AI Article Synopsis
Article Abstract
Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiological and pathological processes. By altering the size and physiochemical properties of modified cysteine residues, sulfenylation can impact the cellular function of proteins in several different ways. Thus, the ability to rapidly and accurately identify putative sulfenylation sites in proteins will provide important insights into redox-dependent regulation of protein function in a variety of cellular contexts. Though bottom-up proteomic approaches, such as tandem mass spectrometry (MS/MS), provide a wealth of information about global changes in the sulfenylation state of proteins, MS/MS-based experiments are often labor-intensive, costly and technically challenging. Therefore, to complement existing proteomic approaches, researchers have developed a series of computational tools to identify putative sulfenylation sites on proteins. However, existing methods often suffer from low accuracy, specificity, and/or sensitivity. In this study, we developed SVM-SulfoSite, a novel sulfenylation prediction tool that uses support vector machines (SVM) to identify key determinants of sulfenylation among five feature classes: binary code, physiochemical properties, k-space amino acid pairs, amino acid composition and high-quality physiochemical indices. Using 10-fold cross-validation, SVM-SulfoSite achieved 95% sensitivity and 83% specificity, with an overall accuracy of 89% and Matthew's correlation coefficient (MCC) of 0.79. Likewise, using an independent test set of experimentally identified sulfenylation sites, our method achieved scores of 74%, 62%, 80% and 0.42 for accuracy, sensitivity, specificity and MCC, with an area under the receiver operator characteristic (ROC) curve of 0.81. Moreover, in side-by-side comparisons, SVM-SulfoSite performed as well as or better than existing sulfenylation prediction tools. Together, these results suggest that our method represents a robust and complementary technique for advanced exploration of protein S-sulfenylation.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062547 | PMC |
| http://dx.doi.org/10.1038/s41598-018-29126-x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Inhibition of Sirtuin Deacylase Activity by Peroxynitrite.
Biochemistry
October 2024
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States.
Sirtuins are a class of enzymes that deacylate protein lysine residues using NAD as a cosubstrate. Sirtuin deacylase activity has been historically regarded as protective; loss of sirtuin deacylase activity potentially increases susceptibility to aging-related disease development. However, which factors may inhibit sirtuins during aging or disease is largely unknown.
View Article and Find Full Text PDFSulfur dioxide inhibits mast cell degranulation by sulphenylation of galectin-9 at cysteine 74.
Front Immunol
July 2024
Department of Pediatrics, Peking University First Hospital, Beijing, China.
Objectives: Mast cell (MC) degranulation is a key process in allergic reactions and inflammatory responses. Aspartate aminotransferase 1 (AAT1)-derived endogenous sulfur dioxide (SO) is an important regulator of MC function. However, the mechanism underlying its role in MC degranulation remains unclear.
View Article and Find Full Text PDFSulfur signaling pathway in cardiovascular disease.
Front Pharmacol
November 2023
Department of Pediatrics, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China.
Hydrogen sulfide (HS) and sulfur dioxide (SO), recognized as endogenous sulfur-containing gas signaling molecules, were the third and fourth molecules to be identified subsequent to nitric oxide and carbon monoxide (CO), and exerted diverse biological effects on the cardiovascular system. However, the exact mechanisms underlying the actions of HS and SO have remained elusive until now. Recently, novel post-translational modifications known as S-sulfhydration and S-sulfenylation, induced by HS and SO respectively, have been proposed.
View Article and Find Full Text PDFHydrogen peroxide-dependent oxidation of ERK2 within its D-recruitment site alters its substrate selection.
iScience
October 2023
Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA.
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are dysregulated in many pervasive diseases. Recently, we discovered that ERK1/2 is oxidized by signal-generated hydrogen peroxide in various cell types. Since the putative sites of oxidation lie within or near ERK1/2's ligand-binding surfaces, we investigated how oxidation of ERK2 regulates interactions with the model substrates Sub-D and Sub-F.
View Article and Find Full Text PDFBiGRUD-SA: Protein S-sulfenylation sites prediction based on BiGRU and self-attention.
Comput Biol Med
September 2023
College of Information Science and Technology, School of Data Science, Qingdao University of Science and Technology, Qingdao, 266061, China; School of Data Science, University of Science and Technology of China, Hefei, 230027, China. Electronic address:
S-sulfenylation is a vital post-translational modification (PTM) of proteins, which is an intermediate in other redox reactions and has implications for signal transduction and protein function regulation. However, there are many restrictions on the experimental identification of S-sulfenylation sites. Therefore, predicting S-sulfoylation sites by computational methods is fundamental to studying protein function and related biological mechanisms.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!