Site-specific methionine oxidation in calmodulin affects structural integrity and interaction with Ca2+/calmodulin-dependent protein kinase II

Calmodulin: The switch button of calcium signaling

Calmodulin (CaM), a calcium sensor, decodes the critical calcium-dependent signals and converts them into the driving force to control various important cellular functions, such as ion transport. This small protein has a short central linker to connect two globular lobes and each unit is composed of a pair of homologous domains (HD) which are responsible for calcium binding. The conformation of each HD is sensitive to the levels of the intracellular Ca²⁺ concentrations while the flexible structure of the central domain enables its interactions with hundreds of cellular proteins. Apart from calcium binding, posttranslational modifications (PTMs) also contribute to the modulations of CaM functions by affecting its protein-protein interaction networks and hence drawing out the various downstream signaling cascades. In this mini-review, we first aim to elucidate the structural features of CaM and then overview the recent studies on the engagements of calcium binding and PTMs in Ca²⁺/CaM-mediated conformational alterations and signaling events. The mechanistic understanding of CaM working models is expected to be a key to decipher the precise role of CaM in cardiac physiology and disease pathology.

Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling

Legumes include several major crops that can fix atmospheric nitrogen in symbiotic root nodules, thus reducing the demand for nitrogen fertilizers and contributing to sustainable agriculture. Global change models predict increases in temperature and extreme weather conditions. This scenario might increase plant exposure to abiotic stresses and negatively affect crop production. Regulation of whole plant physiology and nitrogen fixation in legumes during abiotic stress is complex, and only a few mechanisms have been elucidated. Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) are key players in the acclimation and stress tolerance mechanisms of plants. However, the specific redox-dependent signaling pathways are far from understood. One mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification (PTM) of proteins. Redox-based PTMs occur in the cysteine thiol group (oxidation, S-nitrosylation, S-glutathionylation, persulfidation), and also in methionine (oxidation), tyrosine (nitration), and lysine and arginine (carbonylation/glycation) residues. Unraveling PTM patterns under different types of stress and establishing the functional implications may give insight into the underlying mechanisms by which the plant and nodule respond to adverse conditions. Here, we review current knowledge on redox-based PTMs and their possible consequences in legume and nodule biology.

Elevation of gene expression of calcineurin, calmodulin and calsyntenin in oxidative stress induced PC12 cells

In normal physiological conditions, reactive oxygen and nitrogen species are used as important signaling molecules in the cell. However, in excess it causes the disruption of cell resulting in their death. Oxidative stress causes influx in intracellular calcium levels leading to higher concentrations of calcium in the cell. This accelerated calcium affects both the mitochondria and nuclei leading to excitotoxicity in neurons. Intracellular calcium levels are controlled by voltage dependent calcium channels located in the plasma membrane, calcium stores like endoplasmic/sarcoplasmic reticulum and majorly by calcium binding proteins. Our study was aimed at analyzing the gene expression of major calcium binding proteins namely calcineurin, calmodulin, calreticulin, synaptotagamin and calsyntenin in stress induced PC 12 cells. Rotenone (1 μM), Peroxynitrite (10 μM), H2O2 (100 μM) and High glucose (33 mM) were used to induce oxidative stress in PC12 cells. Results obtained from the study suggest that calcineurin, calmodulin and calsyntenin gene expression were enhanced compared to the control due to oxidative stress. However, synaptotagmin and calreticulin gene expression were down regulated. Further, Akt protein expression (stress marker) was enhanced in PC12 cells with all other stress inducers except in hyperglycemic condition.

The calmodulin redox sensor controls myogenesis

Muscle aging is accompanied by blunted muscle regeneration in response to injury and disuse. Oxidative stress likely underlies this diminished response, but muscle redox sensors that act in regeneration have not yet been characterized. Calmodulin contains multiple redox sensitive methionines whose oxidation alters the regulation of numerous cellular targets. We have used the CRISPR-Cas9 system to introduce a single amino acid substitution M109Q that mimics oxidation of methionine to methionine sulfoxide in one or both alleles of the CALM1 gene, one of three genes encoding the muscle regulatory protein calmodulin, in C2C12 mouse myoblasts. When signaled to undergo myogenesis, mutated myoblasts failed to differentiate into myotubes. Although early myogenic regulatory factors were present, cells with the CALM1 M109Q mutation in one or both alleles were unable to withdraw from the cell cycle and failed to express late myogenic factors. We have shown that a single oxidative modification to a redox-sensitive muscle regulatory protein can halt myogenesis, suggesting a molecular target for mitigating the impact of oxidative stress in age-related muscle degeneration.

An Overview of the Role of Calcium/Calmodulin-Dependent Protein Kinase in Cardiorenal Syndrome

Calcium/calmodulin-dependent protein kinases (CaMKs) are key regulators of calcium signaling in health and disease. CaMKII is the most abundant isoform in the heart; although classically described as a regulator of excitation–contraction coupling, recent studies show that it can also mediate inflammation in cardiovascular diseases (CVDs). Among CVDs, cardiorenal syndrome (CRS) represents a pressing issue to be addressed, considering the growing incidence of kidney diseases worldwide. In this review, we aimed to discuss the role of CaMK as an inflammatory mediator in heart and kidney interaction by conducting an extensive literature review using the database PubMed. Here, we summarize the role and regulating mechanisms of CaMKII present in several quality studies, providing a better understanding for future investigations of CamKII in CVDs. Surprisingly, despite the obvious importance of CaMKII in the heart, very little is known about CaMKII in CRS. In conclusion, more studies are necessary to further understand the role of CaMKII in CRS.

Oxidative post-translational modifications controlling plant-pathogen interaction

Pathogen recognition is linked to the perception of microbe/pathogen-associated molecular patterns triggering a specific and transient accumulation of reactive oxygen species (ROS) at the pathogen attack site. The apoplastic oxidative "burst" generated at the pathogen attack site depends on the ROS-generator systems including enzymes such as plasma membrane NADP (H) oxidases, cell wall peroxidases and lipoxygenase. ROS are cytotoxic molecules that inhibit invading pathogens or signalling molecules that control the local and systemic induction of defence genes. Post-translational modifications induced by ROS are considered as a potential signalling mechanism that can modify protein structure and/or function, localisation and cellular stability. Thus, this review focuses on how ROS are essential molecules regulating the function of proteins involved in the plant response to a pathogen attack through post-translational modifications.

Wheat methionine sulfoxide reductase A4.1 interacts with heme oxygenase 1 to enhance seedling tolerance to salinity or drought stress

Here, a functional characterization of a wheat MSR has been presented: this protein makes a contribution to the plant's tolerance of abiotic stress, acting through its catalytic capacity and its modulation of ROS and ABA pathways. The molecular mechanism and function of certain members of the methionine sulfoxide reductase (MSR) gene family have been defined, however, these analyses have not included the wheat equivalents. The wheat MSR gene TaMSRA4.1 is inducible by salinity and drought stress and in this study, we demonstrate that its activity is restricted to the Met-S-SO enantiomer, and its subcellular localization is in the chloroplast. Furthermore, constitutive expression of TaMSRA4.1 enhanced the salinity and drought tolerance of wheat and Arabidopsis thaliana. In these plants constitutively expressing TaMSRA4.1, the accumulation of reactive oxygen species (ROS) was found to be influenced through the modulation of genes encoding proteins involved in ROS signaling, generation and scavenging, while the level of endogenous abscisic acid (ABA), and the sensitivity of stomatal guard cells to exogenous ABA, was increased. A yeast two-hybrid screen, bimolecular fluorescence complementation and co-immunoprecipitation assays demonstrated that heme oxygenase 1 (HO1) interacted with TaMSRA4.1, and that this interaction depended on a TaHO1 C-terminal domain. In plants subjected to salinity or drought stress, TaMSRA4.1 reversed the oxidation of TaHO1, activating ROS and ABA signaling pathways, but not in the absence of HO1. The aforementioned properties advocate TaMSRA4.1 as a candidate for plant genetic enhancement.

Oxidative Post-translational Modifications Accelerate Proteolytic Degradation of Calprotectin

Oxidative post-translational modifications affect the structure and function of many biomolecules. Herein we examine the biophysical and functional consequences of oxidative post-translational modifications to human calprotectin (CP, S100A8/S100A9 oligomer, MRP8/MRP14 oligomer, calgranulins A/B oligomer). This abundant metal-sequestering protein contributes to innate immunity by starving invading microbial pathogens of transition metal nutrients in the extracellular space. It also participates in the inflammatory response. Despite many decades of study, little is known about the fate of CP at sites of infection and inflammation. We present compelling evidence for methionine oxidation of CP in vivo, supported by using 15N-labeled CP-Ser (S100A8(C42S)/S100A9(C3S)) to monitor for adventitious oxidation following human sample collection. To elucidate the biochemical and functional consequences of oxidative post-translational modifications, we examine recombinant CP-Ser with methionine sulfoxide modifications generated by exposing the protein to hydrogen peroxide. These oxidized species coordinate transition metal ions and exert antibacterial activity. Nevertheless, oxidation of M81 in the S100A9 subunit disrupts Ca(II)-induced tetramerization and, in the absence of a transition metal ion bound at the His6 site, accelerates proteolytic degradation of CP. We demonstrate that native CP, which contains one Cys residue in each full-length subunit, forms disulfide bonds within and between S100A8/S100A9 heterodimers when exposed to hydrogen peroxide. Remarkably, disulfide bond formation accelerates proteolytic degradation of CP. We propose a new extension to the working model for extracellular CP where post-translational oxidation by reactive oxygen species generated during the neutrophil oxidative burst modulates its lifetime in the extracellular space.

Function of the evolutionarily conserved plant methionine-S-sulfoxide reductase without the catalytic residue

In plants, two types of methionine sulfoxide reductase (MSR) exist, namely methionine-S-sulfoxide reductase (MSRA) and methionine-R-sulfoxide reductase (MSRB). These enzymes catalyze the reduction of methionine sulfoxides (MetO) back to methionine (Met) by a catalytic cysteine (Cys) and one or two resolving Cys residues. Interestingly, a group of MSRA encoded by plant genomes does not have a catalytic residue. We asked that if this group of MSRA did not have any function (as fitness), why it was not lost during the evolutionary process. To challenge this question, we analyzed the gene family encoding MSRA in soybean (GmMSRAs). We found seven genes encoding GmMSRAs, which included three segmental duplicated pairs. Among them, a pair of duplicated genes, namely GmMSRA1 and GmMSRA6, was without a catalytic Cys residue. Pseudogenes were ruled out as their transcripts were detected in various tissues and their Ka/Ks ratio indicated a negative selection pressure. In vivo analysis in Δ3MSR yeast strain indicated that the GmMSRA6 did not have activity toward MetO, contrasting to GmMSRA3 which had catalytic Cys and had activity. When exposed to H2O2-induced oxidative stress, GmMSRA6 did not confer any protection to the Δ3MSR yeast strain. Overexpression of GmMSRA6 in Arabidopsis thaliana did not alter the plant's phenotype under physiological conditions. However, the transgenic plants exhibited slightly higher sensitivity toward salinity-induced stress. Taken together, this data suggested that the plant MSRAs without the catalytic Cys are not enzymatically active and their existence may be explained by a role in regulating plant MSR activity via dominant-negative substrate competition mechanism.

Unique methionine-aromatic interactions govern the calmodulin redox sensor

Calmodulin contains multiple redox sensitive methionines whose oxidation alters the regulation of numerous targets. Molecular dynamics simulations were used to define the molecular principles that govern how calmodulin is structurally poised to detect and respond to methionine oxidation. We found that calmodulin's open and closed states were preferentially stabilized by unique, redox sensitive, methionine-aromatic interactions. Key methionine-aromatic interactions were coupled to reorientation of EF hand helices. Methionine to glutamine substitutions designed to mimic methionine oxidation strongly altered conformational transitions by modulating the strength of methionine-aromatic interactions. Together, these results suggest a broadly applicable redox sensing mechanism though which methionine oxidation by cellular oxidants alters the strength of methionine-aromatic interactions critical for functional protein dynamics.

Redox Signaling by Reactive Electrophiles and Oxidants

The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.

Physiological Roles of Plant Methionine Sulfoxide Reductases in Redox Homeostasis and Signaling

Oxidation of methionine (Met) leads to the formation of two S- and R-diastereoisomers of Met sulfoxide (MetO) that are reduced back to Met by methionine sulfoxide reductases (MSRs), A and B, respectively. Here, we review the current knowledge about the physiological functions of plant MSRs in relation with subcellular and tissue distribution, expression patterns, mutant phenotypes, and possible targets. The data gained from modified lines of plant models and crop species indicate that MSRs play protective roles upon abiotic and biotic environmental constraints. They also participate in the control of the ageing process, as shown in seeds subjected to adverse conditions. Significant advances were achieved towards understanding how MSRs could fulfil these functions via the identification of partners among Met-rich or MetO-containing proteins, notably by using redox proteomic approaches. In addition to a global protective role against oxidative damage in proteins, plant MSRs could specifically preserve the activity of stress responsive effectors such as glutathione-S-transferases and chaperones. Moreover, several lines of evidence indicate that MSRs fulfil key signaling roles via interplays with Ca²⁺- and phosphorylation-dependent cascades, thus transmitting ROS-related information in transduction pathways.

Redox Signaling in Neurotransmission and Cognition During Aging

SIGNIFICANCE

Oxidative stress increases in the brain with aging and neurodegenerative diseases. Previous work emphasized irreversible oxidative damage in relation to cognitive impairment. This research has evolved to consider a continuum of alterations, from redox signaling to oxidative damage, which provides a basis for understanding the onset and progression of cognitive impairment. This review provides an update on research linking redox signaling to altered function of neural circuits involved in information processing and memory. Recent Advances: Starting in middle age, redox signaling triggers changes in nervous system physiology described as senescent physiology. Hippocampal senescent physiology involves decreased cell excitability, altered synaptic plasticity, and decreased synaptic transmission. Recent studies indicate N-methyl-d-aspartate and ryanodine receptors and Ca²⁺ signaling molecules as molecular substrates of redox-mediated senescent physiology.

CRITICAL ISSUES

We review redox homeostasis mechanisms and consider the chemical character of reactive oxygen and nitrogen species and their role in regulating different transmitter systems. In this regard, senescent physiology may represent the co-opting of pathways normally responsible for feedback regulation of synaptic transmission. Furthermore, differences across transmitter systems may underlie differential vulnerability of brain regions and neuronal circuits to aging and disease.

FUTURE DIRECTIONS

It will be important to identify the intrinsic mechanisms for the shift in oxidative/reductive processes. Intrinsic mechanism will depend on the transmitter system, oxidative stressors, and expression/activity of antioxidant enzymes. In addition, it will be important to identify how intrinsic processes interact with other aging factors, including changes in inflammatory or hormonal signals. Antioxid. Redox Signal. 28, 1724-1745.

Sulfoxidation Regulation of Musa acuminata Calmodulin (MaCaM) Influences the Functions of MaCaM-Binding Proteins

Sulfoxidation of methionine in proteins by reactive oxygen species can cause conformational alteration or functional impairment, and can be reversed by methionine sulfoxide reductase (Msr). Currently, only a few potential Msr substrates have been confirmed in higher plants. Here, we investigated Msr-mediated sulfoxidation regulation of calmodulin (CaM) and its underlying biological significance in relation to banana fruit ripening and senescence. Expression of MaCaM1 and MaMsrA7 was up-regulated with increased ripening and senescence. We verified that MaCaM1 interacts with MaMsrA7 in vitro and in vivo, and sulfoxidated MaCaM1 could be partly repaired by MaMsrA7 (MaMsrA7 reduces oxidized residues Met77 and Met110 in MaCaM1). Furthermore, we investigated two known CaM-binding proteins, catalase (MaCAT1) and MaHY5-1. MaHY5-1 acts as a transcriptional repressor of carotenoid biosynthesis-related genes (MaPSY1, MaPSY2 and MaPSY3) in banana fruit. MaCaM1 could enhance the catalytic activity of MaCAT1 and the transcriptional repression activity of MaHY5-1 toward MaPSY2. Mimicked sulfoxidation in MaCaM1 did not affect the physical interactions of the protein with MaHY5-1 and MaCAT1, but reduced the catalytic activity of MaCAT1 and the transcriptional repression activity of MaHY5-1. Our data suggest that sulfoxidation modification in MaCaM1 by MaMsrA7 regulates antioxidant response and gene transcription, thereby being involved in regulation of ripening and senescence of banana fruit.

Dioxygen and Metabolism; Dangerous Liaisons in Cardiac Function and Disease

The heart must consume a significant amount of energy to sustain its contractile activity. Although the fuel demands are huge, the stock remains very low. Thus, in order to supply its daily needs, the heart must have amazing adaptive abilities, which are dependent on dioxygen availability. However, in myriad cardiovascular diseases, “fuel” depletion and hypoxia are common features, leading cardiomyocytes to favor low-dioxygen-consuming glycolysis rather than oxidation of fatty acids. This metabolic switch makes it challenging to distinguish causes from consequences in cardiac pathologies. Finally, despite the progress achieved in the past few decades, medical treatments have not improved substantially, either. In such a situation, it seems clear that much remains to be learned about cardiac diseases. Therefore, in this review, we will discuss how reconciling dioxygen availability and cardiac metabolic adaptations may contribute to develop full and innovative strategies from bench to bedside.

Vibrio cholerae ensures function of host proteins required for virulence through consumption of luminal methionine sulfoxide

Vibrio cholerae is a diarrheal pathogen that induces accumulation of lipid droplets in enterocytes, leading to lethal infection of the model host Drosophila melanogaster. Through untargeted lipidomics, we provide evidence that this process is the product of a host phospholipid degradation cascade that induces lipid droplet coalescence in enterocytes. This infection-induced cascade is inhibited by mutation of the V. cholerae glycine cleavage system due to intestinal accumulation of methionine sulfoxide (MetO), and both dietary supplementation with MetO and enterocyte knock-down of host methionine sulfoxide reductase A (MsrA) yield increased resistance to infection. MsrA converts both free and protein-associated MetO to methionine. These findings support a model in which dietary MetO competitively inhibits repair of host proteins by MsrA. Bacterial virulence strategies depend on functional host proteins. We propose a novel virulence paradigm in which an intestinal pathogen ensures the repair of host proteins essential for pathogenesis through consumption of dietary MetO.

Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress

Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport. Next, we analyzed the transcript levels of MRP-coding genes under normal and stress conditions. We found that 57 AtMRPs were responsive either to drought or to high salinity stress in Arabidopsis; 35 GmMRPs were responsive to drought in the leaf of late vegetative or early reproductive stages of soybean. Among the MRP genes with a known function, the majority of the abiotic stress-responsive genes are involved in transcription control and calcium signaling. Finally, Arabidopsis plant which overexpressed an MRP-coding gene, whose transcripts were downregulated by abiotic stress, was more sensitive to paraquat than the control. Taken together, our report indicates that MRPs participate in various vital processes of plants under normal and stress conditions.

Central role for NMDA receptors in redox mediated impairment of synaptic function during aging and Alzheimer's disease

Increased human longevity has magnified the negative impact that aging can have on cognitive integrity of older individuals experiencing some decline in cognitive function. Approximately 30% of the elderly will have cognitive problems that influence their independence. Impaired executive function and memory performance are observed in normal aging and yet can be an early sign of a progressive cognitive impairment of Alzheimer's disease (AD), the most common form of dementia. Brain regions that are vulnerable to aging exhibit the earliest pathology of AD. Senescent synaptic function is observed as a shift in Ca²⁺-dependent synaptic plasticity and similar mechanisms are thought to contribute to the early cognitive deficits associated with AD. In the case of aging, intracellular redox state mediates a shift in Ca²⁺ regulation including N-methyl-d-aspartate (NMDA) receptor hypofunction and increased Ca²⁺ release from intracellular stores to alter synaptic plasticity. AD can interact with these aging processes such that molecules linked to AD, β-amyloid (Aβ) and mutated presenilin 1 (PS1), can also degrade NMDA receptor function, promote Ca²⁺ release from intracellular stores, and may increase oxidative stress. Thus, age is one of the most important predictors of AD and brain aging likely contributes to the onset of AD. The focus of this review article is to provide an update on mechanisms that contribute to the senescent synapse and possible interactions with AD-related molecules, with special emphasis on regulation of NMDA receptors.

Convergent signaling pathways--interaction between methionine oxidation and serine/threonine/tyrosine O-phosphorylation

Oxidation of methionine (Met) to Met sulfoxide (MetSO) is a frequently found reversible posttranslational modification. It has been presumed that the major functional role for oxidation-labile Met residues is to protect proteins/cells from oxidative stress. However, Met oxidation has been established as a key mechanism for direct regulation of a wide range of protein functions and cellular processes. Furthermore, recent reports suggest an interaction between Met oxidation and O-phosphorylation. Such interactions are a potentially direct interface between redox sensing and signaling, and cellular protein kinase/phosphatase-based signaling. Herein, we describe the current state of Met oxidation research, provide some mechanistic insight into crosstalk between these two major posttranslational modifications, and consider the evolutionary significance and regulatory potential of this crosstalk.

Proteomics methods to study methionine oxidation

The oxidation and consequent reduction of protein-bound methionine residues is of great interest in understanding different aspects of how oxidative stress affects protein functions and cellular signaling. To date, few technologies are available for the study of methionine sulfoxides. And, especially the absence of highly specific antibodies has impeded the field in understanding the exact role of methionine oxidation on a proteome-wide level. Nonetheless, the different models where the responsible enzymes for repair of the oxidized methionines have been studied show that there is an important role for this modification in a cellular context. We here review different mass spectrometry based and proteomics methods for characterizing in vivo methionine oxidation.

The physiological role of reversible methionine oxidation

Sulfur-containing amino acids such as cysteine and methionine are particularly vulnerable to oxidation. Oxidation of cysteine and methionine in their free amino acid form renders them unavailable for metabolic processes while their oxidation in the protein-bound state is a common post-translational modification in all organisms and usually alters the function of the protein. In the majority of cases, oxidation causes inactivation of proteins. Yet, an increasing number of examples have been described where reversible cysteine oxidation is part of a sophisticated mechanism to control protein function based on the redox state of the protein. While for methionine the dogma is still that its oxidation inhibits protein function, reversible methionine oxidation is now being recognized as a powerful means of triggering protein activity. This mode of regulation involves oxidation of methionine to methionine sulfoxide leading to activated protein function, and inactivation is accomplished by reduction of methionine sulfoxide back to methionine catalyzed by methionine sulfoxide reductases. Given the similarity to thiol-based redox-regulation of protein function, methionine oxidation is now established as a novel mode of redox-regulation of protein function. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.

Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation

BACKGROUND

Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are typically studied individually, herein we describe the potential for cross-talk and hierarchical regulation.

RESULTS

The proximity of Met to Ser/Thr/Tyr within the proteome has not previously been addressed. In order to consider the possibility of a generalized interaction, we performed a trans-kingdom sequence analysis of known phosphorylation sites in proteins from bacteria, fungi, plants, and animals. The proportion of phosphorylation sites that include a Met within a 13-residue window centered upon Ser/Thr/Tyr is significantly less than the occurrence of Met in proximity to all Ser/Thr/Tyr residues. Met residues are present at all positions (-6 to +6, inclusive) within the 13-residue window that we have considered. Detailed analysis of sequences from eight disparate plant taxa revealed that many conserved phosphorylation sites have a Met residue in the proximity. Results from GO enrichment analysis indicated that the potential for phosphorylation and Met oxidation crosstalk is most prevalent in kinases and proteins involved in signalling.

CONCLUSION

The large proportion of known phosphorylation sites with Met in the proximity fulfils the necessary condition for cross-talk. Kinases/signalling proteins are enriched for Met around phosphorylation sites. These proteins/sites are likely candidates for cross-talk between oxidative signalling and reversible phosphorylation.

Top-down structural analysis of posttranslationally modified proteins by Fourier transform ion cyclotron resonance-MS with hydrogen/deuterium exchange and electron capture dissociation

High-resolution structural characterization of posttranslationally modified proteins represents a challenge for traditional structural biology methods such as crystallography and NMR. In this study, we have used top-down hydrogen/deuterium exchange MS (HDX-MS) with precursor ion selection and electron capture dissociation to determine the impact of oxidative modification on calmodulin (CaM) at an average resolution of 2.5 residues, with complete sequence coverage. The amide deuteration status of native CaM determined by this method correlates well with previously reported crystallographic and NMR data. In contrast, methionine oxidation caused almost complete deuteration of all residues in the protein in 10 s. The oxidative-modification-induced secondary and tertiary structure loss can be largely recovered upon calcium ligation, which also resulted in a substantial increase of amide protection in three of the four calcium-binding loops in oxidatively modified CaM (CaMox ). However, the structure of α-helix VI is not restored by cofactor binding. These results are discussed in terms of different target binding and activation capabilities displayed by CaM and CaMox . The isoform-specific top-down HDX structural analysis strategy demonstrated in this study should be readily applicable to other oxidatively modified proteins and other types of PTMs, and may help decipher the structure and function of specific protein isoforms.

Protein damage, repair and proteolysis

Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression.

Protein flexibility is key to cisplatin crosslinking in calmodulin

Chemical crosslinking in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has significant potential for studying protein structures and protein-protein interactions. Previously, cisplatin has been shown to be a crosslinker and crosslinks multiple methionine (Met) residues in apo-calmodulin (apo-CaM). However, the inter-residue distances obtained from nuclear magnetic resonance structures are inconsistent with the measured distance constraints by crosslinking. Met residues lie too far apart to be crosslinked by cisplatin. Here, by combining FTICR MS with a novel computational flexibility analysis, the flexible nature of the CaM structure is found to be key to cisplatin crosslinking in CaM. It is found that the side chains of Met residues can be brought together by flexible motions in both apo-CaM and calcium-bound CaM (Ca₄-CaM). The possibility of cisplatin crosslinking Ca₄-CaM is then confirmed by MS data. Therefore, flexibility analysis as a fast and low-cost computational method can be a useful tool for predicting crosslinking pairs in protein crosslinking analysis and facilitating MS data analysis. Finally, flexibility analysis also indicates that the crosslinking of platinum to pairs of Met residues will effectively close the nonpolar groove and thus will likely interfere with the binding of CaM to its protein targets, as was proved by comparing assays for cisplatin-modified/unmodified CaM binding to melittin. Collectively, these results suggest that cisplatin crosslinking of apo-CaM or Ca₄-CaM can inhibit the ability of CaM to recognize its target proteins, which may have important implications for understanding the mechanism of tumor resistance to platinum anticancer drugs.

Investigating the hydrogen peroxide quenching capacity of proteins in polyphenol-rich foods

Polyphenols are widely regarded as antioxidants, due in large part to their free radical scavenging activities and their ability to disrupt radical chain propagation. However, recent studies have demonstrated that the oxidation of some polyphenolic compounds, such as the tea-derived compound (-)-epigallocatechin-3-gallate (EGCG), results in the generation of reactive oxygen species that can potentially compromise the oxidative stability of food lipids under some conditions. In this present study, the rate of hydrogen peroxide (H(2)O(2)) generation and its stability, resulting from EGCG oxidation in Tween 80- and sodium caseinate-stabilized oil-in-water (O/W) emulsions in the presence of iron (25 μM Fe(3+) from FeCl(3)), were examined. Observed H(2)O(2) levels in protein-stabilized emulsions were significantly lower across all treatments as compared to surfactant-stabilized emulsions. The lower observed H(2)O(2) concentrations seen in the protein system are likely due to the antioxidant effects of the added proteins, which either prevented the generation of or more likely scavenged the peroxide. All protein-stabilized emulsions containing EGCG showed increases in carbonyl concentrations, a marker of protein oxidation, throughout the study. The H(2)O(2) scavenging activity of aqueous phase and interfacial caseinate and whey protein isolate (WPI) was also evaluated. Both proteins showed concentration-dependent scavenging of H(2)O(2) with caseinate displaying significantly higher scavenging abilities at all concentrations. These results suggest that food proteins may play an important role in mitigating the pro-oxidant effects of polyphenols.

Combined Raman and IR spectroscopic study on the radical-based modifications of methionine

Among damages reported to occur on proteins, radical-based changes of methionine (Met) residues are one of the most important convalent post-translational modifications. The combined application of Raman and infrared (IR) spectroscopies for the characterisation of the radical-induced modifications of Met is described here. Gamma-irradiation was used to simulate the endogenous formation of reactive species such as hydrogen atoms (•H), hydroxyl radicals (•OH) and hydrogen peroxide (H(2)O(2)). These spectroscopic techniques coupled to mass experiments are suitable tools in detecting almost all the main radical-induced degradation products of Met that depend on the nature of the reactive species. In particular, Raman spectroscopy is useful in revealing the radical-induced modifications in the sulphur-containing moiety, whereas the IR spectra allow decarboxylation and deamination processes to be detected, as well as the formation of other degradation products. Thus, some band patterns useful for building a library of spectra-structure correlation for radical-based degradation of Met were identified. In particular, the bands due to the formation of methionine sulfoxide, the main oxidation product of Met, have been identified. All together, these results combine to produce a set of spectroscopic markers of the main processes occurring as a consequence of radical stress exposure, which can be used in a spectroscopic protocol for providing a first assessment of Met modifications in more complex systems such as peptides and proteins, and monitoring their impact on protein structure.