Mapping synthetic binding proteins epitopes on diverse protein targets by protein structure prediction and protein-protein docking

Synthetic binding proteins (SBPs) are a class of artificial proteins engineered from privileged protein scaffolds, which can form highly specific molecular recognition interfaces with a variety of targets. Due to the characteristics of small size, high stability, and good tissue permeability, SBPs have important applications in biomedical research, disease diagnosis and treatment. However, knowledge of SBPs epitopes on the structures of target proteins is still limited, which hinder the development of novel SBPs. In this study, based on the currently available information of SBPs and their targets, 96 pairs of interacting proteins referring to 96 representative SBPs and 80 different targets, were systemically investigated using the state-of-the-art computational modeling techniques including AlphaFold2 protein structure prediction and Rosetta protein-protein docking. As a result, 71 out of the 96 pairs were successfully docked, of which 18, 33, and 20 pairs were defined as models with high, medium, and acceptable quality, respectively. In addition, the interface information was analyzed to decipher the interaction types driven SBPs and targets recognition. Overall, this work not only provides important structural information for understanding the mechanism of action of other SBPs with same protein scaffold, but also for aiding the rational protein engineering and to design of novel SBPs with biomedical applications.