Cytochromes P450 (P450s) constitute a superfamily of phase I enzymes capable of oxidizing and reducing various substrates. P450 2D6 is a polymorphic enzyme, which is absent in 5-9% of the Caucasian population as a result of a recessive inheritance of gene mutations. This deficiency leads to impaired metabolism of a variety of drugs. All drugs metabolized by P450 2D6 contain a basic nitrogen atom, and a flat hydrophobic region coplanar to the oxidation site which is either 5 or 7 A away from the basic nitrogen atom. The aim of this study was to build a three-dimensional structure for the protein and more specifically for the active site of P450 2D6 in order to determine the amino acid residues possibly responsible for binding and/ or catalytic activity. Furthermore, the structural features of the active site can be implemented into the existing small molecule substrate model, thus enhancing its predictive value with respect to possible metabolism by P450 2D6. As no crystal structures are yet available for membrane-bound P450s (such as P450 2D6), the crystal structures of bacterial (soluble) P450 101 (P450cam), P450 102 (P450BM3), and P450 108 (P450terp) have been used to build a three-dimensional model for P450 2D6 with molecular modeling techniques. Several important P450 2D6 substrates were consecutively docked into the active site of the protein model. The energy optimized positions of the substrates in the protein agreed well with the original relative positions of the substrates within the substrate model. This confirms the usefulness of small molecule models in the absence of structural protein data. Furthermore, the derived protein model indicates new leads for experimental validation and extension of the substrate model.

Porcine pancreatic phospholipase A2 interacts with micelles of the substrate analogue n-octadecylphosphocholine to form a specific complex over considerably wide concentration ranges of both lipid and protein. UV absorption difference spectroscopy measurements indicate that the ratio of lipid to protein molecules in the complex is approximately 50. This number is confirmed by using other techniques to study the composition of the complex, namely, ultracentrifugation experiments and light scattering. The latter techniques furthermore demonstrate that the lipid--protein complex consists of 100 lipid and 2 enzyme molecules. Thus, the number of lipid molecules in the free micelle (200) is halved when the complex with phospholipase is being formed. The consequences of the results are discussed in relation to a theoretical model of the lipid--protein interaction.

At alkaline pH porcine pancreatic phospholipase A2 is known to bind two Ca2+ ions per protein molecule. One Ca2+ ion is strongly bound to the active site and is essential for enzyme activity. A second Ca2+ ion binds more weakly to the protein and improves the affinity of the enzyme for lipid-water interfaces severalfold at high pH values. A group having a pK around 6 controls enzyme binding to lipid-water interfaces in the absence of Ca2+. By use of proton titration techniques this group is now identified to be a carboxylate having an abnormally high pK. Its pK shifts to a value around 4.5 in the presence of high Ca2+ concentrations, suggesting that the carboxylate is involved in binding the second Ca2+ ion. The carboxylate was identified to be Glu71 by comparing proton titration experiments on porcine pancreatic phospholipase A2 and an isoenzyme. The isoenzyme differs by only four residues from the most abundant enzyme, lacking the carboxylate at position 71 (Asn for Glu). The isoenzyme also appeared to be devoid of an abnormal carboxylate. Identification of Glu71 as the abnormal carboxylate in the porcine enzyme was substantiated by comparison with enzymes from other sources. Kinetic experiments on the various phospholipases finally demonstrated that enzyme species containing Glu71 bind a second Ca2+ ion to the low-affinity site, whereas enzymes lacking Glu71 also lack this second site. These experiments confirm the suggestion that Glu71 is one of the ligands for Ca2+ in the low-affinity site.