Molecular modeling of luciferyl adenylate deprotonation in the active site of Photinus pyralis luciferase

Firefly bioluminescence is a product of chemical reactions that involve luciferin chromophore oxidation in the active site of luciferase proteins. We perform a series of classical molecular dynamic simulations and combined quantum and molecular mechanics (QM/MM) calculations to expose the molecular mechanism of C4 carbon atom deprotonation in luciferyl adenylate molecule. QM/MM calculations confirm that ND-protonated His245 residue is a suitable proton acceptor in the wild type Photinus pyralis luciferase. Classical molecular dynamic simulations reveal oxygen binding cavities inside the protein including the one located close to the C4 atom of luciferin. In mutant forms that lack direct interactions with the His245 side chain, a proton wire comprising water molecules stimulates either protonation of the phosphate group of the luciferyl adenylate forming an unstable intermediate or keto-enol tautomerization of luciferin. The comparison of the ionization potentials of molecular systems with the ‘deprotonated’ C4 carbon atom revealed that the ionization energy for the enol tautomeric form is close to the system with the His245 proton acceptor. Thus, existence of the keto-enol tautomerization channel might explain bioluminescence in case of absence of the amino acid proton acceptor.