Towards protein-protein docking with significant structural changes using CABS-dock

Abstract

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover, a disruption of hese mechanisms is frequently postulated as a possible cause of diseases such as Alzheimer's or cancer. For many of biologically relevant cases the structure of protein-protein complexes remain unknown. Therefore computational techniques, including molecular docking, have become a valuable part of drug discovery pipelines. Unfortunately, none of the widely used protein-protein docking tools is free from serious limitations. Typically, in docking simulations the protein flexibility is either completely neglected or very limited. Additionally, some knowledge of the approximate location and/or the shape of the active site is also required. Such limitations arise mostly from the enormous number of degrees of freedom of protein-protein systems. In this paper, an efficient computational method for protein-protein docking is proposed and initially tested on a single docking case. The proposed method is based on a two-step procedure. In the first step, CABS-dock web server for protein-peptide docking is used to dock a peptide, which is the appropriate protein fragment responsible for the protein-protein interaction, to the other protein partner. During peptide docking, no knowledge about the binding site, nor the peptide structure, is used and the peptide is allowed to be fully flexible. In the second step, the docked peptide is used in the structural adjustment of protein complex partners. The proposed method allowed us to obtain a high accuracy model, therefore it provides a promising framework for further advances.