The Transition Pathway Between the Closed and Open States of Insulin Degrading Enzyme Shows Two Distinct Motions: Rotation Around a Hinge and Grinding Between Two Domains

Abstract

Insulin Degrading Enzyme (IDE) is involved in the degradation of insulin, amylin, and glucagon, peptides key in controlling blood glucose level. IDE has two ∼55 kDa homologous N- and C-terminal domains (IDE-N and IDE-C), each containing two homologous subdomains (D1 and D2 for IDE-N and D3 and D4 for IDE-C). For IDE to degrade its substrates, both IDE-N and IDE-C must come together for the catalytic cleft to assume a closed conformation. To investigate the mechanism through which IDE transitions between its closed and open conformations, we combined closed state crystal structures with open state CryoEM structures to run molecular dynamics simulations following the string method with swarms of trajectories and bias-exchange umbrella sampling protocols. Our analysis shows that IDE undergoes two distinct modes of motion when opening: a rotation about the hinge joining IDE-N to IDE-C (termed the hinge motion), and a rotation about the dihedral angle between the plane containing D1, D2, and D3 and the plane containing D2, D3, and D4 (termed the grinding motion). This observation matches well with multiple-body analysis performed in Relion used to deduce the protein's motion from available CryoEM data. Whereas the hinge opening motion remains relatively constant throughout the trajectory, the grinding motion appears to stop and restart. Our free energy profile constructed from MD simulations also reveals that IDE passes through a minimum energy state near its closed conformation, and our analysis suggests that this could be attributed to π-π interaction between residues W495 and F218. Our simulations and analysis provide detailed insight into the physical mechanism for the conformational transition between the closed and open states of IDE.