Molecular mechanism of δ-dendrotoxin-potassium channel recognition explored by docking and molecular dynamic simulations

δ-Dendrotoxin, isolated from mamba snake venom, has 57 residues cross-linked by three disulfide bridges. The protein shares a pharmacological activity with other animal toxins, the potent blockade of potassium channels, but is structurally unrelated to toxins of different species. We employed alanine-scanning mutagenesis to explore the molecular mechanism of δ-dendrotoxin binding to potassium channels, using protein-protein docking and molecular dynamic simulations. In our reasonable model of the δ-dendrotoxin-ShaKv1.1 complex, δ-dendrotoxin interacted mainly with the N-terminal region and the turn of two antiparallel β-sheets of the channel. This binding mode could well explain the functional roles of critical residues in δ-dendrotoxin and the ShaKv1.1 channel. Structural analysis indicated that the critical Lys6 residue of δ-dendrotoxin plugged its side chain into a channel selectivity filter. Another two critical δ-dendrotoxin residues, Lys3 and Arg10, were found to contact channel residues through strong polar and nonpolar interactions, especially salt-bridge interactions. As for the ShaKv1.1 channel, the channel turrets were found in the "half-open state," and two of four Glu423 in the turrets of the channel B and D chains could interact, respectively, with Lys3 and Lys26 of δ-dendrotoxin through electrostatic interactions. The essential Asp431 channel residue was found to associate electrostatically with Arg10 of δ-dendrotoxin, and a critical Tyr449 channel residue was just under the channel-interacting surface of δ-dendrotoxin. Together, these novel data may accelerate the structure-function research of toxins in the dendrotoxin family and be of significant value in revealing the diverse interactions between animal toxins and potassium channels.