CYPs Characterization using GRID Molecular Interaction Fields

CYPs Characterization using GRID Molecular Interaction Fields 

The molecular interaction fields (MIF) in the binding site of the cytochromes were obtained using a grid step size of 0.5 A and a self-accommodating dielectric constant [16]. The grid box size for the five isoforms was placed around the active site cavities and carefully refined using the tools available in the GRID software. 

With the enzyme sidechains in fixed positions, the active site volumes computed by the GRID hydrogen probe ranged from 1500 for CYP3A4 to 640 for CYP1A2. With flexible sidechains, the accessible cavity volumes increased from 5% to 10%, probably due to the release of steric hindrance and consequent reduction in steric interaction between the chemical probe and the lateral chains. The explanation put forward is that the cytochromes may use sidechain flexibility to allocate more space when necessary, making sub-pockets or small charmels accessible without changing the structure of the protein backbone. 

In agreement with the GRID findings, site-directed mutagenesis experiments demonstrated that lipophilic interactions are extremely important for binding to take place in the enzyme cavity CYP2C9. In turn, flexibility of sidechains modifies the physicochemical enviroment of the cavity, as well as the protein pharmacopho-ric pattern. 

---

CYPs Characterization using GRID Molecular Interaction Fields I 277... 

---