Charybdotoxin unbinding from the mKv1.3 potassium channel: A Combined computational and experimental study

Rudiger Ettrich^1,2

¹Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, CZ-37333 Nove Hrady, Czech Republic

²Faculty of Sciences, University of South Bohemia, Zamek 136, CZ-37333 Nove Hrady, Czech Republic

Charybdotoxin, belonging to the group of so-called scorpion toxins, is a short peptide able to block many voltage-gated potassium channels, such as mKv1.3, with high affinity. We use a reliable homology model based on the high-resolution crystal structure of the 94% sequence identical homolog Kv1.2 for charybdotoxin docking followed by molecular dynamics simulations to investigate the mechanism and energetics of unbinding, tracing the behavior of the channel protein and charybdotoxin during umbrella-sampling simulations as charybdotoxin is moved away from the binding site [1, 2]. The potential of mean force is constructed from the umbrella sampling simulations and combined with Kd and free energy values gained experimentally using the patch-clamp technique to study the free energy of binding at different ion concentrations and the mechanism of the charybdotoxin-mKv1.3 binding process. A possible charybdotoxin binding mechanism is deduced that includes an initial hydrophobic contact followed by stepwise electrostatic interactions and finally optimization of hydrogen-bonds and salt-bridges. T

R.E. acknowledges the contributions of Morteza Khabiri, Azadeeh Nikouee and Stephan Grissmer and support from the Czech Science Foundation, Grant 13-21053S.

[1] Khabiri, M.; Nikouee, A.; Cwiklik, L.; Grissmer, S.; Ettrich, R.

Journal of Physical Chemistry B 2011 115 (39): 11490–11500.

[2] Nikouee, A.; Khabiri, M.; Grissmer, S.; Ettrich, R. Journal of Physical Chemistry B 2012, 116 (17): 5132-5140.