Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces

Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces

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 d...

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Main Authors: Mohamed, Ruzianisra, Degac, Jennifer, Helms, Volkhard
Format: Online
Language:English
Published: Public Library of Science 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627654/
id pubmed-4627654
recordtype oai_dc
spelling pubmed-46276542015-11-06 Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces Mohamed, Ruzianisra Degac, Jennifer Helms, Volkhard Research Article 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 protein-ligand (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. Public Library of Science 2015-10-30 /pmc/articles/PMC4627654/ /pubmed/26517868 http://dx.doi.org/10.1371/journal.pone.0140965 Text en © 2015 Mohamed et al http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Mohamed, Ruzianisra
Degac, Jennifer
Helms, Volkhard
spellingShingle Mohamed, Ruzianisra
Degac, Jennifer
Helms, Volkhard
Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces
author_facet Mohamed, Ruzianisra
Degac, Jennifer
Helms, Volkhard
author_sort Mohamed, Ruzianisra
title Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces
title_short Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces
title_full Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces
title_fullStr Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces
title_full_unstemmed Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces
title_sort composition of overlapping protein-protein and protein-ligand interfaces
description 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 protein-ligand (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.
publisher Public Library of Science
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627654/
_version_ 1613495437495369728

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