Simulation of the light-induced conformational dynamics in the AppA BLUF domain

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After light absorption by its flavin chromophore (flavin adenine dinucleotide, FAD), the blue light sensitive BLUF (Blue Light sensing Using Flavin) domain of the transcriptional antirepressor protein AppA in Rhb. sphaeroides is conformationally switched on a subnanosecond time scale from a dark-adapted (da) state to a conformationally different light-adapted (la) state. It is the aim of this project to describe this light-induced conformational relaxation dynamics within the framework of molecular mechanics by molecular dynamics simulations. To check the validity of the protein conformations (da, intermediates, la) predicted by the simulations we will compute the associated vibrational spectra for the FAD chromophore in situ using hybrid methods and will compare the results with corresponding experimental data. The hybrid methods combine a quantum mechanical description of the FAD chromophore in the framework of density functional theory with a molecular mechanics model of the protein and solvent environment. The simulations aim at contributing to the clarification of the mechanisms, by which AppA BLUF converts the absorption of light into biochemically detectable information and the regulation of photosynthesis genes. The project requires and aims at close cooperations with other groups within and beyond the Forschergruppe.