Integrative Modeling Identifies a Dual-Function Helix in Full-Length MDM2, Providing Novel Mechanistic Insights

The E3 ubiquitin ligase MDM2, an important oncogene, is a central negative regulator of p53, yet its extensive intrinsically disordered regions have hindered structural characterization of the full-length protein. Here, we integrate AlphaFold ensemble modeling to sample the conformational landscape with all-atom molecular dynamics simulations to characterize structural stability and construct a comprehensive, dynamic model of full-length MDM2. Our analysis identifies a previously uncharacterized autoinhibitory helix (upstream of the central acidic domain) in MDM2 that dynamically masks the N-terminal p53-binding pocket. The dynamic ensembles reveal a multistep unmasking pathway in which the helix pivots away to expose the buried p53-binding pocket. This is followed by a stabilization mechanism whereby, in the bound complex, the same helix repositions to act as an adaptive clamp, anchoring the docked p53. Our study indicates this dynamic gating apparatus to be evolutionarily conserved among MDM2 homologues. These findings provide an atomic-level framework for understanding how MDM2's intrinsic dynamics regulate p53 recognition and suggest new avenues for therapeutic targeting of the p53-MDM2 axis.