Simulation and modeling of the Rhodobacter sphaeroides bacterial reaction center:: Structure and interactions

In this paper, we present the structural and dynamic results of a 3.4 ns molecular dynamics simulation of a reaction center protein immersed in a micelle-like environment formed by a detergent, lauryl dimethyl amino oxide or LDAO, and hydrated by more than 6000 additional water molecules. The whole system,; 40 000 atoms, was simulated using an all-atom force field with refined potential parameters developed by us to describe the protein cofactors and the detergent molecules. LDAO, inserted at the beginning of the run in a configuration far from equilibrium, rearranged forming a micelle attached to the hydrophobic regions of the protein. The micelle is a stable and dynamic structure over the whole trajectory and prevents the protein and the internal cofactors from contacts with water. Comparing our simulated system with the high-resolution crystallographic structure, the deviations of the backbone atoms are small, less than 1.8 Angstrom after 3.4 ns, and the chromophore arrangement geometry is stable and close to X-ray for the whole simulation. Thus, our system constitutes a realistic model to investigate at an atomic level the role of the protein environment on the charge transfer processes taking place in this complex. Related to the functionality of this RC protein, we observe the isomerization of the tyr M210 which is directly coupled with the primary electron transfer. Concerning the branch functionality of the RC, we observe that the computed minimum distance between the chromophores on the L and M side has a different dynamic behavior and is smaller on average for transitions on the L side. This finding might have some bearing on the electron-transfer asymmetry of the primary charge transfer.