Longest ever simulation of an ion channel system

06.07.2007

The pilot grand challenge research project of Professor Ilpo Vattulainen (Tampere University of Technology) and Assistant professor Erik Lindahl's group (Stockholm University) was run successfully on CSC's new supercomputer Cray XT4 (louhi.csc.fi). In studying the dynamics of ion channels Vattulainen and Lindahl completed over 1 microsecond of production simulations of an integral ion channel system consisting of about 120,000 atoms.

The targeted time scale they managed to complete was longer simulation than ever performed before on a comparable system. In research they used a new parallel implementation of the publicly available molecular simulations package Gromacs, developed by Erik Lindahl and others. The simulation was conducted during about a month in the end of the Spring 2007.

– It has shown overwhelming performance and stability on CSC's new
supercomputer during the course of this project - simply a success, Vattulainen and Lindahl say.

According to the scientists, the protein does not show any sign of destabilizing at all. Normally this would not be a particularly important result, but in the light that this simulation is about an order of magnitude longer than ever performed before, it is thus a great confirmation of the accuracy both of the force field, crystal structure (which is very low resolution), physical models, and also the novel techniques to reach these timescales. The lipids snugly line the protein surface and the water fills the protein cavities as expected and at the same time conserving the integrity of the protein and bilayer. There is a wealth of data here to analyze later in terms of exchange of lipids and water. The researchers should for instance be able to address whether some lipid molecules are more tightly bound to the membrane. In addition, the protein moves roughly two times it own size relative to the lipids in the simulation due to natural diffusion, and an additional point of analysis will thus be diffusion of proteins in membrane rather than only lipid mobility. For now the scientists are still focusing on the structural transitions.

– The system showed scaling over 170 processors (~80%) on Louhi, which is almost twice as good as the test result we got on a DDR Infiniband cluster - the SeaStar interconnect of Cray is simply amazing, Lindahl summarizes.

Ion channels an interesting research topic

Ion channels have long been an interesting topic. Although more than 100,000 structures of soluble proteins are already known, only some 100 membrane protein structures have been experimentally determined. However, membrane proteins account for about half of all proteins in the cell. The level of understanding on a remarkable part of the function of proteins and their interactions is still very limited. Experimentally determined structures of proteins will only give a statical picture of the proteins without any dynamics. The dynamics is, however, an important part of the activity of proteins. Computational modeling of this aspect will add considerable value to the experimental work.

– Ion channels are one of the hottest research topics due to their significance for the nervous system, energy storage in cells, and diseases such as epilepsy, among others. The problem is that the mechanisms associated with their structural transitions are poorly understood. This is the very thing where massive simulations create significant added value, illuminating how the opening and closing transitions of ion channels can be controlled, Vattulainen notes.

A call for grand challenge research projects in autumn 2007

During the spring, CSC opened a call for a short-term pilot grand challenge project to be run on CSC's new supercomputer Louhi. Out of five research proposals, the project proposed by Vattulainen and Lindahl was selected due to scientifically important goals and efficient exploitation of the new supercomputer. The experience from the selected pilot case will be taken into account when CSC is preparing a procedure for supporting grand challenge type resource needs. As a result from the successful pilot project CSC will open a call for grand challenge research projects in autumn 2007. The research projects will be able to use a large amount of Louhi's resources.

Further information

• Ilpo Vattulainen, The Tampere University of Technology, Tel: + 358 400 510 592, Email: ilpo.vattulainen at tut.fi

• Erik Lindahl, Stockholm Center for Biomembrane Research, Stockholm
  University, Email: lindahl at sbc.su.se

• A videoclip on the movement of one of the voltage-sensing
  domains relative to the starting structure

CSC

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