#25 · Structural bio & protein design

MD simulations resolve dynamic conformational routes in ezrin, CENP-A, SERINC3 and ExsA

The common thread is molecular dynamics used to trace how local perturbations, such as lipid binding, phosphorylation, or partner engagement, propagate through macromolecular systems. The ezrin study attributes spontaneous CTD dissociation to PI(4,5)P2 binding, with T567 phosphorylation blocking reassociation. The CENP-A nucleosome study uses SIRAH coarse-grained simulations to relate CENP-N-induced N-terminal flexibility and RG loop stabilization to allosteric effects. The SERINC3 study uses TTMetaD enhanced sampling to propose a credit-card mechanism for phosphatidylserine scrambling. The ExsA study reports that the helix-turn-helix motif allosterically stabilizes the ligand-binding domain and identifies new druggable pockets at the NTD/CTD interface. What is new relative to static structure is the explicit description of dynamic routes, though all evidence is simulation-based and the systems differ in resolution and scope.