Mohamed Ruzianisra, Degac Jennifer, Helms Volkhard
Center for Bioinformatics, Saarland University, Building E2 1, P.O. Box 151150, 66041, Saarbruecken, Germany; Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), 42300 Puncak Alam, Selangor, Malaysia.
Center for Bioinformatics, Saarland University, Building E2 1, P.O. Box 151150, 66041, Saarbruecken, Germany.
PLoS One. 2015 Oct 30;10(10):e0140965. doi: 10.1371/journal.pone.0140965. eCollection 2015.
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.
蛋白质-蛋白质相互作用（PPIs）在许多生物过程中发挥着重要作用，并且它们代表了一类重要的治疗干预靶点。然而，靶向PPIs具有挑战性，因为通常没有方便的天然底物可作为小分子设计的起点。在这里，我们探索了来自ABC数据库的174个蛋白质-蛋白质（PP）复合物和161个蛋白质-配体（PL）复合物、来自PIBASE数据库的436个PP复合物和196个PL复合物以及来自Timbal数据库的89个PL复合物的五个非冗余数据集中蛋白质界面的特征。在所有情况下，小分子配体必须结合在各自的PP界面处。我们在所有三个数据集中观察到了相似的氨基酸频率。值得注意的是，PP接触和重叠PL接触的特征也高度相似。
