topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins

Abstract

Transmembrane (TM) proteins have crucial roles in various cellular processes. The location of post-translational modifications (PTMs) on TM proteins is associated with their functional roles in various cellular processes. Given the importance of PTMs in the functioning of TM proteins, this study developed topPTM (available online at http://topPTM.cse.yzu.edu.tw), a new dbPTM module that provides a public resource for identifying the functional PTM sites on TM proteins with structural topology. Experimentally verified TM topology data were integrated from TMPad, TOPDB, PDBTM and OPM. In addition to the PTMs obtained from dbPTM, experimentally verified PTM sites were manually extracted from research articles by text mining. In an attempt to provide a full investigation of PTM sites on TM proteins, all UniProtKB protein entries containing annotations related to membrane localization and TM topology were considered potential TM proteins. Two effective tools were then used to annotate the structural topology of the potential TM proteins. The TM topology of TM proteins is represented by graphical visualization, as well as by the PTM sites. To delineate the structural correlation between the PTM sites and TM topologies, the tertiary structure of PTM sites on TM proteins was visualized by Jmol program. Given the support of research articles by manual curation and the investigation of domain-domain interactions in Protein Data Bank, 1347 PTM substrate sites are associated with protein-protein interactions for 773 TM proteins. The database content is regularly updated on publication of new data by continuous surveys of research articles and available resources.

Figure 1.

The system flowchart of topPTM construction.

Figure 2.

The web interface of a typical topPTM query. (a) Quick search by UniProtKB ID/AC or keywords. (b) Protein information. (c) Amino acid composition in extracellular, TM and intracellular regions of a TM protein. (d) Pathway analysis by mapping the TM protein to KEGG metabolic pathways. (e) Graphical visualization of PTM sites on TM protein with structural topology. (f) Detailed information of PTMs with supported literatures and 3D structures. (g) Jmol visualization of a specific PTM site on tertiary structure.

Figure 3.

A case study of investigating the functions of PTMs on protein structure (PDB ID:1NO8) of human C–C chemokine receptor type 5 (CCR5).