Computational Systems Biology Methods and Protocols.7z

Chapter 14

Computational Prediction of Protein O-GlcNAc Modification

Cangzhi Jia and Yun Zuo

Abstract

Protein O-GlcNAcylation on serine and threonine residues is a significant posttranslational modification.
Experimental techniques can uncover only a small portion of O-GlcNAcylation sites. Several computational
algorithms have been proposed as necessary auxiliary tools to identify potential O-GlcNAcylation sites. This
chapter discusses the metrics and procedures used to assess prediction tools and surveys six computational
tools for the prediction of protein O-GlcNAcylation sites. Analyses of these tools using an independent test
dataset indicated the advantages and disadvantages of the six existing prediction methods. We also discuss
the challenges that may be faced while developing novel predictors in the future.

KeywordsO-GlcNAcylation, Prediction, Sequence information, Features

1 Introduction

O-linked N-acetylglucosamine (O-GlcNAc) was discovered in

early 1984 by the famous biochemist Gerald W. Hart [1].

O-GlcNAcylation on serine and threonine residues of proteins is

recognized as a significant extensive and dynamic posttranslational

modification that occurs in animals, plants, microorganisms, and

viruses. Protein O-GlcNAcylation is completed through the coop-

eration of O-GlcNAc transferase, which is responsible for the addi-

tion of O-GlcNAc, and O-GlcNAcase, which is also responsible for

removal of O-GlcNAc to and from the hydroxyl groups of serine

and threonine residues [2]. The chemical structure of O-GlcNAc

glycosylation is illustrated in Fig.1.

Recent studies have shown that protein O-GlcNAcylation is

involved in multiple cellular processes, such as transcription, trans-

lation, cell signal transduction, and cell stress response. Abnormal

O-GlcNAcylation can lead to diseases, such as cancer, diabetes, and

a variety of neurodegenerative diseases [3, 4]. As a result, research

of protein O-GlcNAcylation is attracting more and more attention.

Although experimental techniques to detect and accurately

localize protein O-GlcNAcylation sites have improved significantly

Tao Huang (ed.),Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754,
https://doi.org/10.1007/978-1-4939-7717-8_14,©Springer Science+Business Media, LLC, part of Springer Nature 2018

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