Key result
Molecular dynamics modelling revealed that the Et4N+ blocker shows several kcal/mol better binding to the KcsA channel than other tetraalkylammonium ions.
Computational modeling demonstrates that Et4N+ has stronger binding to the KcsA potassium channel compared to other tetraalkylammonium ions, matching experimental data.
External tetraalkylammonium ion binding to potassium channels is studied using microscopic molecular modelling methods and the experimental structure of the KcsA channel. Relative binding free energies of the KcsA complexes with Me4N+, Et4N+, and n-Pr4N+ are calculated with the molecular dynamics free energy perturbation approach together with automated ligand docking. The four-fold symmetry of the entrance cavity formed by the Tyr82 residues is found to provide stronger binding for the D2d than for the S4 conformation of the ligands. In agreement with experiment the Et4N+ blocker shows several kcal/mol better binding than the other tetraalkylammonium ions.
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Luzhkov et al. (2003) studied this question. Tetraalkylammonium ions (Me4N+, Et4N+, and n-Pr4N+) was evaluated on Relative binding free energies of the KcsA complexes. Molecular dynamics modelling revealed that the Et4N+ blocker shows several kcal/mol better binding to the KcsA channel than other tetraalkylammonium ions.
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