School of Physics, University of Sydney, Sydney, New South Wales 2006, Australia.
Biochemistry. 2013 Mar 5;52(9):1631-40. doi: 10.1021/bi301257p. Epub 2013 Feb 20.
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.
果蝇 Shaker K(+) 通道是第一个被克隆的电压门控钾通道，因此在这些通道的结构和功能研究中发挥了重要作用。虽然这种作用在离子渗透方面是合理的，但尚不清楚它是否也扩展到配体结合。尽管 Shaker 和 Kv1 通道具有高度的同源性，但κ-芋螺毒素 PVIIA（κ-PVIIA）与 Shaker 具有高亲和力结合，但与 Kv1 通道不结合。在这里，我们通过使用分子动力学（MD）模拟研究κ-PVIIA 与 Shaker 和 Kv1 通道的结合来解决这个问题。通过对接和 MD 精修构建通道-毒素复合物的结构。对每个复合物的结合模式进行了表征，并与可用的突变体数据进行了比较，以验证复合物模型。通过伞状采样 MD 模拟计算 Shaker-κ-PVIIA 复合物解离的平均力势，并确定相应的结合自由能，这为复合物结构提供了进一步的验证。Shaker 和 Kv1 复合物模型的比较表明，在炮塔和扩展区域的几个突变足以消除 Shaker 对 κ-PVIIA 的观察到的敏感性。这项研究表明，Shaker 并不总是 Kv1 通道配体结合的良好模型。它还提供了关于毒素与钾通道结合的见解，这将有助于提高 Kv1 通道的亲和力和选择性。
