Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein

We report the first complete theoretical description of the chain of elementary reactions resulting in chromophore maturation in the green fluorescent protein (GFP). All reaction steps including cyclization, dehydration, and oxidation are characterized at the uniform quantum mechanics/molecular mechanics (QM/MM) computational level using density functional theory in quantum subsystems. Starting from a structure of the wild-type protein with the noncyclized Ser65-Tyr66-Gly67 tripeptide, we modeled cyclization and dehydration reactions. We then added molecular oxygen to the system and modeled the oxidation reaction resulting in the mature protein-bound chromophore. Computationally derived structures of the reaction product and several reaction intermediates agree well with the relevant crystal structures, validating the computational protocol. The highest computed energy barriers at the cyclization-dehydration (17 kcal/mol) and oxidation (21 kcal/mol) steps agree well with the values derived from the kinetics measurements (20.7 and 22.7 kcal/mol, respectively). The simulations provide strong support to the mechanism involving the cyclization-dehydration-oxidation sequence of the chromophore's maturation reactions. The results also establish a solid basis for predictions of maturation mechanisms in other fluorescent proteins.