title: Charybdotoxin unbinding from the mKv1.3 potassium channel: a combined computational and experimental study.
abstract: 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 homologue 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. The potential of mean force is constructed from the umbrella sampling simulations and combined with K(d) 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.
authors.affiliation: Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Morteza
authors.initials: M
authors.lastname: Khabiri
authors.forename: Azadeh
authors.initials: A
authors.lastname: Nikouee
authors.forename: Lukasz
authors.initials: L
authors.lastname: Cwiklik
authors.forename: Stephan
authors.initials: S
authors.lastname: Grissmer
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Ettrich
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018999:Charybdotoxin / Q000737:chemistry* / Q000378:metabolism*; D057927:Hydrophobic and Hydrophilic Interactions; D051664:Kv1.3 Potassium Channel / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D018408:Patch-Clamp Techniques; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D051664:Kv1.3 Potassium Channel; D018999:Charybdotoxin