An unexpected Bis-ligation of S-nitrosothiols

Redox regulation, protein S-nitrosylation, and synapse loss in Alzheimer's and related dementias

Redox-mediated posttranslational modification, as exemplified by protein S-nitrosylation, modulates protein activity and function in both health and disease. Here, we review recent findings that show how normal aging, infection/inflammation, trauma, environmental toxins, and diseases associated with protein aggregation can each trigger excessive nitrosative stress, resulting in aberrant protein S-nitrosylation and hence dysfunctional protein networks. These redox reactions contribute to the etiology of multiple neurodegenerative disorders as well as systemic diseases. In the CNS, aberrant S-nitrosylation reactions of single proteins or, in many cases, interconnected networks of proteins lead to dysfunctional pathways affecting endoplasmic reticulum (ER) stress, inflammatory signaling, autophagy/mitophagy, the ubiquitin-proteasome system, transcriptional and enzymatic machinery, and mitochondrial metabolism. Aberrant protein S-nitrosylation and transnitrosylation (transfer of nitric oxide [NO]-related species from one protein to another) trigger protein aggregation, neuronal bioenergetic compromise, and microglial phagocytosis, all of which contribute to the synapse loss that underlies cognitive decline in Alzheimer's disease and related dementias.

The Chemistry of HNO: Mechanisms and Reaction Kinetics

Azanone (HNO, also known as nitroxyl) is the protonated form of the product of one-electron reduction of nitric oxide (^•NO), and an elusive electrophilic reactive nitrogen species of increasing pharmacological significance. Over the past 20 years, the interest in the biological chemistry of HNO has increased significantly due to the numerous beneficial pharmacological effects of its donors. Increased availability of various HNO donors was accompanied by great progress in the understanding of HNO chemistry and chemical biology. This review is focused on the chemistry of HNO, with emphasis on reaction kinetics and mechanisms in aqueous solutions.

Covalent Chemical Tools for Profiling Post-Translational Modifications

Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs); a process that involves the proteolytic processing or catalytic attachment of diverse functional groups onto proteins. These modifications modulate a host of biological activities and responses. Consequently, anomalous PTMs often correlate to a host of diseases, hence there is a need to detect these transformations, both qualitatively and quantitatively. One technique that has gained traction is the use of robust chemical strategies to label different PTMs. By utilizing the intrinsic chemical reactivity of the different chemical groups on the target amino acid residues, this strategy can facilitate the delineation of the overarching and inclusionary roles of these different modifications. Herein, we will discuss the current state of the art in post-translational modification analysis, with a direct focus on covalent chemical methods used for detecting them.

Protein S-Nitrosation: Biochemistry, Identification, Molecular Mechanisms, and Therapeutic Applications

Protein S-nitrosation (SNO), a posttranslational modification (PTM) of cysteine (Cys) residues elicited by nitric oxide (NO), regulates a wide range of protein functions. As a crucial form of redox-based signaling by NO, SNO contributes significantly to the modulation of physiological functions, and SNO imbalance is closely linked to pathophysiological processes. Site-specific identification of the SNO protein is critical for understanding the underlying molecular mechanisms of protein function regulation. Although careful verification is needed, SNO modification data containing numerous functional proteins are a potential research direction for druggable target identification and drug discovery. Undoubtedly, SNO-related research is meaningful not only for the development of NO donor drugs but also for classic target-based drug design. Herein, we provide a comprehensive summary of SNO, including its origin and transport, identification, function, and potential contribution to drug discovery. Importantly, we propose new views to develop novel therapies based on potential protein SNO-sourced targets.

Specific Reactions of RSNO, HSNO, and HNO and Their Applications in the Design of Fluorescent Probes

Nitric oxide (NO)-derived species play essential roles in regulating cellular responses. Among these species, S-nitrosothiols (including RSNO and HSNO) and nitroxyl (HNO) are especially interesting. Owing to their high reactivity and short survival time, the detection of these molecules in biological settings can be challenging. In this regard, much effort has been invested in exploring novel reactions of RSNO/HSNO/HNO and applying these reactions to develop fluorescence probes. Herein, reported specific reactions of RSNO/HSNO/HNO are summarized and strategies used in the design of fluorescent probes are illustrated. The properties and potential problems of representative probes are also discussed.

A clickable probe for versatile characterization of S-nitrosothiols

S-nitrosation of cysteine thiols (SNOs), commonly referred to as S-nitrosylation, is a cysteine oxoform that plays an important role in cellular signaling and impacts protein function and stability. Direct labeling of SNOs in cells with the flexibility to perform a wide range of cellular and biochemical assays remains a bottleneck as all SNO-targeted probes to date employ a single analytical modality such as biotin or a specific fluorophore. We therefore developed a clickable, alkyne-containing SNO probe 'PBZyn' based on the o-phosphino-benzoyl group warhead that enables multi-modal analysis via click conjugation. We demonstrate the utility of PBZyn to assay SNOs using in situ cellular imaging, protein blotting and affinity purification, as well as mass spectrometry. The flexible PBZyn probe will greatly facilitate investigation into the regulation of SNOs.

Protective mechanisms of hydrogen sulfide in myocardial ischemia

Hydrogen sulfide (H₂ S), which has been identified as the third gaseous signaling molecule after nitric oxide (NO) and carbon monoxide (CO), plays an important role in maintaining homeostasis in the cardiovascular system. Endogenous H₂ S is produced mainly by three endogenous enzymes: cystathionine β-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfur transferase. Numerous studies have shown that H₂ S has a significant protective role in myocardial ischemia. The mechanisms by which H₂ S affords cardioprotection include the antifibrotic and antiapoptotic effects, regulation of ion channels, protection of mitochondria, reduction of oxidative stress and inflammatory response, regulation of microRNA expression, and promotion of angiogenesis. Amplification of NO- and CO-mediated signaling through crosstalk between H₂ S, NO, and CO may also contribute to the cardioprotective effect. Exogenous H₂ S donors are expected to become effective drugs for the treatment of cardiovascular diseases. This review article focuses on the protective mechanisms and potential therapeutic applications of H₂ S in myocardial ischemia.

The Chemical Methods of Disulfide Bond Formation and Their Applications to Drug Conjugates

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The disulfide bond possesses unique chemical and biophysical properties which distinguish it as one of the key structural elements of bioactive proteins and peptides, important drugs and other materials. The chemo-selective synthesis of these structures and the exploration of their function have been of longstanding interest to the chemistry community. The past decades have witnessed significant progress in both areas. This review will summarize the historically established and recently developed chemical methods in disulfide bond formation. The discussion will also be extended to the use of the disulfide linkers in small molecules, and peptide- and protein-drug conjugates. It is hoped that the combined overview of the fundamental chemistries and applications to drug discovery will inspire creative thinking and stimulate future novel uses of these versatile chemistries.

Rational Design of a Dual-Reactivity-Based Fluorescent Probe for Visualizing Intracellular HSNO

Thionitrous acid (HSNO), the smallest S-nitrosothiol, is emerging as a potential key intermediate in cellular redox regulation linking two signaling molecules H₂ S and NO. However, the chemical biology of HSNO remains poorly understood. A major hurdle is the lack of methods for selective detection of HSNO in biological systems. Herein, we report the rational design, synthesis, and evaluation of the first fluorescent probe TAP-1 for HSNO detection. TAP-1 showed high selectivity and sensitivity to HSNO in aqueous media and cells, providing a useful tool for understanding the functions of HSNO in biology.

Phosphite Esters: Reagents for Exploring S-Nitrosothiol Chemistry

The reactions between S-nitrosothiols and phosphite esters, including P(OPh)₃, P(OBn)₃, and P(OEt)₃, were studied. Two different conjugated adducts, thiophosphoramidates and phosphorothioates, were formed, depending on the structures of the S-nitrosothiol substrate (e.g., primary vs tertiary). These reactions proceeded under mild conditions, and the reaction mechanisms were studied using experiments and calculations.

Fluorescent probes for the detection of nitroxyl (HNO)

Nitroxyl (HNO), which according to the IUPAC recommended nomenclature should be named azanone, is the protonated one-electron reduction product of nitric oxide. Recently, it has gained a considerable attention due to the interesting pharmacological effects of its donors. Although there has been great progress in the understanding of HNO chemistry and chemical biology, it still remains the most elusive reactive nitrogen species, and its selective detection is a real challenge. The development of reliable methodologies for the direct detection of azanone is essential for the understanding of important signaling properties of this reactive intermediate and its pharmacological potential. Over the last decade, there has been considerable progress in the development of low-molecular-weight fluorogenic probes for the detection of HNO, and therefore, in this review, we have focused on the challenges and limitations of and perspectives on nitroxyl detection based on the use of such probes.

S-Nitrosothiols: chemistry and reactions

The formation of S-nitrosothiols (SNO) in protein cysteine residues is an important post-translational modification elicited by nitric oxide (NO). This process is involved in virtually every class of cell signaling and has attracted considerable attention in redox biology. On the other hand, their unique structural characters make SNO potentially useful synthons. In this review, we summarized the fundamental chemical/physical properties of SNO. We also highlighted the reported chemical reactions of SNO, including the reactions with phosphine reagents, sulfinic acids, various nucleophiles, SNO-mediated radical additions, and the reactions of acyl SNO species.

Chemical methods for mapping cysteine oxidation

Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.

S-nitrosation of proteins relevant to Alzheimer's disease during early stages of neurodegeneration

Protein S-nitrosation (SNO-protein), the nitric oxide-mediated posttranslational modification of cysteine thiols, is an important regulatory mechanism of protein function in both physiological and pathological pathways. A key first step toward elucidating the mechanism by which S-nitrosation modulates a protein's function is identification of the targeted cysteine residues. Here, we present a strategy for the simultaneous identification of SNO-cysteine sites and their cognate proteins to profile the brain of the CK-p25-inducible mouse model of Alzheimer's disease-like neurodegeneration. The approach-SNOTRAP (SNO trapping by triaryl phosphine)-is a direct tagging strategy that uses phosphine-based chemical probes, allowing enrichment of SNO-peptides and their identification by liquid chromatography tandem mass spectrometry. SNOTRAP identified 313 endogenous SNO-sites in 251 proteins in the mouse brain, of which 135 SNO-proteins were detected only during neurodegeneration. S-nitrosation in the brain shows regional differences and becomes elevated during early stages of neurodegeneration in the CK-p25 mouse. The SNO-proteome during early neurodegeneration identified increased S-nitrosation of proteins important for synapse function, metabolism, and Alzheimer's disease pathology. In the latter case, proteins related to amyloid precursor protein processing and secretion are S-nitrosated, correlating with increased amyloid formation. Sequence analysis of SNO-cysteine sites identified potential linear motifs that are altered under pathological conditions. Collectively, SNOTRAP is a direct tagging tool for global elucidation of the SNO-proteome, providing functional insights of endogenous SNO proteins in the brain and its dysregulation during neurodegeneration.

Proline-based phosphoramidite reagents for the reductive ligation of S-nitrosothiols

S-Nitrosothiols have many biological implications but are rarely used in organic synthesis. In this work we report the development of proline-based phosphoramidite substrates that can effectively convert S-nitrosothiols to proline-based sulfenamides through a reductive ligation process. A unique property of this method is that the phosphine oxide moiety on the ligation products can be readily removed under acidic conditions. In conjugation with the facile preparation of S-nitrosothiols (RSNO) from the corresponding thiols (RSH), this method provides a new way to prepare proline-based sulfenamides from simple thiol starting materials.

Protein S-Nitrosylation as a Therapeutic Target for Neurodegenerative Diseases

At physiological levels, nitric oxide (NO) contributes to the maintenance of normal neuronal activity and survival, thus serving as an important regulatory mechanism in the central nervous system. By contrast, accumulating evidence suggests that exposure to environmental toxins or the normal aging process can trigger excessive production of reactive oxygen/nitrogen species (such as NO), contributing to the etiology of several neurodegenerative diseases. We highlight here protein S-nitrosylation, resulting from covalent attachment of an NO group to a cysteine thiol of the target protein, as a ubiquitous effector of NO signaling in both health and disease. We review our current understanding of this redox-dependent post-translational modification under neurodegenerative conditions, and evaluate how targeting dysregulated protein S-nitrosylation can lead to novel therapeutics.

Design, Synthesis, and Cardioprotective Effects of N-Mercapto-Based Hydrogen Sulfide Donors

Hydrogen sulfide (H2S) is a signaling molecule which plays regulatory roles in many physiological and/or pathological processes. Therefore, regulation of H2S levels could have great potential therapeutic value. In this work, we report the design, synthesis, and evaluation of a class of N-mercapto (N-SH)-based H2S donors. Thirty-three donors were synthesized and tested. Our results indicated that controllable H2S release from these donors could be achieved upon structural modifications. Selected donors (NSHD-1, NSHD-2, and NSHD-6) were tested in cellular models of oxidative damage and showed significant cytoprotective effects. Moreover, NSHD-1 and NSHD-2 were also found to exhibit potent protective effects in a murine model of myocardial ischemia reperfusion (MI/R) injury.

A reductive ligation based fluorescent probe for S-nitrosothiols

A reductive ligation based fluorescent probe () for the detection of S-nitrosothiols (SNO) was developed. The probe showed good selectivity and sensitivity for SNO.

Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation

Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.

Mass spectrometry in studies of protein thiol chemistry and signaling: opportunities and caveats

Mass spectrometry (MS) has become a powerful and widely utilized tool in the investigation of protein thiol chemistry, biochemistry, and biology. Very early biochemical studies of metabolic enzymes have brought to light the broad spectrum of reactivity profiles that distinguish cysteine thiols with functions in catalysis and protein stability from other cysteine residues in proteins. The development of MS methods for the analysis of proteins using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) coupled with the emergence of high-resolution mass analyzers has been instrumental in advancing studies of thiol modifications, both in single proteins and within the cellular context. This article reviews MS instrumentation and methods of analysis employed in investigations of thiols and their reactivity toward a range of small biomolecules. A selected number of studies are detailed to highlight the advantages brought about by the MS technologies along with the caveats associated with these analyses.

Chemical-proteomic strategies to investigate cysteine posttranslational modifications

The unique combination of nucleophilicity and redox-sensitivity that is characteristic of cysteine residues results in a variety of posttranslational modifications (PTMs), including oxidation, nitrosation, glutathionylation, prenylation, palmitoylation and Michael adducts with lipid-derived electrophiles (LDEs). These PTMs regulate the activity of diverse protein families by modulating the reactivity of cysteine nucleophiles within active sites of enzymes, and governing protein localization between soluble and membrane-bound forms. Many of these modifications are highly labile, sensitive to small changes in the environment, and dynamic, rendering it difficult to detect these modified species within a complex proteome. Several chemical-proteomic platforms have evolved to study these modifications and enable a better understanding of the diversity of proteins that are regulated by cysteine PTMs. These platforms include: (1) chemical probes to selectively tag PTM-modified cysteines; (2) differential labeling platforms that selectively reveal and tag PTM-modified cysteines; (3) lipid, isoprene and LDE derivatives containing bioorthogonal handles; and (4) cysteine-reactivity profiling to identify PTM-induced decreases in cysteine nucleophilicity. Here, we will provide an overview of these existing chemical-proteomic strategies and their effectiveness at identifying PTM-modified cysteine residues within native biological systems.

A reductant-resistant and metal-free fluorescent probe for nitroxyl applicable to living cells

Nitroxyl (HNO) is a one-electron reduced and protonated derivative of nitric oxide (NO) and has characteristic biological and pharmacological effects distinct from those of NO. However, studies of its biosynthesis and activities are restricted by the lack of versatile HNO detection methods applicable to living cells. Here, we report the first metal-free and reductant-resistant HNO imaging probe available for use in living cells, P-Rhod. It consists of a rhodol derivative moiety as the fluorophore, linked via an ester moiety to a diphenylphosphinobenzoyl group, which forms an aza-ylide upon reaction with HNO. Intramolecular attack of the aza-ylide on the ester carbonyl group releases a fluorescent rhodol derivative. P-Rhod showed high selectivity for HNO in the presence of various biologically relevant reductants, such as glutathione and ascorbate, in comparison with previous HNO probes. We show that P-Rhod can detect not only HNO enzymatically generated in the horseradish peroxidase-hydroxylamine system in vitro but also intracellular HNO release from Angeli's salt in living cells. These results suggest that P-Rhod is suitable for detection of HNO in living cells.

Mechanism-based triarylphosphine-ester probes for capture of endogenous RSNOs

Nitrosothiols (RSNOs) have been proposed as important intermediates in nitric oxide (NO^•) metabolism, storage, and transport as well as mediators in numerous NO-signaling pathways. RSNO levels are finely regulated, and dysregulation is associated with the etiology of several pathologies. Current methods for RSNO quantification depend on indirect assays that limit their overall specificity and reliability. Recent developments of phosphine-based chemical probes constitute a promising approach for the direct detection of RSNOs. We report here results from a detailed mechanistic and kinetic study for trapping RSNOs by three distinct phosphine probes, including structural identification of novel intermediates and stability studies under physiological conditions. We further show that a triarylphosphine-thiophenyl ester can be used in the absolute quantification of endogenous GSNO in several cancer cell lines, while retaining the elements of the SNO functional group, using an LC–MS-based assay. Finally, we demonstrate that a common product ion (m/z = 309.0), derived from phosphine–RSNO adducts, can be used for the detection of other low-molecular weight nitrosothiols (LMW-RSNOs) in biological samples. Collectively, these findings establish a platform for the phosphine ligation-based, specific and direct detection of RSNOs in biological samples, a powerful tool for expanding the knowledge of the biology and chemistry of NO^•-mediated phenomena.

Direct methods for detection of protein S-nitrosylation

S-nitrosylation of protein cysteine residues is known to be an important mechanism for nitric oxide signaling. However, the detection of protein S-nitrosylation is still challenging due to technical limitations of current methods. This chapter provides a brief review on recent developments of methods, which directly target S-nitroso moieties for detection. We also describe in detail the protocol of an organophosphine-based biotin labeling of protein S-nitroso moieties.

Methods for detection and characterization of protein S-nitrosylation

Reversible protein S-nitrosylation, defined as the covalent addition of a nitroso moiety to the reactive thiol group on a cysteine residue, has received increasing recognition as a critical post-translational modification that exerts ubiquitous influence in a wide range of cellular pathways and physiological processes. Due to the lability of the S-NO bond, which is a dynamic modification, and the low abundance of endogenously S-nitrosylated proteins in vivo, unambiguous identification of S-nitrosylated proteins and S-nitrosylation sites remains methodologically challenging. In this review, we summarize recent advancements and the use of state-of-art approaches for the enrichment, systematic identification and quantitation of S-nitrosylation protein targets and their modification sites at the S-nitrosoproteome scale. These advancements have facilitated the global identification of >3000 S-nitrosylated proteins that are associated with wide range of human diseases. These strategies hold promise to site-specifically unravel potential molecular targets and to change S-nitrosylation-based pathophysiology, which may further the understanding of the potential role of S-nitrosylation in diseases.

Chemical methods for the direct detection and labeling of S-nitrosothiols

SIGNIFICANCE

Posttranslational modification of proteins through phosphorylation, glycosylation, and oxidation adds complexity to the proteome by reversibly altering the structure and function of target proteins in a highly controlled fashion.

RECENT ADVANCES

The study of reversible cysteine oxidation highlights a role for this oxidative modification in complex signal transduction pathways. Nitric oxide (NO), and its respective metabolites (including reactive nitrogen species), participates in a variety of these cellular redox processes, including the reversible oxidation of cysteine to S-nitrosothiols (RSNOs). RSNOs act as endogenous transporters of NO, but also possess beneficial effects independent of NO-related signaling, which suggests a complex and versatile biological role. In this review, we highlight the importance of RSNOs as a required posttranslational modification and summarize the current methods available for detecting S-nitrosation.

CRITICAL ISSUES

Given the limitations of these indirect detection methods, the review covers recent developments toward the direct detection of RSNOs by phosphine-based chemical probes. The intrinsic properties that dictate this phosphine/RSNO reactivity are summarized. In general, RSNOs (both small molecule and protein) react with phosphines to yield reactive S-substituted aza-ylides that undergo further reactions leading to stable RSNO-based adducts.

FUTURE DIRECTIONS

This newly explored chemical reactivity forms the basis of a number of exciting potential chemical methods for protein RSNO detection in biological systems.

Zinc thiolate reactivity toward nitrogen oxides: insights into the interaction of Zn2+ with S-nitrosothiols and implications for nitric oxide synthase

Zinc thiolate complexes containing N(2)S tridentate ligands were prepared to investigate their reactivity toward reactive nitrogen species, chemistry proposed to occur at the zinc tetracysteine thiolate site of nitric oxide synthase (NOS). The complexes are unreactive toward nitric oxide (NO) in the absence of dioxygen, strongly indicating that NO cannot be the species directly responsible for S-nitrosothiol formation and loss of Zn(2+) at the NOS dimer interface in vivo. S-Nitrosothiol formation does occur upon exposure of zinc thiolate solutions to NO in the presence of air, however, or to NO(2) or NOBF(4), indicating that these reactive nitrogen/oxygen species are capable of liberating zinc from the enzyme, possibly through generation of the S-nitrosothiol. Interaction between simple Zn(2+) salts and preformed S-nitrosothiols leads to decomposition of the -SNO moiety, resulting in release of gaseous NO and N(2)O. The potential biological relevance of this chemistry is discussed.

Identification of protein nitrosothiols using phosphine-mediated selective reduction

Regulation of protein function by S-nitrosation of critical cysteines is known to be an important mechanism for nitric oxide signaling. Evidence for this comes from several different experimental approaches including the ascorbate-based biotin switch method. However technical problems with specificity and sensitivity of ascorbate reduction of S-nitrosothiols limit its usefulness and reliability. In the current study we report the use of triphenylphosphine ester derivatives to selectively reduce SNO bonds in proteins. After triphenylphosphine ester reduction, thiols were tagged with biotin or fluorescently labeled maleimide reagents. Importantly we demonstrate that these compounds are specific reductants of SNO in complex biological samples and do not reduce protein disulfides or protein thiols modified by hydrogen peroxide. Reduction proceeds efficiently in cell extracts and in whole fixed cells. Application of this approach allowed us to demonstrate S-nitrosation of specific cellular proteins, label S-nitrosoproteins in whole fixed cells (especially the nuclear compartment) and demonstrate S-nitrosoprotein formation in cells expressing inducible nitric oxide synthase.

Rapid and selective nitroxyl (HNO) trapping by phosphines: kinetics and new aqueous ligations for HNO detection and quantitation

Recent studies distinguish the biological and pharmacological effects of nitroxyl (HNO) from its oxidized/deprotonated product nitric oxide (·NO), but the lack of HNO detection methods limits the understanding its in vivo mechanisms and the identification of endogenous sources. We previously demonstrated that reaction of HNO with triarylphosphines provides aza-ylides and HNO-derived amides, which may serve as stable HNO biomarkers. We now report a kinetic analysis for the trapping of HNO by phosphines, ligations of enzyme-generated HNO, and compatibility studies illustrating the selectivity of phosphines for HNO over other physiologically relevant nitrogen oxides. Quantification of HNO using phosphines is demonstrated using an HPLC-based assay and ligations of phosphine carbamates generate HNO-derived ureas. These results further demonstrate the potential of phosphine probes for reliable biological detection and quantification of HNO.

Strategies and tools to explore protein S-nitrosylation

BACKGROUND

A biochemical pathway by which nitric oxide accomplishes functional diversity is the specific modification of protein cysteine residues to form S-nitrosocysteine. This post-translational modification, S-nitrosylation, impacts protein function, interactions and location. However, comprehensive studies exploring protein signaling pathways or interrelated protein clusters that are regulated by S-nitrosylation have not been performed on a global scale.

SCOPE OF REVIEW

To provide insights to these important biological questions, sensitive, validated and quantitative proteomic approaches are required. This review summarizes current approaches for the global identification of S-nitrosylated proteins.

MAJOR CONCLUSIONS

The application of novel methods for identifying S-nitrosylated proteins, especially when combined with mass-spectrometry based proteomics to provide site-specific identification of the modified cysteine residues, promises to deliver critical clues for the regulatory role of this dynamic posttranslational modification in cellular processes.

GENERAL SIGNIFICANCE

Though several studies have established S-nitrosylation as a regulator of protein function in individual proteins, the biological chemistry and the structural elements that govern the specificity of this modification in vivo are vastly unknown. Additionally, a gap in knowledge exists concerning the potential global regulatory role(s) this modification may play in cellular physiology. By further studying S-nitrosylation at a global scale, a greater appreciation of nitric oxide and protein S-nitrosylation in cellular function can be achieved. This article is part of a Special Issue entitled Regulation of Cellular Processes by S-nitrosylation.

Methodologies for the characterization, identification and quantification of S-nitrosylated proteins

BACKGROUND

Protein S-nitrosylation plays a central role in signal transduction by nitric oxide (NO), and aberrant S-nitrosylation of specific proteins is increasingly implicated in disease.

SCOPE OF REVIEW

Here, methodologies for the characterization, identification and quantification of SNO-proteins are reviewed, focusing on techniques suitable for the structural characterization and absolute quantification of isolated SNO-proteins, the identification and relative quantification of SNO-proteins from complex mixtures as well as the mass spectrometry-based identification and relative quantification of sites of S-nitrosylation (SNO-sites) in proteins.

MAJOR CONCLUSIONS

Structural characterization of SNO-proteins by X-ray crystallography is increasingly being utilized to understand both the relationships between protein structure and Cys thiol reactivity as well as the consequences of S-nitrosylation on protein structure and function. New methods for the proteomic identification and quantification of SNO-proteins and SNO-sites have greatly impacted the ability to study protein S-nitrosylation in complex biological systems.

GENERAL SIGNIFICANCE

The ability to identify and quantify SNO-proteins has long been rate-determining for scientific advances in the field of protein S-nitrosylation. Therefore, it is critical that investigators in the field have a good understand the utility and limitations of modern analytical techniques for SNO-protein analysis. This article is part of a Special Issue entitled: Regulation of cellular processes by S-nitrosylation.

Facile amide formation via S-nitrosothioacids

Here we report a novel amide bond formation strategy from simple thioacid and amine starting materials. The reaction is mediated by unstable but very reactive S-nitrosothioacid intermediates. This fast reaction under mild conditions should be useful in synthesis.

Reductive ligation mediated one-step disulfide formation of S-nitrosothiols

A one-step reductive ligation mediated disulfide formation of S-nitrosothiols was developed. This reaction involves the reaction of the S-nitroso group with phosphine-thioesters to form sulfenamide and thiolate intermediates, which then undergo a fast intermolecular disulfide formation to form stable conjugates. This reaction can be used to design new biosensors of S-nitrosated proteins.

Cysteine-activated hydrogen sulfide (H2S) donors

H(2)S, the newly discovered gasotransmitter, plays important roles in biological systems. However, the research on H(2)S has been hindered by the lack of controllable H(2)S donors that could mimic the slow and continuous H(2)S generation process in vivo. Herein we report a series of cysteine-activated H(2)S donors. Structural modifications of these molecules can regulate the rates of H(2)S generation. These compounds can be useful tools in H(2)S research.

One-pot thioether formation from S-nitrosothiols

Protein S-nitrosation is an important post-translational modification. However, the detection of S-nitrosation is still problematic because S-nitrosation products, that is, S-nitrosothiols, are unstable species. Here a new reaction which can selectively convert unstable S-nitrosothiols to stable thioethers in one-pot under very mild conditions is reported. This reaction has the potential to be applied in the detection of protein S-nitrosation.

Iron acyl thiolato carbonyls: structural models for the active site of the [Fe]-hydrogenase (Hmd)

Phosphine-modified thioester derivatives are shown to serve as efficient precursors to phosphine-stabilized ferrous acyl thiolato carbonyls, which replicate key structural features of the active site of the hydrogenase Hmd. The reaction of Ph(2)PC(6)H(4)C(O)SPh and sources of Fe(0) generates both Fe(SPh)(Ph(2)PC(6)H(4)CO)(CO)(3) (1) and the diferrous diacyl Fe(2)(SPh)(2)(CO)(3)(Ph(2)PC(6)H(4)CO)(2), which carbonylates to give 1. For the extremely bulky arylthioester Ph(2)PC(6)H(4)C(O)SC(6)H(3)-2,6-(2,4,6-trimethylphenyl)(2), oxidative addition is arrested and the Fe(0) adduct of the phosphine is obtained. Complex 1 reacts with cyanide to give Et(4)N[Fe(SPh)(Ph(2)PC(6)H(4)CO)(CN)(CO)(2)] (Et(4)N[2]). (13)C and (31)P NMR spectra indicate that substitution is stereospecific and cis to P. The IR spectrum of [2](-) in ν(CN) and ν(CO) regions very closely matches that for Hmd(CN). XANES and EXAFS measurements also indicate close structural and electronic similarity of Et(4)N[2] to the active site of wild-type Hmd. Complex 1 also stereospecifically forms a derivative with TsCH(2)NC, but the adduct is more labile than Et(4)N[2]. Tricarbonyl 1 was found to reversibly protonate to give a thermally labile derivative, IR measurements of which indicate that the acyl and thiolate ligands are probably not protonated in Hmd.

Chemical methods to detect S-nitrosation

Nitric oxide (NO) is a cell-signaling molecule involved in a number of physiological and pathophysiological processes. Modification of cysteine residues by NO (or NO metabolites), that is S-nitrosation, changes the function of a broad spectrum of proteins. This reaction represents an important post-translational modification that transduces NO-dependent signals. However, the detection and quantification of S-nitrosation in biological samples remain a challenge mainly because of the lability of S-nitrosation products: S-nitrosothiols (SNO). In this review we summarize recent developments of the methods to detect S-nitrosation. Our focus is on the methods which can be used to directly conjugate the site(s) of S-nitrosation.

Facile formation of dehydroalanine from S-nitrosocysteines

A reductive elimination of S-nitrosocysteines using phosphine substrates has been developed. This reaction converts unstable S-nitrosocysteines to dehydroalanine derivatives under very mild conditions. It can potentially be applied for the detection of protein S-nitrosation.