Modification Of Cysteine Residues Research Articles

Electrophilic activation of the nociceptive channel TRPA1 requires a 6000‐fold increase in reactivity at cysteine 621 that is dependent on a neighboring lysine

Mammalian TRPA1 is a cation channel expressed on nociceptive sensory nerves and contributes to pain/nociceptive responses to oxidative stress and inflammation. In particular TRPA1 is rapidly activated by oxidative stress‐associated electrophiles capable of covalent modification of cysteine residues. Putative ‘functionally electrophile‐sensitive’ Cys‐containing proteins must be put into context of antioxidant microenvironments containing mM glutathione and enzymes that accelerate electrophilic‐GSH reactions. Thus the mechanisms underlying the rapid reaction rates of TRPA1 Cys are fundamental to its ability to act as a competent sensor of oxidative stress and electrophilic damage. We have used physiologically relevant concentrations and exposures in both binding studies and functional experiments to offer mechanistic insights into the functional responses of TRPA1 to electrophiles. Human and mouse TRPA1 are rapidly covalently modified by electrophiles and this response is insensitive to TRPA1 inhibition or the absence of polyphosphates. Orthologs and paralogs insensitive to electrophiles display no rapid binding. Mass spectroscopy studies identified only 4 Cys rapidly modified: C273, C621, C665 and C1085. 98% of C621 were modified with 120s of 30uM iodoacetamide treatment. Only 3–4% of the other three Cys were modified. The second order reaction rate of C621 with iodoacetamide is >6000‐fold faster than typical Cys residues. The mutant C621A displays greatly reduced electrophilic binding and is not activated by iodoacetamide. Neighboring basic residues can increase thiol reactivity by promoting the thiolate state. Mutation of K620 eliminated electrophilic binding and electrophile‐induced activation, despite continued presence of C621. This data suggest that TRPA1 possesses a complex reactive Cys profile centering on the extraordinary reactivity of Cys 621, which is determined by its low pKa under the influence of its neighbor Lys 620. The reactivity of C621 is critical to TRPA1's functional sensitivity to oxidative stress. The extraordinary reactivity of TRPA1 C621 is likely fundamental to nociceptive responses to oxidative stress‐associated inflammation.Support or Funding InformationNHLBI R01HL119802 and R01HL119802‐S1

OX133, a monoclonal antibody recognizing protein-bound N-ethylmaleimide for the identification of reduced disulfide bonds in proteins

ABSTRACTIn vivo, enzymatic reduction of some protein disulfide bonds, allosteric disulfide bonds, provides an important level of structural and functional regulation. The free cysteine residues generated can be labeled by maleimide reagents, including biotin derivatives, allowing the reduced protein to be detected or purified. During the screening of monoclonal antibodies for those specific for the reduced forms of proteins, we isolated OX133, a unique antibody that recognizes polypeptide resident, N-ethylmaleimide (NEM)-modified cysteine residues in a sequence-independent manner. OX133 offers an alternative to biotin-maleimide reagents for labeling reduced/alkylated antigens and capturing reduced/alkylated proteins with the advantage that NEM-modified proteins are more easily detected in mass spectrometry, and may be more easily recovered than is the case following capture with biotin based reagents.

Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 2: Peptide Tags and Unnatural Amino Acids.

Molecular imaging using radioisotope- or fluorophore-labeled antibodies is increasingly becoming a critical component of modern precision medicine. Yet despite this promise, the vast majority of these immunoconjugates are synthesized via the random coupling of amine-reactive bifunctional probes to lysines within the antibody, a process that can result in heterogeneous and poorly defined constructs with suboptimal pharmacological properties. In an effort to circumvent these issues, the last 5 years have played witness to a great deal of research focused on the creation of effective strategies for the site-specific attachment of payloads to antibodies. These chemoselective modification methods yield immunoconjugates that are more homogenous and better defined than constructs created using traditional synthetic approaches. Moreover, site-specifically labeled immunoconjugates have also been shown to exhibit superior in vivo behavior compared to their randomly modified cousins. The over-arching goal of this two-part review is to provide a broad yet detailed account of the various site-specific bioconjugation approaches that have been used to create immunoconjugates for positron emission tomography (PET), single photon emission computed tomography (SPECT), and fluorescence imaging. In Part 1, we covered site-specific bioconjugation techniques based on the modification of cysteine residues and the chemoenzymatic manipulation of glycans. In Part 2, we will detail two families of bioconjugation approaches that leverage biochemical tools to achieve site-specificity. First, we will discuss modification methods that employ peptide tags either as sites for enzyme-catalyzed ligations or as radiometal coordination architectures. And second, we will examine bioconjugation strategies predicated on the incorporation of unnatural or non-canonical amino acids into antibodies via genetic engineering. Finally, we will compare the advantages and disadvantages of the modification strategies covered in both parts of the review and offer a brief discussion of the overall direction of the field.

Effect of Cysteamine on Mutant ASL Proteins with Cysteine for Arginine Substitutions

Cysteamine is used to treat cystinosis via the modification of cysteine residues substituting arginine in mutant proteins. We investigated the effect of cysteamine on mutant argininosuccinate lyase (ASL), the second most common defect in the urea cycle. In an established mammalian expression system, 293T cell lysates were produced after transfection with all known cysteine for arginine mutations in the ASL gene (p.Arg94Cys, p.Arg95Cys, p.Arg168Cys, p.Arg379Cys, and p.Arg385Cys), allowing testing of the effect of cysteamine over 48 h in the culture medium as well as for 1 h immediately prior to the enzyme assay. Cysteamine at low concentrations showed no effect on 293T cell viability, ASL protein expression, or ASL activity when applied during cell culture. However, incubation of transfected cells with 0.05 mM cysteamine immediately before the enzyme assay resulted in increased ASL activity of p.Arg94Cys, p.Arg379Cys, and p.Arg385Cys by 64, 20, and 197 %, respectively, and this result was significant (p < 0.01). Cell lysates carrying p.Arg385Cys and treated with cysteamine recover enzyme activity that is similar to the untreated designed mutation p.Arg385Lys, providing circumstantial evidence for the assumed cysteamine-induced change of a cysteine to a lysine analogue. Since 12 % of all known genotypes in ASL deficiency are affected by a cysteine for arginine mutation, we conclude that the potential of cysteamine or of related substances as remedy for this disease should be investigated further.

Chloromethyl-triazole: a new motif for site-selective pseudo-acylation of proteins.

Rapid, site-selective modification of cysteine residues with chloromethyl-triazole derivatives generates pseudo-acyl sLys motifs, mimicking important post-translational modifications. Near-native biotinylation of peptide and protein substrates is shown to be site-selective and modified histone H4 retains functional activity.

Modification of ubiquitin C-terminal hydrolase L1 by reactive lipid species: role in neural regeneration and diseases of aging.

Modification of ubiquitin C-terminal hydrolase L1 by reactive lipid species: role in neural regeneration and diseases of aging.

Label-Free Bottom-Up Proteomic Workflow for Simultaneously Assessing the Target Specificity of Covalent Drug Candidates and Their Off-Target Reactivity to Selected Proteins.

Although designed covalent inhibitors as drug candidates offer several unique advantages over conventional reversible inhibitors, including high potency and the potential for less frequent dosing, there is a general tendency to avoid the covalent mode of action in drug discovery programs due to concerns regarding immune-mediated toxicity that can arise from indiscriminate reactivity with off-target proteins. Therefore, the ability to assess off-target reactivity relative to target specificity is desirable for optimizing covalent drug candidates in the early discovery stage. One concern with current surrogate nucleophile trapping approaches is that they employ a simplistic model nucleophile such as glutathione, which may not reliably reflect the covalent interactions with cellular or extracellular proteins. One way to get a more relevant reactivity assessment is to directly measure the ability of an inhibitor to covalently modify nucelophilic amino acids on biologically relevant proteins, both on- and off-target. In this article, we describe a label-free bottom-up proteomic workflow for simultaneous evaluation of target binding and off-target reactivity of covalent drug candidates to selected proteins at the peptide level. Ibrutinib, a covalent drug targeting the active site of BTK protein, was used as a model compound to demonstrate the feasibility of the workflow. The compound was incubated with a mixture of target protein, Bruton's tyrosine kinase (BTK), and two abundant proteins in blood, hemoglobin (Hb) and human serum albumin (HSA), and then the ibrutinib modification sites were determined utilizing a bottom-up proteomic approach. A non-BTK specific model compound (1) known to modify cysteine residues was also included. By comparing the extent of off-target modifications to the targeted BTK C481 binding in a wide compound concentration range, we were able to determine the concentration where maximum target binding was achieved with minimal off-target reactivity. The generic label-free bottom-up proteomics workflow described in this article should be useful in the rank order assessment of off-target reactivity vs on-target reactivity of covalent drug candidates in the early drug discovery stage.

Redox-Dependent HMGB1 Isoforms as Pivotal Co-Ordinators of Drug-Induced Liver Injury: Mechanistic Biomarkers and Therapeutic Targets.

High-mobility group box 1 (HMGB1) is a critical protein in the coordination of the inflammatory response in drug-induced liver injury (DILI). HMGB1 is released from necrotic hepatocytes and activated immune cells. The extracellular function of HMGB1 is dependent upon redox modification of cysteine residues that control chemoattractant and cytokine-inducing properties. Existing biomarkers of DILI such as alanine aminotransferase (ALT) have limitations such as lack of sensitivity and tissue specificity that can adversely affect clinical intervention. HMGB1 isoforms have been shown to be more sensitive biomarkers than ALT for predicting DILI development and the requirement for liver transplant following acetaminophen (APAP) overdose. Hepatocyte-specific conditional knockout of HMGB1 has demonstrated the pivotal role of HMGB1 in DILI and liver disease. Tandem mass spectrometry (MS/MS) enables the characterization and quantification of different mechanism-dependent post-translationally modified isoforms of HMGB1. HMGB1 shows great promise as a biomarker of DILI. However, current diagnostic assays are either too time-consuming to be clinically applicable (MS/MS) or are unable to distinguish between different redox and acetyl isoforms of HMGB1 (ELISA). Additionally, HMGB1 is not liver specific, so while it outperforms ALT (also not liver specific) as a biomarker for the prediction of DILI development, it should be used in a biomarker panel along with liver-specific markers such as miR-122. A point-of-care test for HMGB1 and the development of redox and acetyl isoform-targeting antibodies will advance clinical utility. Work is ongoing to validate baseline levels of circulating HMGB1 in healthy volunteers.

Post-Translational Nitric Oxide–Dependent Modifications In Immune System

Nitric oxide non classical signalling is exerted through a series of covalent protein post-translational modifications, which include modification of cysteine residues by S-nitrosylation and S-glutathionylation. A key process in adaptive immunity is the immune synapse that tightly couples T cells with antigen presenting cells, triggering antigen recognition by T cells. In this highly regulated process, we have shown that eNOS is activated, inducing protein S-nitrosylation. While both N-Ras and K-Ras are present in T cells, only N-Ras, which colocalizes in the Golgi with eNOS, is S-nitrosylated and activated during the immune synapse, providing an example of short-range selectivity of NO signalling through S-nitrosylation. We have developed proteomic methods to detect S-nitrosylation and reversible cysteine oxidations. We have applied them to detecting S-nitrosylated proteins in macrophage activation, highlighting the role of denitrosylase mechanism, particularly the thioredoxin pathway, in protecting macrophages from self-modification. We have also applied these proteomic methods to studying protein modification in acute hypoxia. In endothelial cells, there is an increase in cysteine oxidation in several proteins that can mediate acute responses to hypoxia prior to the activation of the HIF pathway, and we are currently studying in more detail the role of protein S-nitrosylation. We have also recently shown that acute hypoxia produces a superoxide burst in cells, which can be converted in an oxidative signal through protein cysteine modification, and we are unraveling the molecular mechanisms producing this superoxide burst in mitochondria.

Membrane accessibility of glutathione

Regulation of the ion pumping activity of the Na+,K+-ATPase is crucial to the survival of animal cells. Recent evidence has suggested that the activity of the enzyme could be controlled by glutathionylation of cysteine residue 45 of the β-subunit. Crystal structures so far available indicate that this cysteine is in a transmembrane domain of the protein. Here we have analysed via fluorescence and NMR spectroscopy as well as molecular dynamics simulations whether glutathione is able to penetrate into the interior of a lipid membrane. No evidence for any penetration of glutathione into the membrane was found. Therefore, the most likely mechanism whereby the cysteine residue could become glutathionylated is via a loosening of the α–β subunit association, creating a hydrophilic passageway between them to allow access of glutathione to the cysteine residue. By such a mechanism, glutathionylation of the protein would be expected to anchor the modified cysteine residue in a hydrophilic environment, inhibiting further motion of the β-subunit during the enzyme's catalytic cycle and suppressing enzymatic activity, as has been experimentally observed. The results obtained, therefore, suggest a possible structural mechanism of how the Na+,K+-ATPase could be regulated by glutathione.

A Thiol–Ene Coupling Approach to Native Peptide Stapling and Macrocyclization

We report the discovery of a peptide stapling and macrocyclization method using thiol-ene reactions between two cysteine residues and an α,ω-diene in high yields. This new approach enabled us to selectively modify cysteine residues in native, unprotected peptides with a variety of stapling modifications for helix stabilization or general macrocyclization. We synthesized stapled Axin mimetic analogues and demonstrated increased alpha helicity upon peptide stapling. We then synthesized stapled p53 mimetic analogues using pure hydrocarbon linkers and demonstrated their abilities to block the p53-MDM2 interaction and selectively kill p53 wild-type colorectal carcinoma HCT-116 cells but not p53 null cells. In summary, we demonstrated a robust and versatile peptide stapling method that could be potentially applied to both synthetic and expressed peptides.

A Thiol–Ene Coupling Approach to Native Peptide Stapling and Macrocyclization

AbstractWe report the discovery of a peptide stapling and macrocyclization method using thiol–ene reactions between two cysteine residues and an α,ω‐diene in high yields. This new approach enabled us to selectively modify cysteine residues in native, unprotected peptides with a variety of stapling modifications for helix stabilization or general macrocyclization. We synthesized stapled Axin mimetic analogues and demonstrated increased alpha helicity upon peptide stapling. We then synthesized stapled p53 mimetic analogues using pure hydrocarbon linkers and demonstrated their abilities to block the p53‐MDM2 interaction and selectively kill p53 wild‐type colorectal carcinoma HCT‐116 cells but not p53 null cells. In summary, we demonstrated a robust and versatile peptide stapling method that could be potentially applied to both synthetic and expressed peptides.

Nitrosative Stress in the Nervous System: Guidelines for Designing Experimental Strategies to Study Protein S-Nitrosylation.

Reactive nitrogen species, such as nitric oxide (NO), exert their biological activity in large part through post-translational modification of cysteine residues, forming S-nitrosothiols. This chemical reaction proceeds via a process that we and our colleagues have termed protein S-nitrosylation. Under conditions of normal NO production, S-nitrosylation regulates the activity of many normal proteins. However, in degenerative conditions characterized by nitrosative stress, increased levels of NO lead to aberrant S-nitrosylation that contributes to the pathology of the disease. Thus, S-nitrosylation has been implicated in a wide range of cellular mechanisms, including mitochondrial function, proteostasis, transcriptional regulation, synaptic activity, and cell survival. In recent years, the research area of protein S-nitrosylation has become prominent due to improvements in the detection systems as well as the demonstration that protein S-nitrosylation plays a critical role in the pathogenesis of neurodegenerative and other neurological disorders. To further promote our understanding of how protein S-nitrosylation affects cellular systems, guidelines for the design and conduct of research on S-nitrosylated (or SNO-)proteins would be highly desirable, especially for those newly entering the field. In this review article, we provide a strategic overview of designing experimental approaches to study protein S-nitrosylation. We specifically focus on methods that can provide critical data to demonstrate that an S-nitrosylated protein plays a (patho-)physiologically-relevant role in a biological process. Hence, the implementation of the approaches described herein will contribute to further advancement of the study of S-nitrosylated proteins, not only in neuroscience but also in other research fields.

S-nitrosylation of PDE5 increases its ubiquitin–proteasomal degradation

Phosphodiesterase type 5 (PDE5) expression is upregulated in human failing heart, and overexpression of PDE5 in transgenic mice exacerbates stress-induced left-ventricular dysfunction, suggesting that increased PDE5 expression might contribute to the development of congestive heart failure. However, the underlying mechanisms for increased PDE5 expression are not totally understood. In the present study, we found that PDE5 activity and expression were regulated by S-nitrosylation, a covalent modification of cysteine residues by nitric oxide (NO). S-nitrosylation of PDE5 occurs at Cys220, which is located in the GAFA domain. Upon S-nitrosylation, PDE5 exhibits reduced activity and degradation via the ubiquitin–proteasome system. The decrease in PDE5 expression induced by NO could be blunted by mutation of Cys220 or the phosphorylation site of PDE5 (S102), as well as by pretreatment with H2O2. Conversely, decreased NO bioavailability by nitric oxide synthase (NOS) inhibitors or knockout of NOS3 increased PDE5 expression in cardiomyocytes. Collectively, to the best of our knowledge, our data demonstrate for the first time that S-nitrosylation is one of the mechanisms for PDE5 degradation. This novel regulatory mechanism probably accounts for the increase in PDE5 in the failing heart and other diseases in which NO bioavailability is decreased by oxidative stress.

Quantitative analysis of PPT1 interactome in human neuroblastoma cells.

Mutations in the CLN1 gene that encodes Palmitoyl protein thioesterase 1 (PPT1) or CLN1, cause Infantile NCL (INCL, MIM#256730). PPT1 removes long fatty acid chains such as palmitate from modified cysteine residues of proteins. The data shown here result from isolated protein complexes from PPT1-expressing SH-SY5Y stable cells that were subjected to single step affinity purification coupled to mass spectrometry (AP-MS). Prior to the MS analysis, we utilised a modified filter-aided sample preparation (FASP) protocol. Based on label free quantitative analysis of the data by SAINT, 23 PPT1 interacting partners (IP) were identified. A dense connectivity in PPT1 network was further revealed by functional coupling and extended network analyses, linking it to mitochondrial ATP synthesis coupled protein transport and thioester biosynthetic process. Moreover, the terms: inhibition of organismal death, movement disorders and concentration of lipid were predicted to be altered in the PPT1 network. Data presented here are related to Scifo et al. (J. Proteomics, 123 (2015) 42–53).

Current Review on H2S Signaling

Hydrogen Sulfide, a pungent gas traditionally thought to be toxic to the human body, is now emerging as one of the most important endogenously synthesized gaseous transmitters. Over the course of the past decade, we have witnessed better characterization of its synthetic pathways, discovered how it affects its targets at the molecular level by modifying cysteine residues, a process termed sulfhydration, as well as begun to identify the critical role it plays in the modulation of various cellular processes. In this article, we will review some of these findings.

A Chemical‐Proteomic Platform to Investigate Cysteine S‐Nitrosation

Cysteine residues on proteins play numerous functional roles as catalytic nucleophiles, redox‐active disulfides, or metal‐binding residues. Outside of their direct role in catalysis, cysteines can also regulate protein activity via posttranslational modification by endogenous electrophiles and reactive oxygen species. These modified cysteine residues do not conform to a conserved sequence or structural motif, rendering the global identification of regulatory cysteines a considerable challenge. We hypothesize that cysteines that are hypersensitive to different oxidants or nitrosating agents are likely to be enriched in functional residues that serve to modulate protein activity. To explore this hypothesis, we focused our initial efforts on investigating cysteine susceptibility to nitrosation. S‐nitrosation is a unique posttranslational modification that serves to temporally and spatially control protein activity and localization. In order to identify cysteine residues hypersensitive to nitrosation, we developed a chemical‐proteomic platform that ranks cysteines in the human proteome by sensitivity to a variety of nitric oxide donors. Our proteomic studies identified several known sites of nitrosation, as well as previously unannotated cysteines. We then proceeded to functionally characterize several of the unannotated cysteines using a variety of cell and molecular biology approaches. We show that many of these cysteines are located distal from the active site, and yet mediate essential protein functions such as substrate binding and localization. Overall, our studies aim to unearth novel functional cysteine residues in the proteome, with the long‐term goal of identifying new modes of protein regulation through reactive cysteines.

Reactivity of HNO‐Induced Modifications and Its Relevance to Phospholamban Function

HNO, a potential heart failure therapeutic, is known to post-translationally modify cysteine residues. Among reactive nitrogen oxide species, the modification of cysteine residues to sulfinamides [RS(O)NH2] is unique to HNO. Because this modification can alter protein structure and function, we have examined the reactivity of sulfinamides in several systems, including small organic molecules, peptides, and a protein. At physiological pH and temperature, relevant reactions of sulfinamides involve reduction to free thiols in the presence of excess thiol and hydrolysis to form sulfinic acids [RS(O)OH]. In addition to utilizing ESI-MS and other spectroscopic methods to study sulfinamide reduction, we have applied 15N-edited 1H-NMR techniques to sulfinamide detection and used this method to explore sulfinamide hydrolysis. We have also investigated the effect of local environment on the reactivity of HNO with C-terminal cysteines. Our findings indicate that the nature of HNO-derived modifications of C-terminal cysteines is influenced by the C-terminal carboxylate. HNO has been shown to enhance cardiac sarcoplasmic reticulum Ca2+ cycling independent of the β-adrenergic pathway. In a collaborative project, the effects of HNO on the cardiac protein, phospholamban (PLN) are investigated using 15N-edited NMR methods and biochemistry protocols. This research was supported by the National Science Foundation (CHE-1213438) and Cardioxyl Pharmaceuticals.

Oxidative post-translational modifications of cysteine residues in plant signal transduction.

In plants, fluctuation of the redox balance by altered levels of reactive oxygen species (ROS) can affect many aspects of cellular physiology. ROS homeostasis is governed by a diversified set of antioxidant systems. Perturbation of this homeostasis leads to transient or permanent changes in the redox status and is exploited by plants in different stress signalling mechanisms. Understanding how plants sense ROS and transduce these stimuli into downstream biological responses is still a major challenge. ROS can provoke reversible and irreversible modifications to proteins that act in diverse signalling pathways. These oxidative post-translational modifications (Ox-PTMs) lead to oxidative damage and/or trigger structural alterations in these target proteins. Characterization of the effect of individual Ox-PTMs on individual proteins is the key to a better understanding of how cells interpret the oxidative signals that arise from developmental cues and stress conditions. This review focuses on ROS-mediated Ox-PTMs on cysteine (Cys) residues. The Cys side chain, with its high nucleophilic capacity, appears to be the principle target of ROS. Ox-PTMs on Cys residues participate in various signalling cascades initiated by plant stress hormones. We review the mechanistic aspects and functional consequences of Cys Ox-PTMs on specific target proteins in view of stress signalling events.

Postranslational Modification of Ion Channels in Colonic Inflammation.

Voltage-gated ion channels are key regulators of cell excitability. There is significant evidence that these channels are subject to modulation by redox status of the cells. Here we review the post-translational modifications of ion channels that occur in colonic inflammation. The redox mechanisms involve tyrosine nitration, covalent modification of cysteine residues and sulfhydration by hydrogen sulfide in experimental colitis. In the setting of colonic inflammation, modifications of cysteine and tyrosine are likely to occur at several sites within the same channel complex. In this review we describe alterations in channel function due to specific modifications of tyrosine and cysteine residues by reactive nitrogen, oxygen and hydrogen-sulfide resulting in altered motility.