Latest Results: KcsA Channel

Sample trajectory from a nonequilibrium simulation with 3 volts applied across 80 angstroms (box length). The movie is at 10 frames per second where each frame represents 10 ps of data from a 50 ns trajectory. Left click to open the movie in a browser window, right click and save as... to download the movie which is approx 60 MB in size.

IRK1

This is a cross-section of the latest IRK1 model from Bob Guy. Note the potassium ions (purple spheres) sitting in between the carboxyl groups of the selectivity filter. There are also two water molecules in the model from Bob Guy and these are shown in this picture as well.       Here is a view of the latest IRK1 model from Bob Guy as seen from the top. Note the hole going right throw the channel; the purple spheres at the center are two potassium ions. One can also see the carboxyl groups lining the selectivity filter (the narrowest part of the channel) from this view.       The protonation state of the charge groups in IKR1 is uncertain, however it is known that they will have a significant impact on the conductance measurement. This picture outlines the charge groups present in IRK1.       The protonation state of the charge groups in IKR1 is uncertain, however it is known that they will have a significant impact on the conductance measurement. This picture outlines the charge groups present in IRK1.       The protonation state of the charge groups in IKR1 is uncertain, however it is known that they will have a significant impact on the conductance measurement. This picture outlines the charge groups present in IRK1.

Movies

This movie shows an approximation of what we expect to find using the non-equilibrium approach to determining the conductance. In this video, we have applied a voltage to the potassium ion in order to speed up the transfer rate. Also, the run was conducted at a high temperature to speed up the process as well.       This video is representative of how we conduct the equilibrium approach to determining the conductance. Here, the ion is being mvoed to various positions (windows) along the protein. After monitoring the relative occupancy of various positions, we are able to consturct the potential of mean force (PMF) for the ion crossing the channel. This is the first step in determining the conductance of the channel via the equilibrium approach.