Thiol redox biochemistry: insights from computer simulations

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.

Keywords: Computer simulations; Oxidation; Redox homeostasis; Thiols.

Fig. 1

Most relevant thiol redox reaction pathways. Different routes of oxidation of thiol/thiolate are shown in a schematic way. Thiol acid–base behavior is presented in reaction (I). Reaction (II) shows the one-electron oxidation of thiolates to thiyl radical. Thiolates can be oxidized by hydroperoxides, hypochlorous acid, and chloramines in two-electron oxidation processes that yield the corresponding sulfenic acid (III), which in turn can be further oxidized to sulfinic and sulfonic acids if oxidant is in excess (IV). Inter- and intramolecular disulfides are de-novo formed from the reaction of a sulfenic acid with other thiol (V) and, subsequently, thiol−disulfide exchanges can occur (VI). Protein or protein-like thiolates can also rearrange to a cyclic product called sulfenamide that involves the reaction of the sulfur atom with the backbone’s NH moiety of the preceding residue in the sequence (VII). Thiyl radicals can react with molecular oxygen/superoxide or other thiol, yielding sulfinic acid and disulfides as final products, respectively (reactions VIII and IX). Nitrosothiols can be produced both by radical and non-radical pathways: both thiol–thiolate oxidation by reactive nitrogen species such as dinitrogen trioxide, or thiyl radical recombination with nitric oxide are called S-nitrosation and S-nitrosylation (reactions X and XI). Nitrosothiols can react with other thiols, exchanging the nitroso group in the so-called trans-S-nitrosations (XII) or releasing HNO to form a new disulfide (XIII)

Fig. 2

Intrinsic thiolate reactivities with peroxynitrite (k _2pHind) as a function of thiol pKa (pKa _SH). Low-molecular-weight thiols (filled squares 1–6) show a positive Brønsted correlation, as indicated by the solid red line, consistent with the thiols with a higher pKa being better nucleophiles. Some protein thiols (filled triangles 10–11) react with peroxynitrite, as anticipated according to their thiol pKa. Other protein thiols (filled circles 12–21), react much faster than expected, indicating that protein factors other than thiol pKa are determining this reactivity. 1 L-cysteine (Cys) ethyl ester, 2 Cys methyl ester, 3 penicillamine, 4 Cys, 5 glutathione, 6 mercapto ethyl guanidine, 7 homocysteine, 8 N-acetyl Cys, 9 dihidrolipoic acid, 10 Trypanosoma brucei tryparedoxin, 11 human serum albumin, 12 human arylamine N-acetyltransferase 1, 13 DJ1, 14 TSA2, 15 Mycobacterium tuberculosis AhpC, 16 creatinine kinase, 17 TSA1, 18 GAPDH, 19 red blood cell peroxiredoxin 2 (Prx2), 20 protein-tyrosine phosphatase 1B (PTP1B), 21 human Prx5. Modified from Trujillo et al. (2007) and Ferrer-Sueta et al. (2011)

Fig. 3

Free energy profile obtained by a quantum mechanics–molecular mechanical (QM-MM) umbrella sampling simulation. Free energy (kcal/mol) is plotted versus the reaction coordinate (Å). Illustrative models of the reaction mechanism steps are also depicted. Modified from Zeida et al. (2012)

Fig. 4

Kinetic and QM-MM study of Cys oxidation by peroxynitrite (ONOO^-). a “Bell-shaped” plots of the dependence of k _2pHdep (M^-1 s^-1) as a function of pH, at T = 10, 25, 37, and 50 °C. b Estimated free energies of the reactants, transition states (TS), and products. Illustrative pictures of reactants and products are depicted. Modified from Zeida et al. (2013)

Fig. 5

Energy profile for sulfenamide formation in protein tyrosine phosphatase 1B (PTP1B) for histidine protonated in the epsilon nitrogen (HIE). Cys 215 (as CysSOH) and Ser 216 were treated at the density functional theory level (PBE/dzvp), while the rest of the protein and water molecules were treated classically. Reactant, TS, and products are shown as ball and stick representations. Solid lines distances, dashed lines putative bonds. Modified from Defelipe (in preparation)

Scheme 1

Representation of S-nitrosothiols (RSNOs) in terms of three resonance structures—D, S, and I

Scheme 2

The two reactions studied: transnitrosation and disulfide formation

Fig. 6

a Energetics and optimized species for the transnitrosation reaction between the Cys ethylester (CEE) and the corresponding S-nitrosothiol in gas phase (black) and water (PCM, red) at the B3LYP/6-311 + G* level of theory. b Intermediate assignment from ¹⁵ N nuclear magnetic resonance (NMR) spectrum for the reaction in methanol (reference: nitromethane). c Suggested structure for the intermediate based on ¹H NMR and 2-dimensional correlation spectroscopy (2D COSY), and heteronuclear correlation (HETCOR) NMR spectra. Modified from Perissinotti et al.