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1. pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model

   https://doi.org/10.1186/s12859-023-05164-9  

   Pratyush, Pawel; Pokharel, Suresh; Saigo, Hiroto; KC, Dukka B. (February 2023, BMC Bioinformatics)

   Abstract BackgroundProtein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signaling of all main classes of protein. It is involved in several biological processes including immune response, protein stability, transcription regulation, post translational regulation, DNA damage repair, redox regulation, and is an emerging paradigm of redox signaling for protection against oxidative stress. The development of robust computational tools to predict protein SNO sites would contribute to further interpretation of the pathological and physiological mechanisms of SNO. ResultsUsing an intermediate fusion-based stacked generalization approach, we integrated embeddings from supervised embedding layer and contextualized protein language model (ProtT5) and developed a tool called pLMSNOSite (protein language model-based SNO site predictor). On an independent test set of experimentally identified SNO sites, pLMSNOSite achieved values of 0.340, 0.735 and 0.773 for MCC, sensitivity and specificity respectively. These results show that pLMSNOSite performs better than the compared approaches for the prediction of S-nitrosylation sites. ConclusionTogether, the experimental results suggest that pLMSNOSite achieves significant improvement in the prediction performance of S-nitrosylation sites and represents a robust computational approach for predicting protein S-nitrosylation sites. pLMSNOSite could be a useful resource for further elucidation of SNO and is publicly available athttps://github.com/KCLabMTU/pLMSNOSite. 

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2. S-Nitrosothiols: chemistry and reactions

   https://doi.org/10.1039/c7cc06574d  

   Zhang, Caihong; Biggs, Tyler D.; Devarie-Baez, Nelmi O.; Shuang, Shaomin; Dong, Chuan; Xian, Ming (January 2017, Chem. Commun.)

   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. 

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3. Abscisic acid‐controlled redox proteome of Arabidopsis and its regulation by heterotrimeric Gβ protein

   https://doi.org/10.1111/nph.18348  

   Smythers, Amanda L.; Bhatnagar, Nikita; Ha, Chien; Majumdar, Parinita; McConnell, Evan W.; Mohanasundaram, Boominathan; Hicks, Leslie M.; Pandey, Sona (July 2022, New Phytologist)

   Summary The plant hormone abscisic acid (ABA) plays crucial roles in regulation of stress responses and growth modulation. Heterotrimeric G‐proteins are key mediators of ABA responses. Both ABA and G‐proteins have also been implicated in intracellular redox regulation; however, the extent to which reversible protein oxidation manipulates ABA and/or G‐protein signaling remains uncharacterized.To probe the role of reversible protein oxidation in plant stress response and its dependence on G‐proteins, we determined the ABA‐dependent reversible redoxome of wild‐type and Gβ‐protein null mutantagb1of Arabidopsis.We quantified 6891 uniquely oxidized cysteine‐containing peptides, 923 of which show significant changes in oxidation following ABA treatment. The majority of these changes required the presence of G‐proteins. Divergent pathways including primary metabolism, reactive oxygen species response, translation and photosynthesis exhibited both ABA‐ and G‐protein‐dependent redox changes, many of which occurred on proteins not previously linked to them.We report the most comprehensive ABA‐dependent plant redoxome and uncover a complex network of reversible oxidations that allow ABA and G‐proteins to rapidly adjust cellular signaling to adapt to changing environments. Physiological validation of a subset of these observations suggests that functional G‐proteins are required to maintain intracellular redox homeostasis and fully execute plant stress responses. 

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4. Protic small molecule bioregulators

   https://doi.org/10.1016/j.redox.2025.103921  

   Davis, Amanda G; Pluth, Michael D (December 2025, Redox Biology)

   Small molecule gases such as nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H₂S) have long been recognized as endogenous signaling molecules with diverse physiological roles. Often described as “gasotransmitters”, these molecules complement other small molecule bioregulators (SMBs) that exert biological function across all kingdoms of life. One underappreciated distinction, however, is that many of these molecules – irrespective of whether or not they are gases in their native states outside of biology – exhibit similar molecular signaling potential mediated by protonation-dependent chemical speciation. In this review, we propose the new cross-cutting classification of protic small molecule bioregulators (PSMBs) to describe molecules in which biological function and reactivity are modulated by protonation state. Examples of PSMBs include the canonical gasotransmitter H2S, emerging gasotransmitters (H2Se, HCN), small molecule crosstalk species (e.g., SNO–, SSNO–, SO42–, ONOO–, NO2–, SCN–, OCl–), and other species where protonation state modulation is accessible at physiological pH. Importantly, these species exist in equilibrium between their neutral and anionic forms, with speciation governed by local pH and molecular environment, directly impacting their membrane nucleophilicity, permeability, redox activity, and interaction with metal centers. We describe the evolutionary origins, biosynthesis, and crosstalk of PSMBs, including roles in redox signaling, post-translational modification, and mitochondrial regulation. Reframing these important molecules in a class defined by their protic ability rather than gaseous state does not diminish prior gasotransmitter designations, but rather serves to recognize commonalities in chemical characteristics that drive the unique biological chemistry and regulation. 

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5. Moving beyond the arabidopsis-centric view of G-protein signaling in plants

   https://doi.org/10.1016/j.tplants.2023.07.014  

   Mohanasundaram, Boominathan; Pandey, Sona (December 2023, Trends in Plant Science)

   Heterotrimeric G-protein-mediated signaling is a key mechanism to transduce a multitude of endogenous and environmental signals in diverse organisms. The scope and expectations of plant G-protein research were set by pioneering work in metazoans. Given the similarity of the core constituents, G-protein-signaling mechanisms were presumed to be universally conserved. However, because of the enormous diversity of survival strategies and endless forms among eukaryotes, the signal, its interpretation, and responses vary even among different plant groups. Earlier G-protein research in arabidopsis (Arabidopsis thaliana) has emphasized its divergence from Metazoa. Here, we compare recent evidence from diverse plant lineages with the available arabidopsis G-protein model and discuss the conserved and novel protein components, signaling mechanisms, and response regulation. 

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