Interaction Surfaces of Proteins Involved in Bacterial Chemotaxis with Rigid-Body Docking Decoys

Abstract

To understand protein interaction mechanism, protein interaction interfaces are investigated using properties of protein interaction surfaces derived from sets of protein complex structures generated by rigid-body docking, referred as docking decoys. Because each docking decoys includes information of sets of possible interacting amino acid pairs we used profiles of protein interaction surfaces for improving the precision of protein-protein interaction (PPI) prediction in process of cluster analysis [Uchikoga & Hirokawa 2010 BMC Bioinfo.11:236]. By using profiles of protein interaction surfaces, we have developed methods for exploring docking search spaces in rigid-body docking process, Re-docking scheme [Uchikoga et al. 2013 PLoS ONE 8:e69365]. Protein interaction surfaces of whole decoys would contain clue for understanding protein interaction mechanisms. We then proposed a profile generated by assembling whole docking decoy interaction surfaces, referred as broad interaction surfaces (BIPs). And differences of BIPs between various protein pairs in a docking benchmark dataset were analyzed, indicating that BIPs are different between true and false protein interaction partners [Uchikoga et al. 2016 Biophys. Phisicobiol. 13:105-]. In this work, we apply the BIP method to PPI analysis involved in chemotaxis systems of several bacteria species. We then performed all-to-all docking analysis using a rigid-body docking software MEGADOCK for docking process. Cluster analysis could examine for differences between true interaction protein pairs and false pairs.