This computational project aims to identify the role of large conformational changes in the process of carbon dioxide conversion by photosystem. Photosystem contains several protein units which role is relatively well identified. However, the accessible conformational space of those protein units is poorly understood. Moreover, it is unknown if those conformational fluctuations are the result of photosynthetic process, or they are generic properties of the proteins. Those, we intend to sample accessible conformational space by means of replica-exchange molecular dynamics simulations alongside with normal mode analysis and calculations of spectroscopic properties.
This project is tightly bound to ongoing experimental work in the university, particularly to the experiments at synchrotron facilities. We expect that this project will shed light on the role of large-scale conformational fluctuations on the process of photosynthesis. We also believe project's output will advance us in developing ways to detect structural vibrations which significantly help in design of future experiments.