Towards a predictive model for polymer solubility using the noncovalent interaction index: polyethylene as a case study

In this work we present the development of a novel, quantitative solubility descriptor based on the non-covalent interaction index. It is presented as a more insightful alternative to Hansen's solubility parameters and the COSMO model to assess and predict polymer solubility in different solvents. To this end, we studied the solvation behaviour as a function of the chain length of a single chain of arguably the most simple polymer, polyethylene, in anisole (solvent) and methanol (poor solvent) via molecular dynamics simulations. It was found that in anisole the solute maximized its interface with the solvent, whereas in methanol the macromolecule formed rod-like structures by folding on itself once the chain length surpassed a certain barrier. We assessed this behaviour - which can be related to solubility - quantitatively and qualitatively via well-known descriptors, namely the solvation free energy, and the solvent accessible surface area. In addition, we propose the non-covalent interaction (NCI) index as a versatile descriptor, providing information on the strength, as well as the nature, of the solute-solvent interactions, the solute's intramolecular interactions and on the solute's conformation, both qualitatively and quantitatively. Finally, as a quantitative measure for solubility, defined in this context as the solute's tendency to maximize its interactions with the solvent, we propose two new NCI-based descriptors: the relative integrated NCI density and the integrated NCI difference. The former represents the quantitative difference in solute-solvent interactions between a fully extended coil and the actual conformation during simulation and the latter the quantitative difference between the intermolecular (solute-solvent) and the intramolecular (in the solute) non-covalent interactions. The easy interpretation and calculation of these novel quantities open up the possibility of fast, reliable and insightful high-throughput screening of different (anti)solvent and solute combinations.

Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels

Supramolecular gels form a class of soft materials that has been heavily explored by the chemical community in the past 20 years. While a multitude of experimental techniques has demonstrated its usefulness when characterizing these materials, the potential value of computational techniques has received much less attention. This review aims to provide a complete overview of studies that employ computational tools to obtain a better fundamental understanding of the self-assembly behavior of supramolecular gels or to accelerate their development by means of prediction. As such, we hope to stimulate researchers to consider using computational tools when investigating these intriguing materials. In the concluding remarks, we address future challenges faced by the field and formulate our vision on how computational methods could help overcoming them.

Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities

Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.

The Enigma of 2-Cys Peroxiredoxins: What Are Their Roles?

2-Cys peroxiredoxins are abundant thiol proteins that react efficiently with a wide range of peroxides. Unlike other enzymes, their exceptionally high reactivity does not rely on cofactors. The mechanism of oxidation and reduction of peroxiredoxins places them in a good position to act as antioxidants as well as key players in redox signaling. Understanding of the intimate details of peroxiredoxin functioning is important for translational research.

A dual attack on the peroxide bond. The common principle of peroxidatic cysteine or selenocysteine residues

The (seleno)cysteine residues in some protein families react with hydroperoxides with rate constants far beyond those of fully dissociated low molecular weight thiol or selenol compounds. In case of the glutathione peroxidases, we could demonstrate that high rate constants are achieved by a proton transfer from the chalcogenol to a residue of the active site [Orian et al. Free Radic. Biol. Med. 87 (2015)]. We extended this study to three more protein families (OxyR, GAPDH and Prx). According to DFT calculations, a proton transfer from the active site chalcogenol to a residue within the active site is a prerequisite for both, creating a chalcogenolate that attacks one oxygen of the hydroperoxide substrate and combining the delocalized proton with the remaining OH or OR, respectively, to create an ideal leaving group. The “parking postions” of the delocalized proton differ between the protein families. It is the ring nitrogen of tryptophan in GPx, a histidine in GAPDH and OxyR and a threonine in Prx. The basic principle, however, is common to all four families of proteins. We, thus, conclude that the principle outlined in this investigation offers a convincing explanation for how a cysteine residue can become peroxidatic.

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In some protein families, (seleno)cysteine residues react with hydroperoxides with very high rate constants.

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In GPx, DFT models of the oxidation of the catalytic site support a two-step mechanism for the H₂O₂ reduction.

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This mechanism is here found to operate in other thiol-based enzymes, i.e. OxyR, GAPDH and Prx.

Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide

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.

How Biochemical Environments Fine-Tune a Redox Process: From Theoretical Models to Practical Applications

In this study, we give a new physical insight into how enzymatic environments influence a redox process. This is particularly important in a biochemical context, in which oxidoreductase enzymes and low-molecular-weight cofactors create a microenvironment, fine-tuning their specific redox potential. We present a new theoretical model, quantitatively backed up by quantum chemically calculated data obtained for key biological sulfur-based model reactions involved in preserving the cellular redox homeostasis during oxidative stress. We show that environmental effects can be quantitatively predicted from the thermodynamic cycle linking ΔΔ G(OX/RED)_ref-ligand values to the differential interaction energy ΔΔ G_int of the reduced and oxidized species with the environment. Our obtained data can be linked to hydrogen-bond patterns found in protein active sites. The thermodynamic model is further understood in the framework of molecular orbital theory. The key insight of this work is that the intrinsic properties of neither a redox couple nor the interacting environment (e.g., ligand) are enough by themselves to uniquely predict reduction potentials. Instead, system-environment interactions need to be considered. This study is of general interest as redox processes are pivotal to empower, protect, or damage organisms. Our presented thermodynamic model allows a pragmatically evaluation on the expected influence of a particular environment on a redox process, necessary to fully understand how redox processes take place in living organisms.

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C_P) located in a conserved sequence Pxxx(T/S)xxC_P motif known as C_P-loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C_P-loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C_P-loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C_P-loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C_P-loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C_P-loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C_P-loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C_P-loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles.

Experimentally Dissecting the Origins of Peroxiredoxin Catalysis

AIMS

Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases involved in oxidant defense and signal transduction. Despite much study, the precise roles of conserved residues remain poorly defined. In this study, we carried out extensive functional and structural characterization of 10 variants of such residues in a model decameric bacterial Prx.

RESULTS

Three active site proximal mutations of Salmonella typhimurium AhpC, T43V, R119A, and E49Q, lowered catalytic efficiency with hydrogen peroxide by 4-5 orders of magnitude, but did not affect reactivity toward their reductant, AhpF. pK_a values of the peroxidatic cysteine were also shifted up by 1-1.3 pH units for these and a decamer disruption mutant, T77I. Except for the decamer-stabilizing T77V, all mutations destabilized decamers in the reduced form. In the oxidized form, three mutants-T77V, T43A, and T43S-exhibited stabilized decamers and were more efficiently reduced by AhpF than wild-type AhpC. Crystal structures of most mutants were solved and many showed alterations in stability of the fully folded active site loop.

INNOVATION

This is the first study of Prx mutants to comprehensively assess the effects of mutations on catalytic activities, the active site cysteine pK_a, and the protein structure and oligomeric status.

CONCLUSION

The Arg119 side chain must be properly situated for efficient catalysis, but for other debilitating variants, the functional defects could be explained by structural perturbations and/or associated decamer destabilization rather than direct effects. This underscores the importance of our comprehensive approach. A remarkable new finding was the preference of the reductant for decamers. Antioxid. Redox Signal. 28, 521-536.

Characterisation of conformational and functional features of alkyl hydroperoxide reductase E-like protein

Alkyl hydroperoxide reductase E (AhpE) is a member of the peroxidase family of enzymes that catalyse the reduction of peroxides, however its structural and functional roles are still unclear in details. In this study, we used the Thermococcus kodakarensis AhpE-like protein as a model to investigate structure-function relationships including the molecular properties of DNA binding activity. Multiple sequence alignment, structural comparison and biochemical analyses revealed that TkAhpE includes conserved peroxidase residues in the active site, and exhibits peroxidase activity with structure-dependent holdase chaperone function. Following electrophoretic mobility shift assays and electron microscopy analysis demonstrated distinctive binding features of TkAhpE to the DNA showing that their dimeric conformer can bind to the double-stranded DNA, but not to the single-stranded DNA, indicating its striking molecular features to double-stranded DNA-specific interactions. Based on our results, we provided that TkAhpE is a multifunctional peroxidase displaying structure-dependent molecular chaperone and DNA binding activities.

The thiol of human serum albumin: Acidity, microenvironment and mechanistic insights on its oxidation to sulfenic acid

Human serum albumin (HSA) has a single reduced cysteine residue, Cys34, whose acidity has been controversial. Three experimental approaches (pH-dependence of reactivity towards hydrogen peroxide, ultraviolet titration and infrared spectroscopy) are used to determine that the pK_a value in delipidated HSA is 8.1±0.2 at 37°C and 0.1M ionic strength. Molecular dynamics simulations of HSA in the sub-microsecond timescale show that while sulfur exposure to solvent is limited and fluctuating in the thiol form, it increases in the thiolate, stabilized by a persistent hydrogen-bond (HB) network involving Tyr84 and bridging waters to Asp38 and Gln33 backbone. Insight into the mechanism of Cys34 oxidation by H₂O₂ is provided by ONIOM(QM:MM) modeling including quantum water molecules. The reaction proceeds through a slightly asynchronous S_N2 transition state (TS) with calculated Δ^‡G and Δ^‡H barriers at 298K of respectively 59 and 54kJmol^-1 (the latter within chemical accuracy from the experimental value). A post-TS proton transfer leads to HSA-SO^- and water as products. The structured reaction site cages H₂O₂, which donates a strong HB to the thiolate. Loss of this HB before reaching the TS modulates Cys34 nucleophilicity and contributes to destabilize H₂O₂. The lack of reaction-site features required for differential stabilization of the TS (positive charges, H₂O₂ HB strengthening) explains the striking difference in kinetic efficiency for the same reaction in other proteins (e.g. peroxiredoxins). The structured HB network surrounding HSA-SH with sequestered waters carries an entropic penalty on the barrier height. These studies contribute to deepen the understanding of the reactivity of HSA-SH, the most abundant thiol in human plasma, and in a wider perspective, provide clues on the key aspects that modulate thiol reactivity against H₂O₂.

The Arsenic Detoxification System in Corynebacteria: Basis and Application for Bioremediation and Redox Control

Arsenic (As) is widespread in the environment and highly toxic. It has been released by volcanic and anthropogenic activities and causes serious health problems worldwide. To survive arsenic-rich environments, soil and saprophytic microorganisms have developed molecular detoxification mechanisms to survive arsenic-rich environments, mainly by the enzymatic conversion of inorganic arsenate (As^V) to arsenite (As^III) by arsenate reductases, which is then extruded by arsenite permeases. One of these Gram-positive bacteria, Corynebacterium glutamicum, the workhorse of biotechnological research, is also resistant to arsenic. To sanitize contaminated soils and waters, C. glutamicum strains were modified to work as arsenic "biocontainers." Two chromosomally encoded ars operons (ars1 and ars2) are responsible for As resistance. The genes within these operons encode for metalloregulatory proteins (ArsR1/R2), arsenite permeases (Acr3-1/-2), and arsenate reductases (ArsC1/C2/C1'). ArsC1/C2 arsenate reductases are coupled to the low molecular weight thiol mycothiol (MSH) and to the recently discovered mycoredoxin-1 (Mrx-1) present in most Actinobacteria. This MSH/Mrx-1 redox system protects cells against different forms of stress, including reactive oxygen species (ROS), metals, and antibiotics. ROS can modify functional sulfur cysteines by oxidizing the thiol (-SH) to a sulfenic acid (-SOH). These oxidation-sensitive protein cysteine thiols are redox regulated by the MSH/Mrx-1 couple in Corynebacterium and Mycobacterium. In summary, the molecular mechanisms involved in arsenic resistance system in C. glutamicum have paved the way for understanding the cellular response against oxidative stress in Actinobacteria.

On the Reactions of Thiols, Sulfenic Acids, and Sulfinic Acids with Hydrogen Peroxide

The reaction of thiols with H₂ O₂ is central to many processes essential to life, from protein folding to redox signaling. The initial products are assumed to be sulfenic acids, but their observation, and the kinetic and mechanistic characterization of their subsequent reactions, has proven challenging. The introduction of a 9-fluorotriptycene substituent enabled the use of ¹⁹ F NMR to directly monitor the reaction of a thiol with H₂ O₂ to yield a sulfenic acid, and its subsequent oxidation to sulfinic and sulfonic acids. The oxidations are specific base catalyzed, as revealed by the lack of isotope effects and the dependence of the kinetics on pH but not buffer concentration.