A molecular modeling analysis of polycyclic aromatic hydrocarbon biodegradation by naphthalene dioxygenase

A theoretical analysis was performed to examine the role of naphthalene dioxygenase (NDO) enzymes in determining differences in biodegradability and biodegradation rates of two- to four-ring polycyclic aromatic hydrocarbons (PAHs) via oxygenation and desaturation reactions. Investigation of the thermodynamics of PAH biodegradation reactions catalyzed by NDO revealed that enthalpies of reaction can explain reaction patterns or regioselectivity of the enzyme in limited cases. Molecular modeling analysis of the size and shape constraints of PAH-enzyme interactions suggests that PAHs bigger than approximately four rings and compounds with alpha substituents or other structural features contributing to increased width at the end of the substrate near the active site are expected to have binding difficulties. This explains some regioselectivity observations, in that thermodynamically favorable sites on some PAH molecules cannot be positioned correctly to be oxidized at the active site. The enzyme fit analysis also suggests that slower biodegradation rates are expected for compounds with larger widths because of the unique positioning that is required for reaction to occur. An inverse relationship between a molecular descriptor of compound width and previously obtained biodegradation rates suggests that this descriptor may be valuable for predicting relative biodegradation rates of PAHs with dioxygenases other than NDO.