pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework

Abstract

Thiol groups on cysteines can undergo multiple post-translational modifications (PTMs), acting as a molecular switch to maintain redox homeostasis and regulating a series of cell signaling transductions. Identification of sophistical protein cysteine modifications is crucial for dissecting its underlying regulatory mechanism. Instead of a time-consuming and labor-intensive experimental method, various computational methods have attracted intense research interest due to their convenience and low cost. Here, we developed the first comprehensive deep learning based tool pCysMod for multiple protein cysteine modification prediction, including S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation. Experimentally verified cysteine sites curated from literature and sites collected by other databases and predicting tools were integrated as benchmark dataset. Several protein sequence features were extracted and united into a deep learning model, and the hyperparameters were optimized by particle swarm optimization algorithms. Cross-validations indicated our model showed excellent robustness and outperformed existing tools, which was able to achieve an average AUC of 0.793, 0.807, 0.796, 0.793, and 0.876 for S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation, demonstrating pCysMod was stable and suitable for protein cysteine modification prediction. Besides, we constructed a comprehensive protein cysteine modification prediction web server based on this model to benefit the researches finding the potential modification sites of their interested proteins, which could be accessed at http://pcysmod.omicsbio.info. This work will undoubtedly greatly promote the study of protein cysteine modification and contribute to clarifying the biological regulation mechanisms of cysteine modification within and among the cells.

GSNOR regulates cardiomyocyte differentiation and maturation through protein S-nitrosylation

“…Furthermore, many additional SNOregulatory enzymes remain to be discovered, including S-nitrosylases (SNO synthases and transnitrosylases) and denitrosylases, including but not limited to GSNOR subtypes; in other words, the multiplex enzyme systems [7] regulating protein S-nitrosylation in cardiomyocytes have yet to be fully uncovered. This complexity elevates the impact of the findings presented by Salerno et al [1] , because it links cardiomyocyte differentiation specifically to GSNOR, one of multiple denitrosylase enzymes. In future studies it will be intriguing to explore what role other SNO-processing enzymes may plausibly play in cardiac regeneration and within the purview of stem cell maintenance and proliferation more broadly.…”

“…GSNOR modulates dynamic denitrosylation of hundreds of protein substrates (among > 20,000 in the published literature [2] ) in response to a variety of biological stimuli [3] ; Salerno et al [1] add GSK-3β (glycogen synthase kinase-3β) to this list of SNO substrates. GSK-3β is an essential kinase with multiple roles, particularly in cardiovascular physiology [4] .…”

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S-nitrosoglutathione reductase (GSNOR) is a denitrosylase enzyme responsible for reverting protein Snitrosylation (SNO). In this issue, Salerno et al [1] provide evidence that GSNOR deficiency -and thus elevated protein S-nitrosylation -accelerates cardiomyocyte differentiation and maturation of induced pluripotent stem cells (iPSCs). GSNOR inhibition (GSNOR -/-iPSCs) expedites the epithelial-mesenchymal transition (EMT) and promotes cardiomyocyte progenitor cell proliferation, differentiation, and migration.

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“…S-nitrosylation of GSK-3β inhibits kinase activity independent of canonical inhibitory Ser9 phosphorylation, providing a novel locus of regulation for this important kinase. Salerno et al [1] innovatively demonstrate that S-nitrosylation of GSK-3β is enzymatically regulated by GSNOR in iPSCs during early cardiomyocyte differentiation. Further, they show that GSNOR -/-iPSCs -with elevated Snitrosylation -undergo accelerated cardiomyogenesis, including expedited differentiation, proliferation, migration, and EMT compared to wild-type iPSCs.…”

“…Indeed, no published study has yet investigated functional consequences of individual GSK-3β Cys residue S-nitrosylation, which are likely tightly regulated by specific nitrosylase and denitrosylase enzymes in vivo [7] . Thus, in vitro treatment with exogenous NO donors (GSNO [1] , CysNO [5] , etc.) may not always recapitulate physiology.…”