Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

We report the results of quantum mechanics/molecular mechanics (QM/MM) simulations of structures and absorption spectra of the fluorescent protein IFP1.4 engineered from the chromophore-binding domain of Deinococcus radiodurans (DrCBD). In this work, we focus on different protonation states of the biliverdin chromophore in the red-absorbing form of the protein. To this goal, the protein with the all-protonated chromophore as well as the structures obtained by removal of protons from the biliverdin pyrrole rings to a suitable acceptor within the system are considered. Several quantum chemistry methods to compute the S₀→S₁ excitation energies are used in the QM part to estimate shifts in the absorption band maxima upon chromophore deprotonation.