Effects of pathological mutations on the CHCHD2 monomer structure: A study by AlphaFold3 linked to the generation of conformational ensembles

CHCHD2 is a mitochondrial protein linked to neurodegenerative diseases such as Parkinson's disease (PD), Alzheimer's disease (AD), and frontotemporal dementia (FTD). To investigate the structural effects of disease-associated mutations, we analyzed 19 pathogenic variants using AlphaFold3 and conformational ensemble modeling with AFflecto. While the radius of gyration and end-to-end distances remained largely unchanged, mutations significantly altered secondary structure elements and contact maps, particularly in local folding. Intrinsic disorder and LLPS analyses revealed that mutations modulate the protein's droplet-forming capacity and interaction flexibility. These changes may impact protein-protein interactions, phase behavior, and mitochondrial function. Our findings indicate that pathogenic CHCHD2 mutations cause subtle but functionally relevant structural perturbations rather than global destabilization. This study underscores the importance of ensemble-based modeling in understanding mutation-induced dysfunction in intrinsically disordered proteins involved in neurodegeneration.