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Ould Mohamed L, Abtouche S, Ghoualem Z, Assfeld X. Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling. J Mol Model 2024; 30:180. [PMID: 38780881 DOI: 10.1007/s00894-024-05963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
CONTEXT In cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic mechanisms governing this process remain poorly understood. This study addresses this gap by investigating a disulfide bridge reduction reaction, serving as a model for comprehending electron and proton transfer in biological systems. Six potential mechanisms for reducing the dimethyl disulfide (DMDS) bridge through electron and proton capture were explored. Thermodynamic and kinetic analyses elucidated the sequence of proton and electron addition. MD-PMM, a method that combines molecular dynamics simulations and quantum-chemical calculations, was employed to compute the redox potential of the mechanism. This research provides valuable insights into the mechanisms and redox potentials involved in disulfide bridge reduction within proteins, offering an understanding of phenomena that are challenging to explore experimentally. METHODS All calculations used the Gaussian 09 software package at the MP2/6-311 + g(d,p) theory level. Visualization of the molecular orbitals and electron densities was conducted using Gaussview6. Molecular dynamics simulations were performed using GROMACS with the CHARMM36 force field. The PyMM program (Python Program for QM/MM Simulations Based on the Perturbed Matrix Method) is used to apply the Perturbed Matrix Method to MD simulations.
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Affiliation(s)
- Lina Ould Mohamed
- Laboratoire de Physico Chimie Théorique Et Chimie Informatique, LPCTCI, Faculté de Chimie, USTHB, 16111, Algiers, Algeria
| | - Soraya Abtouche
- Laboratoire de Physico Chimie Théorique Et Chimie Informatique, LPCTCI, Faculté de Chimie, USTHB, 16111, Algiers, Algeria.
| | - Zeyneb Ghoualem
- Laboratoire de Physico Chimie Théorique Et Chimie Informatique, LPCTCI, Faculté de Chimie, USTHB, 16111, Algiers, Algeria
| | - Xavier Assfeld
- Physique et Chimie Théoriques, UMR 7019, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre Lès Nancy Cedex, France
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Li S, Sun H, Sun Y, Han S, Li Q. A theoretical investigation on the hydrodesulphurisation mechanism of hydrogenated thiophene over Cu–Mo-modified FAU zeolite. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2027407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Suyang Li
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, People’s Republic of China
| | - Huai Sun
- School of Chemistry and Chemical Engineering and Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yingxin Sun
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, People’s Republic of China
| | - Sheng Han
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, People’s Republic of China
| | - Qianggen Li
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, People’s Republic of China
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Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase. Proc Natl Acad Sci U S A 2017; 114:E4724-E4733. [PMID: 28559343 DOI: 10.1073/pnas.1618985114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We explore the enzymatic mechanism of the reduction of glutathione disulfide (GSSG) by the reduced a domain of human protein disulfide isomerase (hPDI) with atomistic resolution. We use classical molecular dynamics and hybrid quantum mechanics/molecular mechanics calculations at the mPW1N/6-311+G(2d,2p):FF99SB//mPW1N/6-31G(d):FF99SB level. The reaction proceeds in two stages: (i) a thiol-disulfide exchange through nucleophilic attack of the Cys53-thiolate to the GSSG-disulfide followed by the deprotonation of Cys56-thiol by Glu47-carboxylate and (ii) a second thiol-disulfide exchange between the Cys56-thiolate and the mixed disulfide intermediate formed in the first step. The Gibbs activation energy for the first stage was 18.7 kcal·mol-1, and for the second stage, it was 7.2 kcal·mol-1, in excellent agreement with the experimental barrier (17.6 kcal·mol-1). Our results also suggest that the catalysis by protein disulfide isomerase (PDI) and thiol-disulfide exchange is mostly enthalpy-driven (entropy changes below 2 kcal·mol-1 at all stages of the reaction). Hydrogen bonds formed between the backbone of His55 and Cys56 and the Cys56-thiol result in an increase in the Gibbs energy barrier of the first thiol-disulfide exchange. The solvent plays a key role in stabilizing the leaving glutathione thiolate formed. This role is not exclusively electrostatic, because an explicit inclusion of several water molecules at the density-functional theory level is a requisite to form the mixed disulfide intermediate. In the intramolecular oxidation of PDI, a transition state is only observed if hydrogen bond donors are nearby the mixed disulfide intermediate, which emphasizes that the thermochemistry of thiol-disulfide exchange in PDI is influenced by the presence of hydrogen bond donors.
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Dumont E, Michel C, Sautet P. Unraveling Gold(I)-Specific Action Towards Peptidic Disulfide Cleavage: A DFT Investigation. Chemphyschem 2011; 12:2596-2603. [DOI: 10.1002/cphc.201100336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR CNRS, Institut de Chimie de Lyon, Universit de Lyon, Ecole normale suprieure de Lyon, France.
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Dumont É, Ferré N. Geometrical Embedding Governs a Dramatic Variation of Electron Paramagnetic Resonance Hyperfine Coupling Constants of Disulfide Radical Anions. J Phys Chem B 2011; 115:6776-83. [DOI: 10.1021/jp2021566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Élise Dumont
- Institut de Chimie de Lyon, Université de Lyon, UMR 5182 CNRS LCh École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Nicolas Ferré
- Universite de Provence, UMR 6264 Laboratoire Chimie Provence, Équipe Chimie Théorique, Faculté des Sciences de Saint-Jérôme Case 521, Avenue Escadrille Normandie-Niemen, 13397 Marseille Cedex 20, France
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Wouters MA, Iismaa S, Fan SW, Haworth NL. Thiol-based redox signalling: rust never sleeps. Int J Biochem Cell Biol 2011; 43:1079-85. [PMID: 21513814 DOI: 10.1016/j.biocel.2011.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 03/23/2011] [Accepted: 04/05/2011] [Indexed: 11/30/2022]
Abstract
Cysteine residues in proteins are covalently modified under conditions of oxidative and nitrosative stress by oxidation, nitrosation, glutathionylation and disulfide formation. Modifications induce conformational changes in substrate proteins, effecting signal cascades that evoke a biological response. A growing number of structures with modified cysteines are allowing a piecemeal understanding of the mechanistic aspects of these signalling pathways to emerge. Conformational changes upon conjugation of nitric oxide and glutathione are generally small and often accompanied by a local increase in protein disorder. Burial of nitric oxide is also apparent, which may increase the timeframe of signalling. Conformational changes upon disulfide formation/reduction range from the small to the spectacular. They include order/disorder transitions; oxidation of disulfides following expulsion of metals such as Zn; major reorganisation or "morphing" of portions of the polypeptide backbone; and changes in quaternary structure including domain swapping.
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Dumont É, Laurent AD, Assfeld X, Jacquemin D. Performances of recently-proposed functionals for describing disulfide radical anions and similar systems. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.11.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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How does microhydration impact on structure, spectroscopy and formation of disulfide radical anions? An ab initio investigation on dimethyldisulfide. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dumont É, Laurent AD, Loos PF, Assfeld X. Analyzing the Selectivity and Successiveness of a Two-Electron Capture on a Multiply Disulfide-Linked Protein. J Chem Theory Comput 2009; 5:1700-8. [DOI: 10.1021/ct900093h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Élise Dumont
- Laboratoire de Chimie, UMR 5182 CNRS École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France, and Équipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Adèle D. Laurent
- Laboratoire de Chimie, UMR 5182 CNRS École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France, and Équipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Pierre-François Loos
- Laboratoire de Chimie, UMR 5182 CNRS École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France, and Équipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Chimie, UMR 5182 CNRS École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France, and Équipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
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