Docking of Insulin to its Receptor

Abstract

The human insulin receptor (IR) is a homodimeric membrane-spanning ligand-activated tyrosine kinase. Although a detailed theory describing how binding of the hormone insulin triggers kinase activity of IR remains elusive, the recently published crystal structure of the IR ectodomain offers the unique opportunity to use physical modeling to begin to construct this theory. We present here the results of ∼100 ns of explicit-solvent all-atom molecular dynamics (MD) simulations of IR in both the apo and putative T and R-state insulin docked states. Our simulations confirm the large interdomain flexibility of IR and the stability of its dimeric interfaces. More importantly, however, our simulations demonstrate the evolution of large-scale asymmetry in IR relative to the crystal structure, a result that reflects the structural requirements of a “see-saw” mechanism that guarantees negative homeotropic allostery in insulin binding. This asymmetry also manifests itself in the opening of one of the two equivalent insulin binding pockets and closing of its partner. This result is significant because it allows for the first time computational docking of an intact molecule of insulin into its binding pocket on an intact IR ectodomain. We use a Monte-Carlo docking algorithm followed by MD equilibration to predict bound states of insulin on IR. These simulations allow us to identify unambiguously the residues on IR that form the “site-2” binding epitope which recognizes residues on insulin responsible for its hexamerization.