Computational Studies of Photochemistry in Phytochrome Proteins

In this book chapter, the computational research which has been performed when studying the photochemistry of phytochrome proteins is reviewed. Phytochromes represent a large family of ubiquitous photoreceptor proteins that are considered for various biotechnological applications. A comprehensive understanding of their photochemical properties is essential for their utilization. A brief introduction to phytochromes is given followed by an array of computational studies that cover different aspects of their photochemical properties. This includes the choice of different quantum chemical methods which have been used to calculate the excitation energies, as well as how to accurately model the protein environmental itself and its interaction with the chromophore. Several benchmarking studies with various quantum chemical methods used in excitation energy calculations and their comparisons are summarized. Further benchmarks include the determination of the correct structure of the chromophores found in the protein. Another issue which has been encountered in these studies is accounting for the high dimensionality of the protein environment in calculation of excitation energies. Several procedures used to alleviate this problem, including conformational sampling and the optimization procedures, are discussed. Eventually, new insights from computer simulations such as the resolution of the chromophore conformation or its protonation state are highlighted, augmented by the molecular mechanism for spectral tuning.