Construction and evaluation of a three-dimensional structure of cytochrome P450choP enzyme (CYP105C1)

The purpose of this work was to develop and carefully evaluate improved strategies for constructing reliable 3-D models of P450 isozymes. To this end, a unique combination of steps for building and evaluating a model structure was used to build a homology model of the P450choP isozyme, based on knowledge of the X-ray structures of P450cam, P450terp, P450BM-3 and P450eryF. Specifically, the reliability of this model was examined by systematic comparisons of its conformational, energetic, environmental and packing properties and those of the four reference proteins with corresponding properties from the database of proteins with known structures. The results showed that the examined properties of this model structure are well within the criteria established for reliable structures and are of nearly as good quality as those of the reference proteins. In addition, the result from a 120 ps unconstrained MD simulation of the model with structural waters provided evidence that the model is stable at room temperature. This 3-D model can now be reliably used for explicit characterization of substrate and inhibitor complexes. Most importantly, although it is envisioned that building models for mammalian P450s will be even more challenging, the steps described here should be very useful in future construction of 3-D models of mammalian P450 isozymes.