Proton transport by large-scale molecular simulation
Proton transport plays a key role in cell metabolism, such as the formation of adenosine triphosphate (ATP), the main energy source in biology. The cell membrane surface is a major pathway for proton transport. A long-standing experimentally observed puzzle is how to reconcile fast interfacial proton migration with strong binding to the membrane surface. In close collaboration with Prof. Peter Pohl's experimental group at University of Linz, both energetics and dynamics of an excess proton H+ were investigated by large-scale ab initio molecular dynamics simulations using a minimalistic model (water/hydrophobic interface). With about 1800 atoms in total, this system was one of the largest investigated in biophysics entirely by quantum mechanics (Fig. 1).
It was demonstrated for the first time that the protons can diffuse fast along the second layer of the interfacial water molecules while experiencing sufficient attractive forces to prevent release to bulk water. These findings provide a new perspective on the efficient motion of protons on cell membranes, one of the key questions for understanding bioenergetic processes.
To verify if this mechanism can work also over water/cellular membranes interface, we are investigating proton transfer in four prototype models that includes two kinds of lipids DOPC and DPhPC.
Using a similar approach, we investigated the strikingly efficient proton conduction in the gramicidin A (gA) ion channel, whose measured rate is up to 2×109 H+ s−1. The simulated system comprises almost 2,000 atoms (Fig. 2).