Computational Insights into electrostatics and protonation mechanisms in phytochromes

This dissertation uses constant pH simulations and QM/MM methods to investigate the mechanisms of signal transduction, as well as the correlation of protonation dynamic and structural changes. The study focuses on two bacterial phytochromes (Agp1 and Agp2) and one cyanobacteriochrome (Slr1393g). These photoreceptors bind a chromophore that switches between two parent states. The first part examines the bacterial phytochromes Agp1 and Agp2. For Agp2, electrostatic calculations and constant pH molecular dynamics (MD) simulations were performed. The electrostatic calculations provide insights into the local environment of the chromophore. Sudden changes in electrostatics may influence the overall protein structure and trigger a reaction. To explore the chromophore environment, a functional group called "Stark reporter" is introduced into the protein. Nitrile groups are often used for this purpose, as they are sensitive to small electrostatic changes and exhibit frequency shifts in the IR spectrum when such changes occur. The second part focuses on the correlation between protonation of the propionic side chain C and conformational changes using constant pH MD simulations. The softwares AMBER and GROMACS were used, which approach protonation discretely or continuously, respectively. This allows to compare the two methods. A detailed analysis of the AMBER output was performed using a triangular approach that was developed in the group of M. A. Mroginski. While the latest version of GROMACS cpH MD provides various analysis tools, the dissertation demonstrates why evaluating such complex systems is not straightforward and why not every tool is suitable for this purpose. In the final section, a similar analysis is carried out for the cyanobacteriochrome Slr1393g. Crystal structures exist for both ground states, Pr and Pg, providing a basis for comparative studies.