COMPUTER MODELING OF 3D STRUCTURES OF CYTOCHROME P450S

The understanding of structure-function relationship of enzymes requir es detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequen tly used experimental procedures, are often difficult and time-consumi ng. Thus computer modeling of protein structures has become an increas ingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structure s of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 an d P450eryF have now been determined. However, attempts to obtain the s tructure of mammalian forms by experimental means have thus far not be en successful. Thus, there have been numerous attempts to construct mo dels of mammalian P450s using: homology modeling methods in which the known structures have been used to various extents and in various stra tegies to build models of P450 isozymes. In this paper, we review thes e efforts and then describe a strategy for structure building and asse ssment of 3D models of P450s recently developed in our laboratory that comets many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained mol ecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver micros omal P450 isozyme 2B4, responsible for the oxidative metabolism of div erse xenobiotics including widely used inhalation anesthetics. Using t his 2B4 model, the substrate access channel, substrate binding site an d plausible surface regions for binding with P450 redox partners were identified.