Abstract
Post-translational modification refers to the biological mechanism involved in the enzymatic modification of proteins after being translated in the ribosome. This mechanism comprises a wide range of structural modifications, which bring dramatic variations to the biological function of proteins. One of the recently discovered modifications is succinylation. Although succinylation can be detected through mass spectrometry, its current experimental detection turns out to be a timely process unable to meet the exponential growth of sequenced proteins. Therefore, the implementation of fast and accurate computational methods has emerged as a feasible solution. This paper proposes a novel classification approach, which effectively incorporates the secondary structure and evolutionary information of proteins through profile bigrams for succinylation prediction. The proposed predictor, abbreviated as SSEvol-Suc, made use of the above features for training an AdaBoost classifier and consequently predicting succinylated lysine residues. When SSEvol-Suc was compared with four benchmark predictors, it outperformed them in metrics such as sensitivity (0.909), accuracy (0.875) and Matthews correlation coefficient (0.75).
Highlights
Post-translational modification (PTM) refers to the enzymatic modification of proteins [1]
We propose a new predictor, SSEvol-Suc, which primarily integrates information about the best secondary structure and the position specific scoring matrix (PSSM) for predicting succinylation sites [54, 55]
We evaluated the performance of SSEvol-Suc in terms of four different statistical metrics: sensitivity, specificity, accuracy and Matthews correlation coefficient [15, 36, 77,78,79,80]
Summary
Post-translational modification (PTM) refers to the enzymatic modification of proteins [1] As part of this biological mechanism, one or more amino acids of a protein interact with specific molecular groups. Such interaction functionally changes the amino acids, thereby impacting. Succinylation mainly refers to the addition of a succinyl group to lysine residues This molecular change alters the charge of the lysine to -1, introducing a large structural moiety. Succinylation occurs in both eukaryotic and prokaryotic cells, and is common in enzymes involved in mitochondrial metabolism, amino acid degradation, and fatty acid metabolism. The identification of succinylation sites can provide detailed insights into the function of proteins and their biological interactions
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