Three-dimensional reconstruction of protein networks provides insight into human genetic disease

In an effort to understand molecular mechanisms of human disease and to determine genes responsible, we systematically examine relationships between 3,949 genes, 62,663 mutations and 3,453 associated disorders within the framework of a three-dimensional structurally resolved human interactome, consisting of 4,222 high-quality binary protein-protein interactions with their atomic-resolution interfaces. We find that in-frame mutations (missense point mutations and in-frame insertions and deletions) are enriched on the interaction interfaces of proteins associated with the corresponding disorders, indicating that alteration of specific interactions by in-frame disease mutations is critical in understanding the pathogenesis of many genes. Furthermore, locations of mutations on proteins with regard to interaction interfaces are significantly associated with underlying pathogenic processes and the disease specificity for different mutations of the same gene. Based on these findings, we generate 292 new gene candidates for 694 unknown disease-to-gene associations with proposed molecular mechanism hypotheses, readily expanding our understanding of human genetic diseases and corresponding therapeutic possibilities.