Photosynthesis in silico: Simulations of Photosystem II and the Thylakoid Membrane

Photosynthesis is one of the most fundamental processes on earth. It captures the energy present in light and converts it into chemical bonds. Photosynthesis forms hereby the basis of the energy supply for virtual all organisms on earth. Photosystem II (PSII) is a key player in photosynthesis. This protein complex is embedded in the thylakoid membrane. It splits electrons from water, using the energy present in light. A side product of this project is the oxygen we breath. In this thesis we used molecular dynamics (MD) to study the behavior and dynamics of PSII and the thylakoid membrane. MD is a technique in which you simulate the movement of individual atoms. We did not just use ordinary MD, but coarse grained MD, which allows one to simulate far bigger systems for longer time scales. In our simulations we characterized the thylakoid membrane and we could simulate the transition from a bilayer to an inverted hexagonal phase, this transition is probably important to keep the balance in the membrane. Our simulations of PSII led to the discovery of a new channel in PSII through which electrons are transported. Next to this we observed that some of the pigments are not as strongly bound to the complex as was assumed, in fact some of them even diffuse out of the complex. Another intriguing result is that we observed the tilting of the PSII monomer in the membrane. This has not been observed before, and might related to the repair of the photosystem