| Abstract
| - Computational methods are employed to simulate the interaction of the sea anemone toxin ShK in complexwith the voltage-gated potassium channel Kv1.3 from mice. All of the available 20 structures of ShK in theProtein 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 byusing clustering analysis, screening with expert knowledge, energy minimization, and molecular dynamicsimulations. The quality and validity of the resulting complexes were further evaluated to identify a favorablecomplex structure by 500 ps molecular dynamic simulations and the change of binding free energies witha computational alanine scanning technique. The novel and reasonable ShK-Kv1.3 complex structure wasfound to be different from the traditional model by using the Lys22 residue to block the channel pore. Fromthe resulting structure of the ShK-Kv1.3 complex, ShK mainly associates the channel outer vestibule withits second helical segment. Structural analysis first revealed that the Lys22 residue side chain of the ShKpeptide just hangs between C and D chains of the Kv1.3 channel instead of physically blocking the channelpore. The obvious loss of the ShK Ser20Ala and Tyr23Ala mutant binding ability to the Kv1.3 channel iscaused by the conformational change. The five hydrogen bonds between Arg24 in ShK and H404(A) andD402(D) in Kv1.3 make Arg24 the most crucial for its binding to the Kv1.3 channel. Besides the detailedinteraction between ShK and Kv1.3 at the atom level, the significant conformational change induced by theinteraction between the ShK peptide and the Kv1.3 channel, accompanied by the gradual decrease of bindingfree energies, strongly implies that the binding of the ShK peptide toward the Kv1.3 channel is a dynamicprocess of conformational rearrangement and energy stabilization. All of these can accelerate the developmentof ShK structure-based immunosuppressants.
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