Abstract:

Living Cells have a membrane barrier bordering their perimeter. The existence of this barrier, leads immediately to the question of how transport across the membrane is done selectively. The transport process is characterized typically by a substrate pathway along with associated conformational changes in the protein. From the many different proteins that take part the Ion channels that assist and control the diffusion of ions through biological membranes are ideals to teach students with a very complex but visually fascinating teaching material.

Through the use of Computational Modeling programs like Yasara or VMD and using Molecular Dynamics simulations, we can have a mean of animating static structures, allowing the visualizations of an entire permeation event of a substrate trough a channel, in this case the transport of different ions across a membrane barrier. The diffusion of ions through a channel requires a hydrophilic pathway for perfect ionic coordination. This hydrophilic environment can be provided by coordinating groups of the protein, such as the carboxylic atoms in the selectivity filter of the ion channel, or by transient hydration of the ionic conduction pathway, such as that encountered around the activation gate of the ion channel.

The use of IXTLI, a 3d immersion auditorium with a 180° screen and interactive controls, allow us to show the dynamics of the proteins in several positions and depth. In such a way that the images show are extremely complex structures of the lipid membrane with water molecules on both size. Giving distinct representation to each element, we can visualize them very easily. Visualizing the core of the channel allow us to see the way in which it is working. Various elements can be subtracted from the visualization screen, and we can focus on the gate. Many ion channels consist of Tetramers, to get inside; one of the chains is subtracted, and appreciate how the different groups move the ions thought the channels.

Keywords:

3D visualization, Molecular Modeling, Ion channels, Molecular Dynamics.