xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures

The identification of protein surfaces required for interaction with other biomolecules broadens our understanding of protein function, their regulation by post-translational modification, and the deleterious effect of disease mutations. Protein interaction interfaces are often identifiable as patches of conserved residues on a protein's surface. However, finding conserved accessible surfaces on folded regions requires an understanding of the protein structure to discriminate between functional and structural constraints on residue conservation. With the emergence of deep learning methods for protein structure prediction, high-quality structural models are now available for any protein. In this study, we introduce tools to identify conserved surfaces on AlphaFold2 structural models. We define autonomous structural modules from the structural models and convert these modules to a graph encoding residue topology, accessibility, and conservation. Conserved surfaces are then extracted using a novel eigenvector centrality-based approach. We apply the tool to the human proteome identifying hundreds of uncharacterised yet highly conserved surfaces, many of which contain clinically significant mutations. The xProtCAS tool is available as open-source Python software and an interactive web server.

Automated summary

The identification of protein surfaces required for interaction with other biomolecules broadens our understanding of protein function and their regulation, as well as the impact of disease mutations. This study introduces tools to identify conserved surfaces on AlphaFold2 structural models, resulting in the discovery of numerous uncharacterized yet highly conserved surfaces in the human proteome.