The Allosteric Communication Network in the Activation of Antithrombin by Heparin

The allosteric activation of antithrombin (AT) involves a conformational shift from a native, repressed (R) to a heparin-bound, activated (AH) state. Using computational structural analysis, we identified an evolutionarily conserved allosteric communication network (ACN) comprising the residues H120, Y131, and Y166, which undergo key structural displacements during this transition. Site-directed mutagenesis of these residues markedly enhanced AT native reactivity toward FXa and reduced thermal stability, indicating their role in stabilizing the R state. These findings support a three-step "slingshot" model in which the ACN functions as a molecular lock that restrains stored conformational energy, preventing premature activation. Heparin binding disengages this lock, triggering a cascade of structural changes that propagate from the heparin-binding site (HBS) to the reactive center loop (RCL). Additional mutational analyses of residues bridging the β-sheet A (βsA) and the RCL/exosite domains revealed a delicate energetic balance involving the S380 insertion and E381-R197 salt bridge, which collectively tune the activation threshold. Molecular dynamics simulations of ACN mutants further revealed increased flexibility at both HBS and RCL domains, consistent with concerted allosteric coupling. Together, these results provide new mechanistic insights into the structural basis of AT activation and suggest avenues for engineering heparin-independent AT variants.