Charybdotoxin unbinding from the mKv1.3 potassium channel: a combined computational and experimental study
| Autor: | Azadeh Nikouee, Morteza Khabiri, Lukasz Cwiklik, R. Ettrich, Stephan Grissmer |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Patch-Clamp Techniques
Charybdotoxin Molecular Sequence Data Static Electricity Molecular Dynamics Simulation complex mixtures chemistry.chemical_compound Molecular dynamics Computational chemistry Materials Chemistry Homology modeling Amino Acid Sequence Physical and Theoretical Chemistry Binding site Potential of mean force Binding Sites Kv1.3 Potassium Channel Chemistry Potassium channel Surfaces Coatings and Films Protein Structure Tertiary Docking (molecular) Biophysics Thermodynamics Umbrella sampling Hydrophobic and Hydrophilic Interactions Sequence Alignment Protein Binding |
| Zdroj: | The journal of physical chemistry. B. 115(39) |
| ISSN: | 1520-5207 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|