Abstract
BackgroundPost-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis. In the recent times, there has been many reported PTMs. Out of the many modifications, phosphoglycerylation has become particularly the subject of interest. The experimental procedure for identification of phosphoglycerylated residues continues to be an expensive, inefficient and time-consuming effort, even with a large number of proteins that are sequenced in the post-genomic period. Computational methods are therefore being anticipated in order to effectively predict phosphoglycerylated lysines. Even though there are predictors available, the ability to detect phosphoglycerylated lysine residues still remains inadequate.ResultsWe have introduced a new predictor in this paper named EvolStruct-Phogly that uses structural and evolutionary information relating to amino acids to predict phosphoglycerylated lysine residues. Benchmarked data is employed containing experimentally identified phosphoglycerylated and non-phosphoglycerylated lysines. We have then extracted the three structural information which are accessible surface area of amino acids, backbone torsion angles, amino acid’s local structure conformations and profile bigrams of position-specific scoring matrices.ConclusionEvolStruct-Phogly showed a noteworthy improvement in regards to the performance when compared with the previous predictors. The performance metrics obtained are as follows: sensitivity 0.7744, specificity 0.8533, precision 0.7368, accuracy 0.8275, and Mathews correlation coefficient of 0.6242. The software package and data of this work can be obtained from https://github.com/abelavit/EvolStruct-Phogly or www.alok-ai-lab.com
Highlights
Post-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis
We introduce an original predictor called EvolStruct-Phogly which employs a set of features comprising structural properties and evolutionary information for distinguishing phosphoglycerylated and non-phosphoglycerylated lysine residues
This predictor considers a total of eight structural properties which are the accessible surface area (ASA), the backbone torsion angles, and amino acid probability to local structure conformations [33, 34] and position-specific scoring matrix (PSSM) of proteins together with profile bigram [35] of amino acids for predicting phosphoglycerylated and non-phosphoglycerylated lysine residues
Summary
Post-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis. The experimental procedure for identification of phosphoglycerylated residues continues to be an expensive, inefficient and time-consuming effort, even with a large number of proteins that are sequenced in the post-genomic period. Post-translational modification (PTM) signifies the biological process responsible for the enzymatic change in proteins after its translation in the ribosome. There has been a stir of interest in these types of modifications across numerous organisms due to the progressive efforts of high-throughput proteomics in areas of site-specific PTM and protein altering enzymes [1]. The modification of amino acids, as well as regulatory enzymes, have resulted in numerous human diseases including neurodegenerative disorders, rheumatic arthritis, coeliac disease, essential hypertension and high blood pressure, multiple sclerosis and coronary heart diseases
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