Features of S-nitrosylation based on statistical analysis and molecular dynamics simulation: cysteine acidity, surrounding basicity, steric hindrance and local flexibility

S-nitrosoproteomics profiling elucidates the regulatory mechanism of S-nitrosylation on beef quality

This study aimed to quantitively profile the S-nitrosylation in beef semimembranosus (SM) with different treatments (nitric oxide donor or nitric oxide synthase inhibitor) by applying iodoTMT-based nitrosoproteomics. Results showed that 2096 S-nitrosylated cysteine sites in 368 proteins were detected in beef SM. Besides, differential SNO-modified proteins were screened, some of which were involved in crucial biochemical pathways, including calcium-releasing-related proteins, energy metabolic enzymes, myofibrils, and cytoskeletal proteins. GO analysis indicated that differential proteins were localized in a wide range of cellular compartments, such as cytoplasm, organelle, and mitochondrion, providing a prerequisite for S-nitrosylation exerting broad roles in post-mortem muscles. Furthermore, KEGG analysis validated that these proteins participated in the regulation of diverse post-mortem metabolic processes, especially glycolysis. To conclude, changes of S-nitrosylation levels in post-mortem muscles could impact the structure and function of crucial muscle proteins, which lead to different levels of muscle metabolism and ultimately affect beef quality.

Ribonucleotide reductase: Implications of thiol S-nitrosylation and tyrosine nitration for different subunits

Ribonucleotide reductase (RNR) is a multi-subunit enzyme responsible for catalyzing the rate-limiting step in the production of deoxyribonucleotides essential for DNA synthesis and repair. The active RNR complex is composed of multimeric R1 and R2 subunits. The RNR catalysis involves the formation of tyrosyl radicals in R2 subunits and thiyl radicals in R1 subunits. Despite the quaternary structure and cofactor diversity, all the three classes of RNR have a conserved cysteine residue at the active site which is converted into a thiyl radical that initiates the substrate turnover, suggesting that the catalytic mechanism is somewhat similar for all three classes of the RNR enzyme. Increased RNR activity has been associated with malignant transformation, cancer cell growth, and tumorigenesis. Efforts concerning the understanding of RNR inhibition in designing potent RNR inhibitors/drugs as well as developing novel approaches for antibacterial, antiviral treatments, and cancer therapeutics with improved radiosensitization have been made in clinical research. This review highlights the precise and potent roles of NO in RNR inhibition by targeting both the subunits. Under nitrosative stress, the thiols of the R1 subunits have been found to be modified by S-nitrosylation and the tyrosyl radicals of the R2 subunits have been modified by nitration. In view of the recent advances and progresses in the field of nitrosative modifications and its fundamental role in signaling with implications in health and diseases, the present article focuses on the regulations of RNR activity by S-nitrosylation of thiols (R1 subunits) and nitration of tyrosyl residues (R2 subunits) which will further help in designing new drugs and therapies.

Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis

The fungi Paracoccidioides brasiliensis and Paracoccidioides lutzii are the causative agents of paracoccidioidomycosis (PCM), a systemic mycosis endemic to Latin America. This fungus is considered a facultative intracellular pathogen that is able to survive and replicate inside macrophages. The survival of the fungus during infection depends on its adaptability to various conditions, such as nitrosative/oxidative stress produced by the host immune cells, particularly alveolar macrophages. Currently, there is little knowledge about the Paracoccidioides spp. signaling pathways involved in the fungus evasion mechanism of the host defense response. However, it is known that some of these pathways are triggered by reactive oxygen species and reactive nitrogen species (ROS/RNS) produced by host cells. Considering that the effects of NO (nitric oxide) on pathogens are concentration dependent, such effects could alter the redox state of cysteine residues by influencing (activating or inhibiting) a variety of protein functions, notably S-nitrosylation, a highly important NO-dependent posttranslational modification that regulates cellular functions and signaling pathways. It has been demonstrated by our group that P. brasiliensis yeast cells proliferate when exposed to low NO concentrations. Thus, this work investigated the modulation profile of S-nitrosylated proteins of P. brasiliensis, as well as identifying S-nitrosylation sites after treatment with RNS. Through mass spectrometry analysis (LC-MS/MS) and label-free quantification, it was possible to identify 474 proteins in the S-nitrosylated proteome study. With this approach, we observed that proteins treated with NO at low concentrations presented a proliferative response pattern, with several proteins involved in cellular cycle regulation and growth being activated. These proteins appear to play important roles in fungal virulence. On the other hand, fungus stimulated by high NO concentrations exhibited a survival response pattern. Among these S-nitrosylated proteins we identified several potential molecular targets for fungal disease therapy, including cell wall integrity (CWI) pathway, amino acid and folic acid metabolisms. In addition, we detected that the transnitrosylation/denitrosylation redox signaling are preserved in this fungus. Finally, this work may help to uncover the beneficial and antifungal properties of NO in the P. brasiliensis and point to useful targets for the development of antifungal drugs.

S-Nitrosation impairs activity of stress-inducible aldehyde dehydrogenases from Arabidopsis thaliana

Nitric oxide (NO) is an intracellular messenger that mediates stress responses. Several plant aldehyde dehydrogenase (ALDH) genes are expressed during abiotic stress conditions to reduce the level of cytotoxic aldehydes. We investigated a possible interference between NO and ALDHs, using the isoform ALDH3H1 of Arabidopsis thaliana as model. The physiological NO donor; S-nitrosoglutathione (GSNO), inhibits ALDH3H1 in a time- and concentration-dependent manner. Mutagenesis and ESI-MS/MS analyses show that all Cys residues of ALDH3H1 are targets of GSNO-mediated S-nitrosation. Chemical labelling indicates that the deactivation is due to the conversion of the catalytic thiol into a catalytically non-active nitrosothiol. GSNO has the same effect on the chloroplastic ALDH3I1, suggesting that susceptibility of the catalytic Cys to NO is a common feature of ALDHs. S-Nitrosation and enzymatic inhibition of ALDH were reverted by reducing agents. Our study proves that the function of ALDHs does not exclusively depend on transcriptional regulation, with stress-induced expression, but may be also susceptible to posttranslational regulation through S-nitrosation. We discuss the potential involvement of S-nitrosoglutathione reductase (GSNOR), binding specific cofactors and reducing partners in a protective system of ALDHs in vivo, which will be experimentally corroborated in our forthcoming study.

S-Nitrosylation: An Emerging Paradigm of Redox Signaling

Nitric oxide (NO) is a highly reactive molecule, generated through metabolism of L-arginine by NO synthase (NOS). Abnormal NO levels in mammalian cells are associated with multiple human diseases, including cancer. Recent studies have uncovered that the NO signaling is compartmentalized, owing to the localization of NOS and the nature of biochemical reactions of NO, including S-nitrosylation. S-nitrosylation is a selective covalent post-translational modification adding a nitrosyl group to the reactive thiol group of a cysteine to form S-nitrosothiol (SNO), which is a key mechanism in transferring NO-mediated signals. While S-nitrosylation occurs only at select cysteine thiols, such a spatial constraint is partially resolved by transnitrosylation, where the nitrosyl moiety is transferred between two interacting proteins to successively transfer the NO signal to a distant location. As NOS is present in various subcellular locales, a stress could trigger concerted S-nitrosylation and transnitrosylation of a large number of proteins involved in divergent signaling cascades. S-nitrosylation is an emerging paradigm of redox signaling by which cells confer protection against oxidative stress.

S-Nitrosylation of α1-Antitrypsin Triggers Macrophages Toward Inflammatory Phenotype and Enhances Intra-Cellular Bacteria Elimination

Background: Human α1-antitrypsin (hAAT) is a circulating anti-inflammatory serine-protease inhibitor that rises during acute phase responses. in vivo, hAAT reduces bacterial load, without directly inhibiting bacterial growth. In conditions of excess nitric-oxide (NO), hAAT undergoes S-nitrosylation (S-NO-hAAT) and gains antibacterial capacity. The impact of S-NO-hAAT on immune cells has yet to be explored.

Aim: Study the effects of S-NO-hAAT on immune cells during bacterial infection.

Methods: Clinical-grade hAAT was S-nitrosylated and then compared to unmodified hAAT, functionally, and structurally. Intracellular bacterial clearance by THP-1 macrophages was assessed using live Salmonella typhi. Murine peritoneal macrophages were examined, and signaling pathways were evaluated. S-NO-hAAT was also investigated after blocking free mambranal cysteine residues on cells.

Results: S-NO-hAAT (27.5 uM) enhances intracellular bacteria elimination by immunocytes (up to 1-log reduction). S-NO-hAAT causes resting macrophages to exhibit a pro-inflammatory and antibacterial phenotype, including release of inflammatory cytokines and induction of inducible nitric oxide synthase (iNOS) and TLR2. These pro-inflammatory effects are dependent upon cell surface thiols and activation of MAPK pathways.

Conclusions: hAAT duality appears to be context-specific, involving S-nitrosylation in a nitric oxide rich environment. Our results suggest that S-nitrosylation facilitates the antibacterial activity of hAAT by promoting its ability to activate innate immune cells. This pro-inflammatory effect may involve transferring of nitric oxide from S-NO-hAAT to a free cysteine residue on cellular targets.

A bioinformatics study on characteristics, metabolic pathways, and cellular functions of the identified S-nitrosylated proteins in postmortem pork muscle

This study aimed to determine the characteristics, metabolic pathways and cellular functions of S-nitrosylated proteins from pork postmortem muscle using bioinformatics analysis. The results showed that S-nitrosylated proteins had a broad range of molecular weight and pI value and were mainly located in the functional region of secondary structure. The motif revealed the lysine (K) positioned at -5, -7, +1 and +5 through the S-nitrosocysteine while "C-X-X-C" was identified as the motif for non-S-nitrosylation-modified cysteine. The proteins were widely localized in cell compartments and mostly belonged to enzymes participating in the metabolic process. Glycolysis was the most significant pathways of S-nitrosylated proteins in postmortem muscle. The cell death of muscle cells was predicted to be inhibited by S-nitrosylation with the potential influence on the apoptosis. Those identified pathways and cellular functions of S-nitrosylation are proposed to have a profound influence on meat quality and should be highly regarded.

Proteomic Analysis of Thiol Modifications and Assessment of Structural Changes in Hemoglobin Induced by the Aniline Metabolites N-Phenylhydroxylamine and Nitrosobenzene

MS-based proteomic analysis was combined with in silico quantum mechanical calculations to improve understanding of protein adduction by N-phenylhydroxylamine (PhNHOH) and nitrosobenzene (NOB), metabolic products of aniline. In vitro adduction of model peptides containing nucleophilic sidechains (Cys, His, and Lys) and selected proteins (bovine and human hemoglobin and β-lactoglobulin-A) were characterized. Peptide studies identified the Cys thiolate as the most reactive nucleophile for these metabolites, a result consistent with in silico calculations of reactivity parameters. For PhNHOH, sulfinamides were identified as the primary adduction products, which were stable following tryptic digestion. Conversely, reactions with NOB yielded an additional oxidized adduct, the sulfonamide. In vitro exposure of human whole blood to PhNHOH and NOB demonstrated that only sulfinamides were formed. In addition to previously reported adduction of β⁹³Cys of human Hb, two novel sites of adduction were found; α¹⁰⁴Cys and β¹¹²Cys. We also report CD and UV-Vis spectroscopy studies of adducted human Hb that revealed loss of α-helical content and deoxygenation. The results provide additional understanding of the covalent interaction of aromatic amine metabolites with protein nucleophiles.

Biological effects of α-adrenergic phentolamine on erythrocyte hemeprotein: Molecular insights from biorecognition behavior, protein dynamics and flexibility

Phentolamine is one of the most representative nonselective α-adrenoreceptor blocking agents, which have been proved to be owned various pharmacological actions. Unfortunately, whether erythrocytes in the veins intervene in biological behaviors of such drug are largely obscured. With the aid of multiple biophysical techniques, this scenario was to detailed explore the potential biorecognition between phentolamine and the hemeprotein in the cytosol of erythrocytes, and the influences of dynamic characters of protein during the bioreaction. Steady-state and time-resolved fluorescence data manifested that the biomolecular recognition of phentolamine by hemeprotein was processed through the biopolymer-drug adduct with a moderate strength of 10⁴M^-1. Such procedure causes a reduction in fluorescence intensity of the aromatic tryptophan (Trp) residues, and the R-T transition of the globular protein occurred concurrently. Circular dichroism demonstrated the conclusions of fluorescence essays, viz. biorecognition can induce fairly structural transformation (self-regulation) of protein conformation. Furthermore, one could find that a specific domain for phentolamine is located at the polypeptide chains α₁β₂ interface, and hydrogen bonds, π-conjugated and hydrophobic effects are discovered to be held the lowest energy state of the biomacromolecule-drug biosystem, which overtly matches the outcomes of wet experiments. Meanwhile, several crucial residues such as Trp-37 and Arg-40 were confirmed to have directly noncovalent interactions with phentolamine, and the effect of the heme group on the biomolecule-drug recognition is minimal. Further analyses of molecular dynamics simulation supported that the inherent protein flexibility may notably elicit alterations in some key noncovalent bonds between biomacromolecule and drug during the dynamic biointeraction, which might primarily be attributed to the torsion of drug structure and the conformational changes of essential residues. Undoubtedly, this research will not only help to thoroughly unearth the pharmacological profiles of phentolamine, but to elaborate the impacts of the intrinsic features (i.e. dynamics and flexibility) of critically cellular proteins on the biological conducts of active α-adrenergic blockers.

Protein S-nitrosylation: specificity and identification strategies in plants

The role of nitric oxide (NO) as a major regulator of plant physiological functions has become increasingly evident. To further improve our understanding of its role, within the last few years plant biologists have begun to embrace the exciting opportunity of investigating protein S-nitrosylation, a major reversible NO-dependent post-translational modification (PTM) targeting specific Cys residues and widely studied in animals. Thanks to the development of dedicated proteomic approaches, in particular the use of the biotin switch technique (BST) combined with mass spectrometry, hundreds of plant protein candidates for S-nitrosylation have been identified. Functional studies focused on specific proteins provided preliminary comprehensive views of how this PTM impacts the structure and function of proteins and, more generally, of how NO might regulate biological plant processes. The aim of this review is to detail the basic principle of protein S-nitrosylation, to provide information on the biochemical and structural features of the S-nitrosylation sites and to describe the proteomic strategies adopted to investigate this PTM in plants. Limits of the current approaches and tomorrow's challenges are also discussed.