From Thiol to Sulfonic Acid: Modeling the Oxidation Pathway of Protein Thiols by Hydrogen Peroxide

Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation

Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.

Positive Regulation of Interleukin-1β Bioactivity by Physiological ROS-Mediated Cysteine S-Glutathionylation

Reactive oxygen species (ROS)-induced cysteine S-glutathionylation is an important posttranslational modification (PTM) that controls a wide range of intracellular protein activities. However, whether physiological ROS can modulate the function of extracellular components via S-glutathionylation is unknown. Using a screening approach, we identified ROS-mediated cysteine S-glutathionylation on several extracellular cytokines. Glutathionylation of the highly conserved Cys-188 in IL-1β positively regulates its bioactivity by preventing its ROS-induced irreversible oxidation, including sulfinic acid and sulfonic acid formation. We show this mechanism protects IL-1β from deactivation by ROS in an in vivo system of irradiation-induced bone marrow (BM) injury. Glutaredoxin 1 (Grx1), an enzyme that catalyzes deglutathionylation, was present and active in the extracellular space in serum and the BM, physiologically regulating IL-1β glutathionylation and bioactivity. Collectively, we identify cysteine S-glutathionylation as a cytokine regulatory mechanism that could be a therapeutic target in the treatment of various infectious and inflammatory diseases.

Impact of SCILL catalysts for the S-S coupling of thiols to disulfides

This study reports the behaviour of SCILL based catalysts in the oxidative S-S coupling of aliphatic and aromatic thiols, namely 1-butanethiol and thiophenol, to dibutyl disulfide and diphenyl disulfide. A range of ionic liquids (1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide) and metal supported catalysts (5% Pt/SiO₂; 5% Ru/SiO₂; 5% Ru/C; 5% Pt/OMS-2) were used to prepare the SCILL catalysts and all were found to be active for the reaction following the trend 5% Pt-OMS-2 > 5% Pt/SiO₂ > 5% Ru/C > 5% Ru/SiO₂. The presence of SCILL catalysts afforded high selectivity to the disulfide, and the activity of the SCILL catalyst was dependent on the ionic liquid used. A significant increase in the stability of all the supported metal catalysts was found in the presence of the ionic liquid, and there was no change in the selectivity towards disulfides. This demonstrated that the ionic liquids protect the active sites of the catalyst against sulfation, thus providing more stable and active catalysts.

NitroxylFluor: A Thiol-Based Fluorescent Probe for Live-Cell Imaging of Nitroxyl

Detection of nitroxyl (HNO), the transient one-electron reduced form of nitric oxide, is a significant challenge owing to its high reactivity with biological thiols (with rate constants as high as 10⁹ M^-1 s^-1). To address this, we report a new thiol-based HNO-responsive trigger that can compete against reactive thiols for HNO. This process forms a common N-hydroxysulfenamide intermediate that cyclizes to release a masked fluorophore leading to fluorescence enhancement. To ensure that the cyclization step is rapid, our design capitalizes on two established physical organic phenomena; the alpha-effect and the Thorpe-Ingold effect. Using this new trigger, we developed NitroxylFluor, a selective HNO-responsive fluorescent probe. Treatment of NitroxylFluor with an HNO donor results in a 16-fold turn-on. This probe also exhibits excellent selectivity over various reactive nitrogen, oxygen, and sulfur species and efficacy in the presence of thiols (e.g., glutathione in mM concentrations). Lastly, we successfully performed live cell imaging of HNO using NitroxylFluor.

Understanding seed-mediated growth of gold nanoclusters at molecular level

The continuous development of total synthesis chemistry has allowed many organic and biomolecules to be produced with known synthetic history–that is, a complete set of step reactions in their synthetic routes. Here, we extend such molecular-level precise reaction routes to nanochemistry, particularly to a seed-mediated synthesis of inorganic nanoparticles. By systematically investigating the time−dependent abundance of 35 intermediate species in total, we map out relevant step reactions in a model size growth reaction from molecularly pure Au₂₅ to Au₄₄ nanoparticles. The size growth of Au nanoparticles involves two different size−evolution processes (monotonic LaMer growth and volcano-shaped aggregative growth), which are driven by a sequential 2-electron boosting of the valence electron count of Au nanoparticles. Such fundamental findings not only provide guiding principles to produce other sizes of Au nanoparticles (e.g., Au₃₈), but also represent molecular-level insights on long-standing puzzles in nanochemistry, including LaMer growth, aggregative growth, and digestive ripening.

Synthetic nanochemistry currently lacks the molecular step-by-step routes afforded to organic chemistry by total synthesis. Here, the authors track the seeded growth of atom-precise gold nanoclusters using mass spectrometry, revealing that the clusters evolve through a series of intermediates in two-electron steps.

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.

Oxidatively-generated damage to DNA and proteins mediated by photosensitized UVA

UVA accounts for about 95% of the solar ultraviolet (UV) radiation that reaches Earth and most likely contributes to human skin cancer risk. In contrast to UVB, which comprises the remaining 5% and is absorbed by DNA nucleobases to cause direct photodamage, UVA damages DNA indirectly. It does this largely through its interactions with cellular chromophores that act as photosensitisers to generate reactive oxygen species. Exogenously supplied chemicals, including some widely-prescribed medicines, may also act as photosensitisers and these drugs are associated with an increased risk of sun-related cancer. Because they amplify the effects of UVA on cells, they provide a means to investigate the mechanisms and effects of UVA-induced photodamage. Here, we describe some of the major lesions induced by two groups of UVA photosensitisers, the DNA thionucleotides and the fluoroquinolone antibiotics. In thionucleotides, replacement of the oxygen atoms of canonical nucleobases by sulfur converts them into strong UVA chromophores that can be incorporated into DNA. The fluoroquinolones are also UVA chromophores. They are not incorporated into DNA and induce a different range of DNA damages. We also draw attention to the potentially important contribution of photochemical protein damage to the cellular effects of photosensitised UVA. Proteins targeted for oxidation damage include DNA repair factors and we suggest that UVA-mediated protein damage may contribute to sunlight-induced cancer risk.

Biochemical basis of sulphenomics: how protein sulphenic acids may be stabilized by the protein microenvironment

Among protein residues, cysteines are one of the prominent candidates to ROS-mediated and RNS-mediated post-translational modifications, and hydrogen peroxide (H₂ O₂ ) is the main ROS candidate for inducing cysteine oxidation. The reaction with H₂ O₂ is not common to all cysteine residues, being their reactivity an utmost prerequisite for the sensitivity towards H₂ O₂ . Indeed, only deprotonated Cys (i.e. thiolate form, S^- ) can react with H₂ O₂ leading to sulphenic acid formation (SOH), which is considered as a major/central player of ROS sensing pathways. However, cysteine sulphenic acids are generally unstable because they can be further oxidized to irreversible forms (sulphinic and sulphonic acids, SO₂ H and SO₃ H, respectively), or alternatively, they can proceed towards further modifications including disulphide bond formation (SS), S-glutathionylation (SSG) and sulphenamide formation (SN). To understand why and how cysteine residues undergo primary oxidation to sulphenic acid, and to explore the stability of cysteine sulphenic acids, a combination of biochemical, structural and computational studies are required. Here, we will discuss the current knowledge of the structural determinants for cysteine reactivity and sulphenic acid stability within protein microenvironments.

Oxygen-dependent activation of Cu,Zn-superoxide dismutase-1

Copper zinc superoxide dismutase (Sod1) is a critical enzyme in limiting reactive oxygen species in both the cytosol and the mitochondrial intermembrane space.

Coping with inevitable accidents in metabolism

Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.

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.

Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana

AIMS

Cysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively).

RESULTS

Although AtGAPC1 and AtGAPA have almost identical 3D structure and similar acidity of their catalytic Cys149, AtGAPC1 is more sensitive to H2O2 and prone to irreversible oxidation than AtGAPA. As a result, sulfenic acid is more stable in AtGAPA.

INNOVATION

Based on crystallographic structures of AtGAPC1 and AtGAPA, the reaction potential energy surface for Cys149 oxidation by H2O2 was calculated by QM. In both enzymes, sulfenic acid formation was characterized by a lower energy barrier than sulfinate formation, and sulfonate formation was prevented by very high energy barriers. Activation energies for both oxidation steps were lower in AtGAPC1 than AtGAPA, supporting the higher propensity of AtGAPC1 toward irreversible oxidation.

CONCLUSIONS

QM/MM calculations coupled to fingerprinting analyses revealed that two Arg of AtGAPA (substituted by Gly and Val in AtGAPC1), located at 8-15 Å distance from Cys149, are the major factors responsible for sulfenic acid stability, underpinning the importance of long-distance polar interactions in tuning sulfenic acid stability in native protein microenvironments.

Bisphenol A degradation by a new acidic nano zero-valent iron diatomite composite

A new nano zero-valent iron material that generates acidic conditionsin situexhibits a high removal efficiency of BPA under natural pH conditions.

Rich synthetic and structural chemistry of polynuclear Pb(ii)–Cu(i)/Ag(i) heterobimetallic thiolate clusters, their decomposition and generation of a Cu(ii) hydrosulfide variant

Thermal decomposition of Pb(ii)–Cu(i)/Ag(i) heterobimetallic thiolate clusters yielded PbS nanoparticles along with a sought-after Cu(ii) hydrosulfide complex.