Structural and functional impact of the POLD1 Ser605del variant in MDPL syndrome: insights from protein-protein interactions

Background: Mandibular hypoplasia, Deafness, Progeroid features, and Lipodystrophy (MDPL) syndrome is a very rare genetic disorder linked to variants in the POLD1 gene, which encodes the catalytic subunit of DNA polymerase delta, a key enzyme involved in DNA replication and repair. Most patients carry a recurrent in frame deletion (p.Ser605del) within the active site of the p125 subunit. Despite its rarity, understanding the functional consequences of the Ser605del variant has broad implications for aging-related diseases and genome stability. Methods: We combined structural modelling, molecular dynamics simulations, and protein–protein interaction (PPIs) analyses to evaluate the impact of Ser605del in the catalytic activity of DNA polymerase delta. Bioinformatic tools were applied to characterize its interaction network. RT-q PCR and Western Blot were performed to assess expression levels of POLD1, TRF1, and PARP1 in human dermal fibroblasts (HDFs) of three MDPL patients of different ages. Cells were monitored at different passages, both in basal condition and after damage by X irradiation. POLD1/TRF1 interaction was confirmed by immunoprecipitation analyses. Results: Using molecular docking, molecular dynamics simulations and thermodynamic analyses, we found that Ser605del affects the DNA-binding site, impairing dTTP binding. The deletion alters short linear motifs involved in protein–protein interactions (PPIs), allowing the acquisition of a F/Y-X-L-X-P (FSLYP) consensus sequence with TRF1, a telomeric protein. In silico analyses highlighted a stronger interaction between the Ser605del POLD1 variant and TRF1. Experiments on MDPL fibroblasts confirmed a stronger POLD1–TRF1 binding and revealed dysregulation of PARP1, involved in telomere maintenance. Following X-ray irradiation, aimed at exacerbating the cellular phenotype, we observed a decreasing trend in these markers, which reached statistical significance particularly in one older patient. Conclusions: We identified a novel short linear motif (FSLYP) in the Ser605del POLD1 protein that mediates abnormal interaction with TRF1, revealing a structural and functional link between POLD1 and telomere biology, contributing to premature aging phenotypes. This work provides new insights into MDPL pathogenesis and lays the foundation for future research into aging-related therapies.