Theoretical Studies of Cytochrome P450

Abstract: The cytochromes P450 are a large enzyme family that is found in all living organisms and takes part in both endogenous and exogenous metabolism. They are primarily mono-oxygenases and perform a wide range of reactions. In contrast to many other enzymes, they have been optimised to react with a wide range of substrates instead of having high reaction rates. In the active site, these enzymes have a haem group, a porphyrin ring with an iron ion in the centre, and a cysteine amino acid bound to the iron. During the reaction cycle, this complex is turned into a highly oxidative complex, which enables the enzyme to oxidise even aliphatic carbons. We study various aspects of the functionality of these enzymes and other related haem-containing proteins with theoretical methods. For example, we discuss how nature has tuned the functionality of different haem proteins by using different axial ligands, and go into depth on the elusive properties of a mobile proton in haem peroxidases. Furthermore, we study the transition state in aliphatic hydroxylation, nitrogen oxidation, sulphur oxidation, and sulphoxide oxidation in cytochrome P450 with density functional theory and suggest a qualitative model to predict the activation energy of the aliphatic hydroxylation reaction. By constructing a transition-state force field and combining it with the qualitative model, we study the hydroxylation reactivity of two drugs in two cytochrome P450 isoforms. Finally, using molecular dynamics, we provide the first calculation of the free energy for moving a substrate molecule from bulk water solution into the active site of a cytochrome P450, and we also study the dynamics of water molecules in the active-site cavity.