Why the Drosophila Shaker K+ Channel Is Not a Good Model for Ligand Binding to Voltage-Gated Kv1 Channels

The Drosophila Shaker K+ channel is the first cloned voltage-gated potassium channel and has, therefore, played an important role in structural and functional studies of those channels. While such a role is well justified for ion permeation, it is not clear whether this also extends to ligand binding. Despite the high degree of homology among Shaker and Kv1 channels, kappa-conotoxin PVIIA (kappa-PVIIA) binds to Shaker with high affinity but not to Kv1 channels. Here we address this issue by studying binding of kappa-PVIIA to Shaker and Kv1 channels using molecular dynamics (MD) simulations. The structures of the channel toxin complexes are constructed via docking and refinement with MD. The binding mode of each complex is characterized and compared to available mutagenesis data to validate the complex models. The potential of mean force for dissociation of the Shaker-kappa-PVIIA complex is calculated from umbrella sampling MD simulations, and the corresponding binding free energy is determined, which provides further validation of the complex structure. Comparison of the Shaker and Kv1 complex models shows that a few mutations in the turret and extended regions are sufficient to abolish the observed sensitivity of Shaker to kappa-PVIIA. This study demonstrates that Shaker is not always a good model for Kv1 channels for ligand binding. It also provides insights into the binding of the toxin to potassium channels that will be useful for improving affinity and selectivity properties of Kv1 channels.