Theoretical investigation of the protein regulation on the energy transfer in photosystem II

Photosynthesis is an essential biological process whereby the solar energy is captured and converted through a series of events to the biochemical energy stored by organisms. Among all the photosystems, photosystem II is special considering it is the origin of the oxygen production on the earth. It is a protein-pigment complex with two-fold symmetry. For each monomer, it contains around 20 protein subunits, among which D1 and D2 are the core reaction center. Several cofactors including chlorophyll-a, pheophytin-a, plastoquinone-9 molecules located in D1/D2 are arranged in two branches while only one pathway is active in electron transfer with nearly unitary quantum yield. Despite of its significance, the process has not been fully explored. In the past years, the X-ray crystallography structures provide the basis to study the system. However, the experimental structures are static while the dynamics of the protein environment may play an important role in mediating the energy transfer process. In this regard, molecular dynamic simulation that could model the dynamics by considering the protein environment at atomic resolution may complement experiments and provide information together with the environment. The aim of this work is to figure out why only one pathway is active in the electron transfer although the two branches share a very similar structural composition. It is found out that the environmental electric field composed by protein point charge is important to enlarge the excitation energy difference of the chlorophyll-a molecules between the two chains. It is expected this contributes to the initial excitation energy distribution and the following charge separation pathway choice