UTILIZATION OF MOLECULAR DYNAMIC METHODS FOR IDENTIFICATION OF STABLE CYP1A2-CYTochrome B5 BINARY COMPLEXES

Jeřábek P., Stiborová M., Martínek V.

 

Department of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 40 Prague 2, Czech Republic

 

Cytochrome P450 (CYP) represents a large group of enzymes oxidizing drugs and chemical carcinogens. Eukaryotic CYPs interact with other membrane proteins located in the endoplasmic reticulum. Cytochrome b5 (cyt b5), which is also present in endoplasmic reticulum (ER), may enhance, inhibit or have no effect on enzymatic activity of CYPs, depending on the particular CYP isoform and the substrate. Hence, the cyt b5 has the potential to significantly modulate CYP mediated metabolism of xenobiotics. The cyt b5-mediated modulation of CYP activity is attributed to the formation of specific protein-protein interaction. Exact 3D structure of the binary complex has not been experimentally determined. However, indirect data based on mutagenesis studies and chemical cross-links indicate that the convex and acidic surface of cyt b5 binds to the basic concave surface of a CYP.

Presented study is focused on prediction of the CYP1A2-cyt b5 binary complex structure, using contemporary methods of theoretical chemistry. In the first step, flexible protein-protein docking method implemented in HADDOCK software was employed to obtain a set of plausible orientations of soluble domains of both cytochromes. Further several individuals were selected according to rough estimations of binding energies and mutual orientations of both protein structures. These binary complexes were subjected to stability evaluation using classical molecular dynamic method implemented in NAMD software. Further we employed steered molecular dynamic protocol. This method was used in order to compare binding free energies of individual CYP1A2-cyt b5 complexes obtained by protein-protein docking.

Supported by GACR (203/09/0812, P207/12/0627, 305/09/H008) and Charles University in Prague (UNCE #42). Also the access to the METACentrum supercomputing facilities provided under the programme LM2010005 funded by the Ministry of Education, Youth, and Sports of the Czech Republic is highly appreciated.