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Molecular Dynamics Simulation of Ionic Channels

© Adam Hughes

In approaching a new area of simulation studies, a scientist is faced with many decisions in order to begin making meaningful progress toward his goal. One of the most common problems is that the intended focus of a research project is often beyond the reach of currently available simulation technology and computer power. In this case, the researcher can either decide to move on to something less challenging, try to develop new techniques that directly address the target problem, or attempt to find a simpler system that is still representative of the main features of the original idea. This latter approach tends to lead to the most continued progress towards a goal, as taking these incremental steps can help "shape" the technology into more advanced forms, while providing more immediate feedback than jumping to an entirely different paradigm.

A good example of this situation can be seen in some recent work by researchers at the Laboratory of Molecular Biophysics at the University of Oxford in Oxford, England (the group's homepage can be viewed at http://biop.ox.ac.uk/www/lj2000/sansom/s... who wanted to conduct simulation studies of ionic channels in lipid bilayers. When these channels are formed by complex protein structures, the resulting electrochemical environment makes it possible for certain chemical species to move quickly into the bilayers. Ionic channels are vital to many biological functions at the cellular layer, but their structures are not well understood. In addition, due to the complexity of their constituent proteins, ionic channels are generally difficult to simulate via molecular dynamics (MD), or other similar classical techniques (simulation via quantum methods would be prohibitively computationally expensive).

In order to begin to gain insight into the phenomenon of ionic channels while employing well-understood theoretical methods, the Oxford researchers decided to study the M2 protein from the influenza virus. This protein is simple relative to other candidate proteins, but it still forms the ionic channels which are the target of the study. In order to generate the models to be studied, the scientists used simulated annealing (another classical method) to move the proteins into the correct starting configurations. The rest of the simulation system was basically an equilibrated configuration also obtained through MD simulation. Once the systems were set up, the scientists conducted MD simulations with periodic boundary conditions, under constant pressure.

We won't delve into the results of these studies, for anyone wishing to see them and the concomitant conclusions of the authors may visit the web page above. However, it is encouraging to note that several trends and general insights can be gathered from these simulations that help to explain what's going on in ionic channels. Using

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