Abstract

Post Translational Modification (PTM) is defined as the modification of amino acids along the protein sequences after the translation process. These modifications significantly impact on the functioning of proteins. Therefore, having a comprehensive understanding of the underlying mechanism of PTMs turns out to be critical in studying the biological roles of proteins. Among a wide range of PTMs, sumoylation is one of the most important modifications due to its known cellular functions which include transcriptional regulation, protein stability, and protein subcellular localization. Despite its importance, determining sumoylation sites via experimental methods is time-consuming and costly. This has led to a great demand for the development of fast computational methods able to accurately determine sumoylation sites in proteins. In this study, we present a new machine learning-based method for predicting sumoylation sites called SumSec. To do this, we employed the predicted secondary structure of amino acids to extract two types of structural features from neighboring amino acids along the protein sequence which has never been used for this task. As a result, our proposed method is able to enhance the sumoylation site prediction task, outperforming previously proposed methods in the literature. SumSec demonstrated high sensitivity (0.91), accuracy (0.94) and MCC (0.88). The prediction accuracy achieved in this study is 21% better than those reported in previous studies. The script and extracted features are publicly available at: https://github.com/YosvanyLopez/SumSec.

Highlights

  • Post Translational Modifications (PTMs) are enzymatic alterations of proteins after the translation process in which a macromolecule binds to a particular amino acid at a specific location [1]

  • Is currently considered as the most accurate methods for sumoylation site prediction problem and outperforms all the other method found in the literature

  • We proposed a new machine learning model called SumSec to predict sumoylation sites as one of the most important post translational modifications

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Summary

Introduction

Post Translational Modifications (PTMs) are enzymatic alterations of proteins after the translation process in which a macromolecule binds to a particular amino acid at a specific location [1]. Among different PTMs, sumoylation is one of the most recent and important types discovered far It is defined as the binding of small ubiquitin-like modifier (or SUMO), which are small proteins in the cell. Because of this, determining those lysines that constitute sumoylation sites is of particular interest This PTM is important due to its wide spectrum of critical cellular functions, such as nuclear-cytosolic transport, transcriptional regulation, protein stability, response to stress, neurodegeneration, immune-related diseases, and certain types of cancers [10,11,12,13,14,15,16,17]

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