Abstract
Post-translational modifications (PTMs) are crucial steps in protein synthesis and are important factors contributing to protein diversity. PTMs play important roles in the regulation of gene expression, protein stability and metabolism. Lysine residues in protein sequences have been found to be targeted for both types of PTMs: sumoylations and acetylations; however, each PTM has a different cellular role. As experimental approaches are often laborious and time consuming, it is challenging to distinguish the two types of PTMs on lysine residues using computational methods. In this study, we developed a method to discriminate between sumoylated lysine residues and acetylated residues. The method incorporated several features: PSSM conservation scores, amino acid factors, secondary structures, solvent accessibilities and disorder scores. By using the mRMR (Maximum Relevance Minimum Redundancy) method and the IFS (Incremental Feature Selection) method, an optimal feature set was selected from all of the incorporated features, with which the classifier achieved 92.14% accuracy with an MCC value of 0.7322. Analysis of the optimal feature set revealed some differences between acetylation and sumoylation. The results from our study also supported the previous finding that there exist different consensus motifs for the two types of PTMs. The results could suggest possible dominant factors governing the acetylation and sumoylation of lysine residues, shedding some light on the modification dynamics and molecular mechanisms of the two types of PTMs, and provide guidelines for experimental validations.
Highlights
Post-translational modifications (PTMs) are crucial steps in protein synthesis and are important factors contributing to protein diversity
Among the various types of PTMs, lysine acetylation and sumoylation are emerging as two major types for both nuclear and cytoplasmic proteins, and they are related to several human diseases such as metabolic disorders and cancers [1,2,3]
Discovered on core histones approximately half a century ago, lysine acetylation has been found to be involved in multiple cellular processes such as transcriptional control, epigenetic program shaping, cytoskeleton organization, and energy metabolism regulation [4,5,6,7]
Summary
Post-translational modifications (PTMs) are crucial steps in protein synthesis and are important factors contributing to protein diversity. Discovered on core histones approximately half a century ago, lysine acetylation has been found to be involved in multiple cellular processes such as transcriptional control, epigenetic program shaping, cytoskeleton organization, and energy metabolism regulation [4,5,6,7]. This type of reversible modification begins with the catalysis of lysine acetyltransferases (KATs, or histone acetyltransferases (HATs)), by adding the acetyl-group of an acetyl-CoA to the epsilon-amino group of an internal lysine residue. Lysine acetylation and deacetylation have been associated with chromatin [4,10] but have been found to be related to cytoplasmic proteins in recent studies [5,11]
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