Structural and functional effects of disease mutations in the interface of human membrane protein complexes

Membrane proteins are integral to the regulation and maintenance of vital cellular functions. Mutations in these proteins have been implicated in a wide range of diseases, including cancer and metabolic disorders. While previous studies have shown a preferential enrichment of disease-associated mutations at protein-protein interaction (PPI) interfaces, their distribution and impact in membrane proteins remain largely unexplored. In this study, we present a comprehensive structure-based analysis of pathogenic missense mutations in human α-helical membrane proteins, integrating biophysical, functional, and inheritance annotations. Our findings reveal that mutations localized at membrane protein interfaces are significantly enriched in pathogenic variants and tend to cause synergistic disruptions in both binding and stability, resulting in greater functional impairment. Notably, non-interface residues that are in close spatial proximity to interaction interfaces are also enriched in disease mutations, suggesting a potential allosteric effect of pathogenicity. We also uncovered distinct mutation patterns across various classifications, with a notable enrichment of disease mutations in multi-pass membrane proteins, particularly within the transporter functional class. In contrast to other disease classes, which showed strong enrichment at protein interfaces, cancer-associated variants were depleted at interfaces and showed weaker binding effects, indicating alternative pathogenic pathways. Furthermore, analysis of inheritance patterns and molecular mechanisms revealed that autosomal dominant mutations, particularly those acting via dominant-negative mechanisms, are preferentially localized at interfaces. Thus, this study underscores the importance of structure-based, multi-parametric approaches in interpreting pathogenic mutations and guiding the development of targeted therapeutic strategies for membrane protein-related diseases.