Folding Forum

Sodium channels initiate signaling in neurons and other cells which go on to become sensations of pleasure and pain, as well as thoughts and feelings. Sodium channel malfunction has been linked with cardiac arrhythmia, epilepsy, and neuropathic pain. These projects simulate a whole voltage-gated sodium channel in a bi-lipid membrane based on crystal structures deduced only recently (2013). The channel is made up of four homologous domain which form a pore through the membrane. The "top" (extracellular) end of the pore selects for sodium ions only. The "bottom" (intracellular) region can be open or closed. Each pore domain is linked to a voltage-sensing domain, which causes the channel to open or close based on the electrical environment of the membrane. We aim to study the dynamics of transitions between the open and closed states mediated by the voltage sensing domains. Our experimental collaborators will probe sodium channel function through the use of natural toxins secreted by frogs in the Amazon rainforest. By combining theory and experiment, we can propose and test derivatives of these toxins which have positive therapeutic effects.


Runs: 5000
Clones: 1
Gens: 1562
Base: 1000
Timeout 0.5 days
Deadline: 1 day
number of atoms: ~175k
OS: Windows / Linux / OS X
CPUs >= 3
CPUs <= 48