Pokyny pro elektronické podávání abstrakt

Flexibility and plasticity of the structures of cytochromes P450 as a property determining their function

T. Smith¹, E. Mc Donnald² 

¹ Palacky University, Pharmacology, Olomouc, Czech Republic
² Charles University, Biochemistry, Prague, Czech Republic

Versatility of functions as well as of substrates of cytochromes P450 should be reflected in their ability to accommodate molecules of various size and shape. Active sites of cytochromes P450 hence differ in their flexibility and plasticity of the corresponding parts of the structure. Examples discussed here are cytochromes P450 known to metabolize various drugs and their analogs, namely, cytochromes P450 3A4, 2C9 and 2D6. Experimental data obtained by spectroscopic methods (absorption spectroscopy at high hydrostatic pressure and resonance Raman data) are correlated with results of molecular dynamic simulations carried out using the AMBER package with parm99 force field. Starting structures were essentially based on these taken from the PDB database; simulations were made at normal (0.1 MPa) and high pressure (300 MPa). The results indicate a decrease in radius of gyration as well as the overall B-factor decrease under high pressure. A correlation has been found between the experimentally obtained coefficient describing a shift of the Soret band with pressure (related to compressibility of the active site) and coordination numbers of water molecules and backbone atoms in the active site around the axial ligand (carbon monoxide). The data show that the spectral changes under pressure reflect structural changes in the close proximity (less than 0.5 nm) of the heme. The compressibility of the active site apparently increase with number of water molecules in the active site, and decrease with number of non-polar protein backbone atoms close to the heme. Raman spectral data reflect the situation in the active site by presence of heme vinyl vibrations assigned to two vinyl conformations, with two conformations present in the spectrum indicating a more flexible structure in the active site as e.g. in the case of CYP3A4. The data both experimental and obtained from the simulations hence document an essential necessity of plasticity/flexibility of enzyme active site for proper functioning of an enzyme, here cytochrome(s) P450.