Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study

This licentiate thesis presents computational chemistry studies on photochemical properties of phytochrome and firefly luciferase chromophores. Phytochromes are bilin-containing proteins that based on the ambient light environment regulate a number of physiological and developmental processes in bacteria, cyanobacteria, fungi and plants. From the viewpoint of computational modeling, however, only a few studies have been devoted to these systems. In this thesis, two systematic studies comparing calculated and experimental UV-vis spectra of bilin chromophores in protein and solution environments are presented. The first study focuses on how hybrid quantum mechanics/molecular mechanics methods are best applied to calculate absorption spectra of a bacteriophytochrome. The second study, in turn, investigates the performance of a number of quantum chemical methods in calculating absorption and emission spectra of sterically locked bilin chromophores. Firefly luciferase catalyzes a chemical reaction in which the electronically excited oxyluciferin is formed and subsequently emits light. Depending on the conditions, oxyluciferin can exist in a number of different chemical forms. To date, there is no consensus regarding which of these that most significantly contributes to the light emission. In this thesis, the most probable form of the light emitter is predicted by calculating excited-state pKE and pKa values, in aqueous solution, of the various equilibrium reactions relevant for the oxyluciferin system.