Molecular mechanism of the sea anemone toxin ShK recognizing the Kv1.3 channel explored by docking and molecular dynamic simulations.

Computational methods are employed to simulate the interaction of the sea anemone toxin ShK in complex with the voltage-gated potassium channel Kv1.3 from mice. All of the available 20 structures of ShK in the Protein Data Bank were considered for improving the performance of the rigid protein docking of ZDOCK. The traditional and novel binding modes were obtained among a large number of predicted complexes by using clustering analysis, screening with expert knowledge, energy minimization, and molecular dynamic simulations. The quality and validity of the resulting complexes were further evaluated to identify a favorable complex structure by 500 ps molecular dynamic simulations and the change of binding free energies with a computational alanine scanning technique. The novel and reasonable ShK-Kv1.3 complex structure was found to be different from the traditional model by using the Lys22 residue to block the channel pore. From the resulting structure of the ShK-Kv1.3 complex, ShK mainly associates the channel outer vestibule with its second helical segment. Structural analysis first revealed that the Lys22 residue side chain of the ShK peptide just hangs between C and D chains of the Kv1.3 channel instead of physically blocking the channel pore. The obvious loss of the ShK Ser20Ala and Tyr23Ala mutant binding ability to the Kv1.3 channel is caused by the conformational change. The five hydrogen bonds between Arg24 in ShK and H404(A) and D402(D) in Kv1.3 make Arg24 the most crucial for its binding to the Kv1.3 channel. Besides the detailed interaction between ShK and Kv1.3 at the atom level, the significant conformational change induced by the interaction between the ShK peptide and the Kv1.3 channel, accompanied by the gradual decrease of binding free energies, strongly implies that the binding of the ShK peptide toward the Kv1.3 channel is a dynamic process of conformational rearrangement and energy stabilization. All of these can accelerate the development of ShK structure-based immunosuppressants.