Abstract
As one of the most important and ubiquitous post-translational modifications (PTMs) of proteins, S-nitrosylation plays important roles in a variety of biological processes, including the regulation of cellular dynamics and plasticity. Identification of S-nitrosylated substrates with their exact sites is crucial for understanding the molecular mechanisms of S-nitrosylation. In contrast with labor-intensive and time-consuming experimental approaches, prediction of S-nitrosylation sites using computational methods could provide convenience and increased speed. In this work, we developed a novel software of GPS-SNO 1.0 for the prediction of S-nitrosylation sites. We greatly improved our previously developed algorithm and released the GPS 3.0 algorithm for GPS-SNO. By comparison, the prediction performance of GPS 3.0 algorithm was better than other methods, with an accuracy of 75.80%, a sensitivity of 53.57% and a specificity of 80.14%. As an application of GPS-SNO 1.0, we predicted putative S-nitrosylation sites for hundreds of potentially S-nitrosylated substrates for which the exact S-nitrosylation sites had not been experimentally determined. In this regard, GPS-SNO 1.0 should prove to be a useful tool for experimentalists. The online service and local packages of GPS-SNO were implemented in JAVA and are freely available at: http://sno.biocuckoo.org/.
Highlights
The 1998 Nobel Prize for Physiology or Medicine was awarded for seminal discoveries that showed nitric oxide (NO) to be a freely-diffusible signaling molecule and second messenger which regulates the production of cyclic GMP and plays essential roles in the cardiovascular system
We developed a novel algorithm of GPS 1.0 & 1.10 (Group-based Phosphorylation Scoring) for the prediction of kinase-specific phosphorylation sites [29,30]
We developed a simple approach of matrix mutation (MaM), which mutated the initial matrix of BLOSUM62 into the optimal matrix having the highest leave-oneout performance [24]
Summary
The 1998 Nobel Prize for Physiology or Medicine was awarded for seminal discoveries that showed nitric oxide (NO) to be a freely-diffusible signaling molecule and second messenger which regulates the production of cyclic GMP (cGMP) and plays essential roles in the cardiovascular system. Recent reports have proposed that S-nitrosylation can modulate protein stability [7], activities [8] and trafficking [9,10], and play an important role in a variety of biological processes, including transcriptional regulation [7], cell signaling [11], apoptosis [8], and chromatin remodeling [12]. Aberrant S-nitrosylation has been implicated in numerous diseases and cancers [1,2,8]. In this regard, experimental identification of S-nitrosylated proteins together with their sites would serve as a foundation of understanding the molecular mechanisms and regulatory roles of S-nitrosylation
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