Predicting Binding Affinities for the Binding Domain of Hyperpolarization-Activated Cyclic Nucleotide-Gated Channel Isoforms Using Free-Energy Perturbation

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are are a family of voltage-gated, cyclic-nucleotide modulated Na+/K+ channels that regulate spontaneous rhythmic electrical activity in both the heart and the brain. Understanding differences in the responsiveness to cyclic adenosine monophosphate (cAMP) modulation between HCN isoforms would offer insight into the specific binding interactions that drive channel activation. Using all-atom molecular dynamics (MD) simulations and the free-energy perturbation (FEP) approach, we determined the absolute binding free energy of cAMP to the the cyclicnucleotide-binding domain (CNBD) of HCN isoforms 1-4. By studying the free-energy of ligand binding to the various isoforms of HCN, our study advances the understanding of HCN channel activation and modulation mechanisms. Overall, our work offers insight into explaining differences in channel sensitivity across the isoforms of HCN.