Paper Citing NAMD - Abstract
Chen, Rong; Chung, Shin-Ho
Molecular Dynamics Simulations of Scorpion Toxin Recognition by the Ca2+-Activated Potassium Channel K(Ca)3.1
BIOPHYSICAL JOURNAL, 105:1829-1837, OCT 15 2013
The Ca2+-activated channel of intermediate-conductance (K(Ca)3.1) is a target for antisickling and immunosuppressant agents. Many small peptides isolated from animal venoms inhibit K(Ca)3.1 with nanomolar affinities and are promising drug scaffolds. Although the inhibitory effect of peptide toxins on K(Ca)3.1 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(Ca)3.1 are examined in atomic detail using molecular dynamics (MD) simulations. Employing a homology model of K(Ca)3.1, 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(Ca)3.1 and OSK1-K(Ca)3.1 complexes are then constructed using MD simulations biased with distance restraints. The ChTx-K(Ca)3.1 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(Ca)3.1 determined experimentally are reproduced within fivefold using potential of mean force calculations. Making use of the knowledge we gained by studying the ChTx-K(Ca)3.1 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(Ca)3.1 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(Ca)3.1, and demonstrates the power of computational methods in the design of novel toxins.
