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Proton race in the simulated cell

June 06, 2012 - The Proceedings of the National Academy of Sciences journal (PNAS) has just published online (later it will appear in the regular issue) the article:

Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion

by some members of IAS-5 in collaboration with Peter Pohl's group of the University of Linz.

The article has also raised the attention of the local press. Here, you can find the original press release (in German) and below the English translation.

Proton race in the cell simulated

How protons move on the cell membrane walls is one of the key questions for understanding bioenergetic processes. Scientists in Jülich and Linz have found now important insights into the transport processes through experimental studies and computer simulations in a simplified model. They discovered an interfacial layer, where the proton can move effectively unhampered, without loosing its binding to the membrane surface. The results were published online in the current issue of the PNAS journal (DOI: 10.1073/pnas.1121227109).
Proton transport plays a key role in cell metabolism, such as the formation of adenosine triphosphate (ATP), the main energy source in cells of all known organisms. Specific enzymes act as "proton pump". They control these processes by establishing a proton gradient, that is a different proton concentration inside and outside the cell, e.g. of mitochondria. The membrane surface is a major pathway for the proton transport. The protons migrate there amazingly fast, almost as fast as in pure water. The mechanism that prevents protons to be slowed down by binding to the membrane surface has remained unknown up to now.
Scientists from the German Research School for Simulation Sciences and the "Computational Biomedicine" group of the Institute for Advanced Simulation (IAS-5) at the Forschunzentrum Jülich together with Peter Pohl’s Austrian group from the Institute of Biophysics at the University of Linz report in PNAS decisive progresses in solving this riddle, by using a minimalistic model system. For this purpose they monitored proton dynamics on the interface between water and a hydrophobic, water-repellent surface (n-decane) by so-called microfluorometrical experiments. Subsequently, the process was studied by extensive molecular dynamics simulations, which take quantum mechanical interactions between atoms and molecules into account, performed on the JUGENE supercomputer in Jülich.
The team showed that the protons preferentially stick to the hydrophobic surface. However, those located only one water layer away from the surface migrate very quickly and yet experience sufficient attractive forces to prevent releasing to the bulk water. The calculations were supported by the Partnership for the Advanced Computing in Europe PRACE. On a single standard PC, the calculations required by this study would have taken almost 5,000 years while the parallel supercomputer JUGENE in Jülich needed “only'' 100 day to use the 40 million processor hours at disposal.

Proton migration along a hydrophobic surfaceProton migration along a hydrophobic surface (at left in the green stick representation). The proton, identified by the yellow sphere, jumps from one water molecule (red and white sticks) to another close to the first. When the proton is found in the first water layer next to the interface, it sticks to the surface and cannot move laterally. Once the proton migrates to the second water layer, it can jump to neighbouring water molecules and move along the surface without disappearing into the bulk water.


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