Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450...

In this work, a model for the interaction between CYP2B4 and the FMN domain of rat P450-oxidoreductase is built using as template the structure of a bacterial redox complex. Amino acid residues identified in the literature as cytochrome P450 (CYP)-redox partner interfacial residues map to the interface in our model. Our model supports the view that the bacterial template represents a specific electron transfer complex and moreover provides a structural framework for explaining previous experimental data. We have used our model in an exhaustive search for complementary pairs of mammalian CYP and P450-oxidoreductase (POR) charge clusters. We quantitatively show that among the previously defined basic clusters, the 433K-434R cluster is the most dominant (32.3% of interactions) and among the acidic clusters, the 207D-208D-209D cluster is the most dominant (29%). Our analysis also reveals the previously not described basic cluster 343R-345K (16.1% of interactions) and 373K (3.2%) and the acidic clusters 113D-115E-116E (25.8%), 92E-93E (12.9%), 101D (3.2%) and 179E (3.2%). Cluster pairings among the previously defined charge clusters include the pairing of cluster 421K-422R to cluster 207D-208D-209D. Moreover, 433K-434R and 207D-208D-209D, respectively the dominant positively and negatively charged clusters, are uncorrelated. Instead our analysis suggests that the newly identified cluster 113D-115E-116E is the main partner of the 433K-434R cluster while the newly described cluster 343R-345K is correlated to the cluster 207D-208D-209D.