Revealing Dynamics-Mediated Effects of Pathogenic Missense Mutations on Menin Protein Function

Understanding how disease-causing missense mutations (DCMMs) affect protein function is fundamental. As protein dynamics is increasingly recognized as a key regulator of protein function, it is essential to incorporate dynamics into the once heavily emphasized structure-function framework to explain the effects of DCMMs. Although research in this area is emerging, evidence supporting a definitive role of dynamics in mediating the DCMM effects on protein function remains limited. Here, we used Menin─a mutation-prone scaffold protein involved in various pathologies─as a model system to explore the DCMMs' effects on Menin's dynamics and on Menin's interaction with a disordered JunD peptide. By performing MD simulations on 24 clinically confirmed DCMMs coupled with Rosetta conformation energy calculations, we showed that DCMMs do not necessarily destabilize protein stability. Instead, they induce similar dynamic changes in the protein. Using multireplica umbrella sampling to compare binding affinities, we show that DCMMs reduce Menin-JunD affinity by disrupting the conserved dissociation pathway observed in wild-type Menin. The underlying mechanism was revealed through allosteric analysis, which showed that, despite being located far from the JunD binding site, DCMMs uniformly disturbed the coupling between Menin residue E179 and the binding pocket, and forced maintenance of E197-pocket coupling restored the impaired Menin-JunD interactions in DCMMs. Together, these data demonstrate that DCMMs affect Menin-JunD interactions via changing protein dynamics, with allostery playing a crucial role, necessitating the incorporation of dynamics to better explain the effects of DCMMs.