Abstract
Post-translational modification (PTM) increases the functional diversity of proteins by introducing new functional groups to the side chain of amino acid of a protein. Among all amino acid residues, the side chain of lysine (K) can undergo many types of PTM, called K-PTM, such as “acetylation”, “crotonylation”, “methylation” and “succinylation” and also responsible for occurring multiple PTM in the same lysine of a protein which leads to the requirement of multi-label PTM site identification. However, most of the existing computational methods have been established to predict various single-label PTM sites and a very few have been developed to solve multi-label issue which needs further improvement. Here, we have developed a computational tool termed mLysPTMpred to predict multi-label lysine PTM sites by 1) incorporating the sequence-coupled information into the general pseudo amino acid composition, 2) balancing the effect of skewed training dataset by Different Error Cost method, and 3) constructing a multi-label predictor using a combination of support vector machine (SVM). This predictor achieved 83.73% accuracy in predicting the multi-label PTM site of K-PTM types. Moreover, all the experimental results along with accuracy outperformed than the existing predictor iPTM-mLys. A user-friendly web server of mLysPTMpred is available at http://research.ru.ac.bd/mLysPTMpred/.
Highlights
The structural and functional diversities of proteins as well as plasticity and dynamics of living cells are significantly dominated by the post-translational modifications (PTMs) [1]
Some lysine residues in proteins can undergo multiple K-PTMs which lead to the requirement of multi-label PTM site identification
The identification of multiple K-PTM sites in proteins has become a vital question in cellular physiology and pathology, which in turns, helps in providing some valuable evidence for both biomedical research and drug development [6, 9]
Summary
The structural and functional diversities of proteins as well as plasticity and dynamics of living cells are significantly dominated by the post-translational modifications (PTMs) [1]. PTMs are responsible for expanding the genetic code and for regulating cellular physiology [2,3,4]. It changes the properties of a protein by proteolytic cleavage or adding a modifying group to one or more amino acids [5, 6]. Some lysine residues in proteins can undergo multiple K-PTMs which lead to the requirement of multi-label PTM site identification. This kind of multiplex lysine residues in proteins may have some exceptional functions that require special attention [9]. The identification of multiple K-PTM sites in proteins has become a vital question in cellular physiology and pathology, which in turns, helps in providing some valuable evidence for both biomedical research and drug development [6, 9]
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