Composition of overlapping protein-protein and protein-ligand interfaces

• Published in: PLoS ONE
• Main Author: Mohamed R.; Degac J.; Helms V.
• Format: Article
• Language: English
• Published: Public Library of Science 2015
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84951058673&doi=10.1371%2fjournal.pone.0140965&partnerID=40&md5=463f13dd2ce87ea8b8e07a5a9a47a250

Protein-protein interactions (PPIs) play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP) complexes, and 161 proteinligand (PL) complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar. © 2015 Mohamed et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.