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

Abstract

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, κ-conotoxin PVIIA (κ-PVIIA) binds to Shaker with high affinity but not to Kv1 channels. Here we address this issue by studying binding of κ-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-κ-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 κ-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.

Efficient enzymatic cyclization of an inhibitory cystine knot‐containing peptide

“…Although Shaker has been used as a model for studying other K V channels due to the high degree of homology, our results suggest that a ligand of Shaker does not necessarily bind to other K V channels. Similar experimental or modeling results were also obtained previously using K V 1.1 and K V 1.2, (Boccaccio et al, ; Mahdavi and Kuyucak, ; Shon et al, ). Finally, neither peptide is active on rNa V 1.4 or hNa V 1.6.…”

“…The molecular model used for the studies of interaction between the Shaker K + channel and linear κ‐PVIIA was kindly provided by Mhadavi and Kuyucak (Mahdavi and Kuyucak, ). A model of the interaction between cyc‐PVIIA and the Shaker K + channel was built by homology with Modeller 9v13 (Sali and Blundell, ) using the model of Mhadavi and Kuyucak and the solution structure of cyc‐PVIIA as templates.…”

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

“…(1) Small molecule conformational sampling [73][74][75][76]; (2) Protein-folding [77][78][79] and large-scale protein conformational sampling [80][81][82][83]; (3) Protein-protein/peptide-peptide interactions [84][85][86][87][88][89][90][91][92]; (4) DNA conformational changes [93] and DNA-DNA interactions [94][95][96]; (5) Binding and association free-energies [97][98][99][100][101][102][103][104][105][106][107]; (6) Adsorption on and permeation through lipid bilayers [108][109][110][111][112][113][114][115][116][117] …”

Computational Studies of Marine Toxins Targeting Ion Channels

“…In a more recent study of κ -PVIIA binding to Shaker and Kv1 channels [61], a correct model of Shaker was used and the results obtained from the Shaker- κ -PVIIA complex model were in general agreement with the experiments. Similar protocols as in ShK were employed in creating the complex model.…”

“…In a follow-up study, conformational restraints were used to prevent the deformation of the toxin, which enabled calculation of the absolute binding free energy within chemical accuracy of 1 kcal/mol [53]. Since then, the PMF method has been used in several computational studies of toxin binding to ion channels [54,55,56,57,58,59,60,61]. As long as a validated complex structure was employed in the PMF calculations, the absolute binding free energy was obtained within chemical accuracy in all cases.…”