SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids

Anal Biochem. 2017 Jun 15;527:24-32. doi: 10.1016/j.ab.2017.03.021. Epub 2017 Mar 28.

Abstract

Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles and local structure conformations were incorporated. We used the k-nearest neighbors cleaning treatment for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred to as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathew's correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively.

Keywords: Amino acids; Lysine succinylation; Prediction; Protein sequences; Structural features.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Amino Acids / metabolism*
  • Animals
  • Humans
  • Lysine / metabolism*
  • Models, Statistical*
  • Protein Processing, Post-Translational*
  • Proteome / genetics
  • Proteome / metabolism*
  • Rodentia / genetics
  • Rodentia / metabolism
  • Succinic Acid / metabolism*

Substances

  • Amino Acids
  • Proteome
  • Succinic Acid
  • Lysine