Insights into Substrate Protonation and Solvent Accessibility in the Active Site of Fatty Acid Photodecarboxylase

Fatty acid photodecarboxylase catalyzes the light-driven decarboxylation of fatty acids into hydrocarbons via electron transfer (ET) from the substrate to the flavin adenine dinucleotide cofactor, proceeding through either proton-coupled ET or hydrogen-atom transfer. Through quantum mechanics/molecular mechanics calculations, we show that only the deprotonated fatty acid supports the charge-transfer states required to initiate catalysis. Molecular dynamics simulations combined with graph-theory-based analysis reveal that the crystallographic water site, Wat1, is consistently occupied by a stable, yet dynamically exchanging, population of water molecules. We also identify transient, solvent-accessible water channels connecting the active site to the bulk solvent, potentially facilitating proton transfer and water exchange. These findings support the notion that beyond preserving the structural integrity of the active site, this water population may also enable the flexible modulation of electron and proton transfer through an adaptive hydrogen-bonding network.