Molecular Dynamics Simulations of Scorpion Toxin Recognition by the Ca2+-Activated Potassium Channel KCa3.1

The Ca²⁺-activated channel of intermediate-conductance (K_Ca3.1) is a target for antisickling and immunosuppressant agents. Many small peptides isolated from animal venoms inhibit K_Ca3.1 with nanomolar affinities and are promising drug scaffolds. Although the inhibitory effect of peptide toxins on K_Ca3.1 has been examined extensively, the structural basis of toxin-channel recognition has not been understood in detail. Here, the binding modes of two selected scorpion toxins, charybdotoxin (ChTx) and OSK1, to human K_Ca3.1 are examined in atomic detail using molecular dynamics (MD) simulations. Employing a homology model of K_Ca3.1, we first determine conduction properties of the channel using Brownian dynamics and ascertain that the simulated results are in accord with experiment. The model structures of ChTx-K_Ca3.1 and OSK1-K_Ca3.1 complexes are then constructed using MD simulations biased with distance restraints. The ChTx-K_Ca3.1 complex predicted from biased MD is consistent with the crystal structure of ChTx bound to a voltage-gated K⁺ channel. The dissociation constants (K_d) for the binding of both ChTx and OSK1 to K_Ca3.1 determined experimentally are reproduced within fivefold using potential of mean force calculations. Making use of the knowledge we gained by studying the ChTx-K_Ca3.1 complex, we attempt to enhance the binding affinity of the toxin by carrying out a theoretical mutagenesis. A mutant toxin, in which the positions of two amino acid residues are interchanged, exhibits a 35-fold lower K_d value for K_Ca3.1 than that of the wild-type. This study provides insight into the key molecular determinants for the high-affinity binding of peptide toxins to K_Ca3.1, and demonstrates the power of computational methods in the design of novel toxins.