CoDIAC: A comprehensive approach for interaction analysis provides insights into SH2 domain function and regulation

Protein domains are conserved structural and functional units that serve as the building blocks of proteins. Through evolutionary expansion, domain families are represented by multiple members in diverse configurations with other domains, evolving new specificities for their interacting partners. Here, we developed a structure-based interface analysis to map domain interfaces from experimental and predicted structures, including interfaces with macromolecules and intraprotein interfaces. We hypothesized that contact mapping of domains could yield insights into domain selectivity and the conservation of domain-domain interfaces across proteins and identify conserved posttranslational modifications (PTMs) relative to interaction interfaces, enabling the inference of specific effects as a result of PTMs or mutations. We designed this modular approach as an open-source Python package called Comprehensive Domain Interface Analysis of Contacts (CoDIAC) and applied it to the family of human Src homology 2 (SH2) domains, a modular unit central to phosphotyrosine-mediated signaling. CoDIAC revealed coordinated regulation of SH2 domain binding interfaces by tyrosine and serine/threonine phosphorylation and acetylation that may underlie binding selectivity. These findings suggest that multiple signaling systems can regulate protein activity and SH2 domain interactions in a coordinated manner. Applying CoDIAC to the study of other protein domains should provide insights into their binding interfaces and molecular interactions.