Computational Studies on the cAMP Modulation of the HCN2 Channel

Abstract

Hyperpolarization-activated cyclic nucleotide-gated 2 (HCN2) ion channels play a fundamental role in electric signaling in nerves, muscles, and synapses; however, their ligand gating mechanism is not well understood. Through collaboration between experimental and computational methods, this study brings insight into the mechanism of cyclic adenosine monophosphate (cAMP) modulation of the HCN2 channel (residues 443-636) by exploring the monomer and tetramer dynamics in the apo and holo states. We applied all-atom and coarse-grained molecular dynamics on molecular systems containing HCN2 with and without cAMP. Starting from the holo structure resolved by X-ray crystallography, our simulations guide the protein into its apo state. Along this pathway, we observed unfolding of the C'-helix and loss of contact between A’ and B’ helices in the C-linker and the cyclic nucleotide binding domain (CNBD). In addition, by using tmFRET distances as restraints, we were able to capture structural changes in the CNBD. Our results corroborate recent experimental studies showing the outward movement of the C-helix in the absence of cAMP.