Dynamics of the substrate binding pocket in the presence of an inhibitor covalently attached to a fungal lipase

Influence of a lipid interface on protein dynamics in a fungal lipase

Lipases catalyze lipolytic reactions and for optimal activity they require a lipid interface. To study the effect of a lipid aggregate on the behavior of the enzyme at the interfacial plane and how the aggregate influences an attached substrate or product molecule in time and space, we have performed molecular dynamics simulations. The simulations were performed over 1 to 2 ns using explicit SPC water. The interaction energies between protein and lipid are mainly due to van der Waals contributions reflecting the hydrophobic nature of the lipid molecules. Estimations of the protonation state of titratable residues indicated that the negative charge on the fatty acid is stabilized by interactions with the titratable residues Tyr-28, His-143, and His-257. In the presence of a lipid patch, the active site lid opens wider than observed in the corresponding simulations in an aqueous environment. In that lid conformation, the hydrophobic residues Ile-85, Ile-89, and Leu-92 are embedded in the lipid patch. The behavior of the substrate or product molecule is sensitive to the environment. Entering and leaving of substrate molecules could be observed in presence of the lipid patch, whereas the product forms strong hydrogen bonds with Ser-82, Ser-144, and Trp-88, suggesting that the formation of hydrogen bonds may be an important contribution to the mechanism by which product inhibition might take place.