title: SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.
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.
authors.affiliation: Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan; Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan. Electronic address: yosvany.lopez.alvarez@gmail.com.
authors.forename: Yosvany
authors.initials: Y
authors.lastname: López
authors.affiliation: Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, USA. Electronic address: abdollah.dehzangi@uiowa.edu.
authors.forename: Abdollah
authors.initials: A
authors.lastname: Dehzangi
authors.affiliation: School of Engineering & Advanced Technology, Massey University, New Zealand.
authors.forename: Sunil Pranit
authors.initials: SP
authors.lastname: Lal
authors.affiliation: School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, Queensland 4215, Australia.
authors.forename: Ghazaleh
authors.initials: G
authors.lastname: Taherzadeh
authors.affiliation: Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Michaelson
authors.affiliation: School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, Queensland 4215, Australia; Institute for Integrated and Intelligent Systems, Griffith University, Australia.
authors.forename: Abdul
authors.initials: A
authors.lastname: Sattar
authors.affiliation: Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan; Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; CREST, JST, Tokyo 113-8510, Japan.
authors.forename: Tatsuhiko
authors.initials: T
authors.lastname: Tsunoda
authors.affiliation: Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Institute for Integrated and Intelligent Systems, Griffith University, Australia.
authors.forename: Alok
authors.initials: A
authors.lastname: Sharma
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism*; D000818:Animals; D006801:Humans; D008239:Lysine / Q000378:metabolism*; D015233:Models, Statistical; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D012377:Rodentia / Q000235:genetics / Q000378:metabolism; D019802:Succinic Acid / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D020543:Proteome; D019802:Succinic Acid; D008239:Lysine
keywords: Amino acids; Lysine succinylation; Prediction; Protein sequences; Structural features