboratorio de Expresión y Plegado de Proteínas
- Departamento de Ciencia y Tecnología
- Universidad Nacional de Quilmes
- Buenos Aires
- Argentina
| | - Ari Zeida
- Departamento de Bioquímica y Centro de Investigaciones Biomédicas (CEINBIO)
- Facultad de Medicina
- Universidad de la República
- Montevideo
- Uruguay
| | - William A. Agudelo
- Fundación Instituto de Inmunología de Colombia (FIDIC)
- Bogotá D.C
- Colombia
| | - Mónica R. Montes
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB)
- “Prof. Dr Alejandro C. Paladini”
- Universidad de Buenos Aires and CONICET
- Ciudad Autónoma de Buenos Aires
- Argentina
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica
- Instituto de Química Biológica and CEINBIO
- Facultad de Ciencias
- Universidad de la República
- Montevideo
| | - Javier Santos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Ciudad Autónoma de Buenos Aires
- Argentina
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3)
- Departamento de Fisiología y Biología Molecular y Celular
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19
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Semelak JA, Battistini F, Radi R, Trujillo M, Zeida A, Estrin DA. Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide. J Chem Inf Model 2019; 60:843-853. [PMID: 31718175 DOI: 10.1021/acs.jcim.9b00817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, we employ a multiscale quantum-classical mechanics (QM/MM) scheme to investigate the chemical reactivity of sulfenic acids toward hydrogen peroxide, both in aqueous solution and in the protein environment of the peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE). The reaction of oxidation of cysteine with hydrogen peroxides, catalyzed by peroxiredoxins, is usually accelerated several orders of magnitude in comparison with the analogous reaction in solution. The resulting cysteine sulfenic acid is then reduced in other steps of the catalytic cycle, recovering the original thiol. However, under some conditions, the sulfenic acid can react with another equivalent of oxidant to form a sulfinic acid. This process is called overoxidation and has been associated with redox signaling. Herein, we employed a multiscale scheme based on density function theory calculations coupled to the classical AMBER force field, developed in our group, to establish the molecular basis of thiol overoxidation by hydrogen peroxide. Our results suggest that residues that play key catalytic roles in the oxidation of MtAhpE are not relevant in the overoxidation process. Indeed, the calculations propose that the process is unfavored by this particular enzyme microenvironment.
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Affiliation(s)
- J A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
| | - F Battistini
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , 08028 Barcelona , Spain
| | - R Radi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - M Trujillo
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - A Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - D A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
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20
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Abstract
Life on Earth evolved in the presence of hydrogen peroxide, and other peroxides also emerged before and with the rise of aerobic metabolism. They were considered only as toxic byproducts for many years. Nowadays, peroxides are also regarded as metabolic products that play essential physiological cellular roles. Organisms have developed efficient mechanisms to metabolize peroxides, mostly based on two kinds of redox chemistry, catalases/peroxidases that depend on the heme prosthetic group to afford peroxide reduction and thiol-based peroxidases that support their redox activities on specialized fast reacting cysteine/selenocysteine (Cys/Sec) residues. Among the last group, glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) are the most widespread and abundant families, and they are the leitmotif of this review. After presenting the properties and roles of different peroxides in biology, we discuss the chemical mechanisms of peroxide reduction by low molecular weight thiols, Prxs, GPxs, and other thiol-based peroxidases. Special attention is paid to the catalytic properties of Prxs and also to the importance and comparative outlook of the properties of Sec and its role in GPxs. To finish, we describe and discuss the current views on the activities of thiol-based peroxidases in peroxide-mediated redox signaling processes.
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Affiliation(s)
| | | | | | | | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 2160 Buenos Aires , Argentina
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21
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Cuevasanta E, Benchoam D, Ferrer-Sueta G, Zeida A, Denicola A, Alvarez B, Möller MN. Commentary on "Using resonance synchronous spectroscopy to characterize the reactivity and electrophilicity of biologically relevant sulfane sulfur". Evidence that the methodology is inadequate because it only measures unspecific light scattering. Redox Biol 2019; 26:101281. [PMID: 31351822 PMCID: PMC6831858 DOI: 10.1016/j.redox.2019.101281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 11/25/2022] Open
Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay; Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay.
| | - Dayana Benchoam
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay
| | - Gerardo Ferrer-Sueta
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay
| | - Ana Denicola
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay
| | - Matías N Möller
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, 11800, Uruguay; Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay.
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22
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Cuevasanta E, Reyes AM, Zeida A, Mastrogiovanni M, De Armas MI, Radi R, Alvarez B, Trujillo M. Kinetics of formation and reactivity of the persulfide in the one-cysteine peroxiredoxin from Mycobacterium tuberculosis. J Biol Chem 2019; 294:13593-13605. [PMID: 31311857 DOI: 10.1074/jbc.ra119.008883] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/12/2019] [Indexed: 12/20/2022] Open
Abstract
Hydrogen sulfide (H2S) participates in prokaryotic metabolism and is associated with several physiological functions in mammals. H2S reacts with oxidized thiol derivatives (i.e. disulfides and sulfenic acids) and thereby forms persulfides, which are plausible transducers of the H2S-mediated signaling effects. The one-cysteine peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE-SH) reacts fast with hydroperoxides, forming a stable sulfenic acid (MtAhpE-SOH), which we chose here as a model to study the interactions between H2S and peroxiredoxins (Prx). MtAhpE-SOH reacted with H2S, forming a persulfide (MtAhpE-SSH) detectable by mass spectrometry. The rate constant for this reaction was (1.4 ± 0.2) × 103 m-1 s-1 (pH 7.4, 25 °C), six times higher than that reported for the reaction with the main low-molecular-weight thiol in M. tuberculosis, mycothiol. H2S was able to complete the catalytic cycle of MtAhpE and, according to kinetic considerations, it could represent an alternative substrate in M. tuberculosis. MtAhpE-SSH reacted 43 times faster than did MtAhpE-SH with the unspecific electrophile 4,4'-dithiodipyridine, a disulfide that exhibits no preferential reactivity with peroxidatic cysteines, but MtAhpE-SSH was less reactive toward specific Prx substrates such as hydrogen peroxide and peroxynitrite. According to molecular dynamics simulations, this loss of specific reactivity could be explained by alterations in the MtAhpE active site. MtAhpE-SSH could transfer its sulfane sulfur to a low-molecular-weight thiol, a process likely facilitated by the low pKa of the leaving thiol MtAhpE-SH, highlighting the possibility that Prx participates in transpersulfidation. The findings of our study contribute to the understanding of persulfide formation and reactivity.
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Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay .,Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Aníbal M Reyes
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay .,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María Inés De Armas
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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23
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Machado MR, Zeida A, Darré L, Pantano S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019; 9:20180085. [PMID: 31065347 PMCID: PMC6501346 DOI: 10.1098/rsfs.2018.0085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
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Affiliation(s)
- Matías R. Machado
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Institut Pasteur de Montevideo, Functional Genomics Unit, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
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Canessa Fortuna A, Zerbetto De Palma G, Aliperti Car L, Armentia L, Vitali V, Zeida A, Estrin DA, Alleva K. Gating in plant plasma membrane aquaporins: the involvement of leucine in the formation of a pore constriction in the closed state. FEBS J 2019; 286:3473-3487. [DOI: 10.1111/febs.14922] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/25/2019] [Accepted: 05/08/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Agustina Canessa Fortuna
- Facultad de Farmacia y Bioquímica Instituto de Química y Fisicoquímica Biológica (IQUIFIB) CONICET Universidad de Buenos Aires Argentina
- Departamento de Fisicomatemática Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Argentina
| | - Gerardo Zerbetto De Palma
- Facultad de Farmacia y Bioquímica Instituto de Química y Fisicoquímica Biológica (IQUIFIB) CONICET Universidad de Buenos Aires Argentina
- Departamento de Fisicomatemática Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Argentina
- Instituo de Biotecnología Universidad Nacional de Hurlingham Villa Tesei Argentina
| | - Lucio Aliperti Car
- Laboratorio de Fisiología de Proteínas IQUIBICEN y Facultad de Ciencias Exactas y Naturales CONICET Universidad de Buenos Aires Argentina
| | - Luciano Armentia
- Departamento de Fisicomatemática Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Argentina
| | - Victoria Vitali
- Facultad de Farmacia y Bioquímica Instituto de Química y Fisicoquímica Biológica (IQUIFIB) CONICET Universidad de Buenos Aires Argentina
- Departamento de Fisicomatemática Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Argentina
| | - Ari Zeida
- Departamento de Bioquímica Facultad de Medicina Center for Free Radical and Biomedical Research Universidad de la República Montevideo Uruguay
| | - Darío A. Estrin
- DQIAQF‐INQUIMAE Facultad de Ciencias Exactas y Naturales CONICET Universidad de Buenos Aires Argentina
| | - Karina Alleva
- Facultad de Farmacia y Bioquímica Instituto de Química y Fisicoquímica Biológica (IQUIFIB) CONICET Universidad de Buenos Aires Argentina
- Departamento de Fisicomatemática Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Argentina
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25
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Pedron FN, Bartesaghi S, Estrin DA, Radi R, Zeida A. A computational investigation of the reactions of tyrosyl, tryptophanyl, and cysteinyl radicals with nitric oxide and molecular oxygen. Free Radic Res 2018; 53:18-25. [DOI: 10.1080/10715762.2018.1541322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Federico N. Pedron
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Buenos Aires, Argentina
| | - Silvina Bartesaghi
- Departamento de Bioquímica, Universidad de la República, Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Universidad de la República, Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Bioquímica, Universidad de la República, Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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26
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Marcolongo JP, Zeida A, Semelak JA, Foglia NO, Morzan UN, Estrin DA, González Lebrero MC, Scherlis DA. Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code. Front Chem 2018; 6:70. [PMID: 29619365 PMCID: PMC5871697 DOI: 10.3389/fchem.2018.00070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/05/2018] [Indexed: 12/13/2022] Open
Abstract
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
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Affiliation(s)
- Juan P Marcolongo
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ari Zeida
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jonathan A Semelak
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolás O Foglia
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Uriel N Morzan
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario A Estrin
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariano C González Lebrero
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Damián A Scherlis
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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27
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Marcolongo JP, Zeida A, Slep LD, Olabe JA. Thionitrous Acid/Thionitrite and Perthionitrite Intermediates in the “Crosstalk” of NO and H 2 S. ADVANCES IN INORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.adioch.2017.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Reyes AM, Vazquez DS, Zeida A, Hugo M, Piñeyro MD, De Armas MI, Estrin D, Radi R, Santos J, Trujillo M. PrxQ B from Mycobacterium tuberculosis is a monomeric, thioredoxin-dependent and highly efficient fatty acid hydroperoxide reductase. Free Radic Biol Med 2016; 101:249-260. [PMID: 27751911 DOI: 10.1016/j.freeradbiomed.2016.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/16/2016] [Accepted: 10/06/2016] [Indexed: 12/23/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is the intracellular bacterium responsible for tuberculosis disease (TD). Inside the phagosomes of activated macrophages, M. tuberculosis is exposed to cytotoxic hydroperoxides such as hydrogen peroxide, fatty acid hydroperoxides and peroxynitrite. Thus, the characterization of the bacterial antioxidant systems could facilitate novel drug developments. In this work, we characterized the product of the gene Rv1608c from M. tuberculosis, which according to sequence homology had been annotated as a putative peroxiredoxin of the peroxiredoxin Q subfamily (PrxQ B from M. tuberculosis or MtPrxQ B). The protein has been reported to be essential for M. tuberculosis growth in cholesterol-rich medium. We demonstrated the M. tuberculosis thioredoxin B/C-dependent peroxidase activity of MtPrxQ B, which acted as a two-cysteine peroxiredoxin that could function, although less efficiently, using a one-cysteine mechanism. Through steady-state and competition kinetic analysis, we proved that the net forward rate constant of MtPrxQ B reaction was 3 orders of magnitude faster for fatty acid hydroperoxides than for hydrogen peroxide (3×106vs 6×103M-1s-1, respectively), while the rate constant of peroxynitrite reduction was (0.6-1.4) ×106M-1s-1 at pH 7.4. The enzyme lacked activity towards cholesterol hydroperoxides solubilized in sodium deoxycholate. Both thioredoxin B and C rapidly reduced the oxidized form of MtPrxQ B, with rates constants of 0.5×106 and 1×106M-1s-1, respectively. Our data indicated that MtPrxQ B is monomeric in solution both under reduced and oxidized states. In spite of the similar hydrodynamic behavior the reduced and oxidized forms of the protein showed important structural differences that were reflected in the protein circular dichroism spectra.
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Affiliation(s)
- Aníbal M Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Diego S Vazquez
- Instituto de Química y Físicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires and CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martín Hugo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - M Dolores Piñeyro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Unidad de Biología Molecular-Institut Pasteur Montevideo, Montevideo, Uruguay
| | - María Inés De Armas
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Darío Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Javier Santos
- Instituto de Química y Físicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Universidad de Buenos Aires and CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay.
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Marcolongo JP, Morzan UN, Zeida A, Scherlis DA, Olabe JA. Nitrosodisulfide [S 2NO] - (perthionitrite) is a true intermediate during the "cross-talk" of nitrosyl and sulfide. Phys Chem Chem Phys 2016; 18:30047-30052. [PMID: 27774554 DOI: 10.1039/c6cp06314d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nitrosodisulfide S2NO- is a controversial intermediate in the reactions of S-nitrosothiols with HS- that produce NO and HNO. QM-MM molecular dynamics simulations combined with TD-DFT analysis contribute to a clear identification of S2NO- in water, acetone and acetonitrile, accounting for the UV-Vis signatures and broadening the mechanistic picture of N/S signaling in biochemistry.
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Affiliation(s)
- Juan P Marcolongo
- Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina.
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30
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Issoglio FM, Campolo N, Zeida A, Grune T, Radi R, Estrin DA, Bartesaghi S. Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations. Biochemistry 2016; 55:5907-5916. [DOI: 10.1021/acs.biochem.6b00822] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Federico M. Issoglio
- Departamento
de Química Inorgánica, Analítica y Química-Física
and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Ari Zeida
- Departamento
de Química Inorgánica, Analítica y Química-Física
and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Tilman Grune
- German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, Department of Molecular Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | | | - Dario A. Estrin
- Departamento
de Química Inorgánica, Analítica y Química-Física
and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvina Bartesaghi
- Departamento
de Educación Médica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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31
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Bringas M, Semelak J, Zeida A, Estrin DA. Theoretical investigation of the mechanism of nitroxyl decomposition in aqueous solution. J Inorg Biochem 2016; 162:102-108. [DOI: 10.1016/j.jinorgbio.2016.06.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 11/24/2022]
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Ramírez CL, Zeida A, Jara GE, Roitberg AE, Martí MA. Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm. J Chem Theory Comput 2015; 10:4609-17. [PMID: 26588154 DOI: 10.1021/ct500672d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accurate and well converged results at a moderate computational cost is still an open challenge. Here, we present and thoroughly test a hybrid differential relaxation algorithm (HyDRA), which allows faster equilibration of the classical environment during the nonequilibrium steering of a (bio)chemical reaction. We show and discuss why (in the context of Jarzynski's Relationship) this method allows obtaining accurate free energy profiles with smaller number of independent trajectories and/or faster pulling speeds, thus reducing the overall computational cost. Moreover, due to the availability and straightforward implementation of the method, we expect that it will foster theoretical studies of key enzymatic processes.
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Affiliation(s)
- Claudia L Ramírez
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
| | - Ari Zeida
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
| | - Gabriel E Jara
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
| | - Adrián E Roitberg
- Quantum Theory Project and Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Marcelo A Martí
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
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33
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Zeida A, Reyes AM, Lichtig P, Hugo M, Vazquez DS, Santos J, González Flecha FL, Radi R, Estrin DA, Trujillo M. Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis. Biochemistry 2015; 54:7237-47. [DOI: 10.1021/acs.biochem.5b00758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aníbal M. Reyes
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Martín Hugo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | | | | | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Madia Trujillo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
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Cuevasanta E, Zeida A, Carballal S, Wedmann R, Morzan UN, Trujillo M, Radi R, Estrin DA, Filipovic MR, Alvarez B. Insights into the mechanism of the reaction between hydrogen sulfide and peroxynitrite. Free Radic Biol Med 2015; 80:93-100. [PMID: 25555671 DOI: 10.1016/j.freeradbiomed.2014.12.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022]
Abstract
Hydrogen sulfide and peroxynitrite are endogenously generated molecules that participate in biologically relevant pathways. A revision of the kinetic features of the reaction between peroxynitrite and hydrogen sulfide revealed a complex process. The rate constant of peroxynitrite decay, (6.65 ± 0.08) × 10(3) M(-1) s(-1) in 0.05 M sodium phosphate buffer (pH 7.4, 37°C), was affected by the concentration of buffer. Theoretical modeling suggested that, as in the case of thiols, the reaction is initiated by the nucleophilic attack of HS(-) on the peroxide group of ONOOH by a typical bimolecular nucleophilic substitution, yielding HSOH and NO2(-). In contrast to thiols, the reaction then proceeds to the formation of distinct products that absorb near 408 nm. Experiments in the presence of scavengers and carbon dioxide showed that free radicals are unlikely to be involved in the formation of these products. The results are consistent with product formation involving the reactive intermediate HSSH and its fast reaction with a second peroxynitrite molecule. Mass spectrometry and UV-Vis absorption spectra predictions suggest that at least one of the products is HSNO2 or its isomer HSONO.
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Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Química Inorgánica, Analítica, y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Sebastián Carballal
- Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Rudolf Wedmann
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Uriel N Morzan
- Departamento de Química Inorgánica, Analítica, y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Madia Trujillo
- Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Rafael Radi
- Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica, y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Milos R Filipovic
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, 91058 Erlangen, Germany.
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Universidad de la República, 11800 Montevideo, Uruguay.
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35
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Zeida A, Reyes AM, Lebrero MCG, Radi R, Trujillo M, Estrina DA. The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step. Chem Commun (Camb) 2014; 50:10070-3. [PMID: 25045760 PMCID: PMC4336542 DOI: 10.1039/c4cc02899f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes. The first step in the catalytic cycle of all Prxs is the oxidation of a cysteine residue to sulfenic acid, which occurs 10(3)-10(7) times faster than in free cysteine. We present an experimental kinetics and hybrid QM/MM investigation to explore the reaction of Prxs with H2O2 using alkyl hydroperoxide reductase E from Mycobacterium tuberculosis as a Prx model. We report for the first time the thermodynamic activation parameters of H2O2 reduction using Prx, which show that protein significantly lowers the activation enthalpy, with an unfavourable entropic effect, compared to the uncatalyzed reaction. The QM/MM simulations show that the remarkable catalytic effects responsible for the fast H2O2 reduction in Prxs are mainly due to an active-site arrangement, which establishes a complex hydrogen bond network activating both reactive species.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Anibal M. Reyes
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Mariano C. G. Lebrero
- IQUIFIB-Dpto. Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
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Zeida A, Guardia CM, Lichtig P, Perissinotti LL, Defelipe LA, Turjanski A, Radi R, Trujillo M, Estrin DA. Thiol redox biochemistry: insights from computer simulations. Biophys Rev 2014; 6:27-46. [PMID: 28509962 PMCID: PMC5427810 DOI: 10.1007/s12551-013-0127-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/03/2013] [Indexed: 12/13/2022] Open
Abstract
Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Carlos M Guardia
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Pablo Lichtig
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Laura L Perissinotti
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada, T2N 2N4
| | - Lucas A Defelipe
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina.
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Dans PD, Darré L, Machado MR, Zeida A, Brandner AF, Pantano S. Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-3-319-02624-4_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Zeida A, Machado MR, Dans PD, Pantano S. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 86:021903. [PMID: 23005781 DOI: 10.1103/physreve.86.021903] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 06/01/2012] [Indexed: 06/01/2023]
Abstract
Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ~80% of the DNA curvature present in experimentally solved structures.
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Affiliation(s)
- Ari Zeida
- Institut Pasteur de Montevideo, Calle Mataojo 2020, Montevideo, Codigo Postal 11400, Uruguay
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Zeida A, Babbush R, Lebrero MCG, Trujillo M, Radi R, Estrin DA. Molecular basis of the mechanism of thiol oxidation by hydrogen peroxide in aqueous solution: challenging the SN2 paradigm. Chem Res Toxicol 2012; 25:741-6. [PMID: 22303921 DOI: 10.1021/tx200540z] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The oxidation of cellular thiol-containing compounds, such as glutathione and protein Cys residues, is considered to play an important role in many biological processes. Among possible oxidants, hydrogen peroxide (H(2)O(2)) is known to be produced in many cell types as a response to a variety of extracellular stimuli and could work as an intracellular messenger. This reaction has been reported to proceed through a S(N)2 mechanism, but despite its importance, the reaction is not completely understood at the atomic level. In this work, we elucidate the reaction mechanism of thiol oxidation by H(2)O(2) for a model methanethiolate system using state of the art hybrid quantum-classical (QM-MM) molecular dynamics simulations. Our results show that the solvent plays a key role in positioning the reactants, that there is a significant charge redistribution in the first stages of the reaction, and that there is a hydrogen transfer process between H(2)O(2) oxygen atoms that occurs after reaching the transition state. These observations challenge the S(N)2 mechanism hypothesis for this reaction. Specifically, our results indicate that the reaction is driven by a tendency of the slightly charged peroxidatic oxygen to become even more negative in the product via an electrophilic attack on the negative sulfur atom. This is inconsistent with the S(N)2 mechanism, which predicts a protonated sulfenic acid and hydroxyl anion as stable intermediates. These intermediates are not found. Instead, the reaction proceeds directly to unprotonated sulfenic acid and water.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
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Dans PD, Zeida A, Machado MR, Pantano S. A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. J Chem Theory Comput 2010; 6:1711-25. [PMID: 26615701 DOI: 10.1021/ct900653p] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coarse-grain (CG) techniques allow considerable extension of the accessible size and time scales in simulations of biological systems. Although many CG representations are available for the most common biomacromolecules, very few have been reported for nucleic acids. Here, we present a CG model for molecular dynamics simulations of DNA on the multi-microsecond time scale. Our model maps the complexity of each nucleotide onto six effective superatoms keeping the "chemical sense" of specific Watson-Crick recognition. Molecular interactions are evaluated using a classical Hamiltonian with explicit electrostatics calculated under the framework of the generalized Born approach. This CG representation is able to accurately reproduce experimental structures, breathing dynamics, and conformational transitions from the A to the B form in double helical fragments. The model achieves a good qualitative reproduction of temperature-driven melting and its dependence on size, ionic strength, and sequence specificity. Reconstruction of atomistic models from CG trajectories give remarkable agreement with structural, dynamic, and energetic features obtained from fully atomistic simulation, opening the possibility to acquire nearly atomic detail data from CG trajectories.
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Affiliation(s)
- Pablo D Dans
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Matías R Machado
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
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