title: Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study.
abstract: Cytochrome P450 BM-3 from Bacillus megaterium is an extensively studied enzyme for industrial applications. A major focus of current protein engineering research is directed to improving the catalytic performance of P450 BM-3 toward nonnatural substrates of industrial importance in the presence of organic solvents or cosolvents. For the latter reason, it is important to study the effect of organic cosolvent molecules on the structure and dynamics of the enzyme, in particular, the effect of cosolvent molecules on the active site's structure and dynamics. In this paper, we have studied, using molecular dynamics (MD) simulations, the F87A mutant of P450 BM-3 in the presence of DMSO as cosolvent, to understand the role of the F87A substitution for its catalytic activity. This mutant exhibits an altered regioselectivity and substrate specificity compared with wild-type; however, it has lower tolerance toward DMSO. The simulation results offer an explanation for the DMSO sensitivity of the F87A mutant. Our simulation results show that the F87 side chain prevents the disturbance of the water molecule bound to the heme iron by DMSO molecules. The absence of the phenyl ring in F87A mutant promotes interactions of the DMSO molecule with the heme iron resulting in water displacement by DMSO at the catalytic heme center.
authors.affiliation: School of Engineering and Science, International University Bremen, Campus Ring 1, D-28759, Bremen, Germany. d.roccatano@iu-bremen.de
authors.forename: Danilo
authors.initials: D
authors.lastname: Roccatano
authors.forename: Tuck Seng
authors.initials: TS
authors.lastname: Wong
authors.forename: Ulrich
authors.initials: U
authors.lastname: Schwaneberg
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
mesh_terms: D001410:Bacillus megaterium / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D003198:Computer Simulation; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry*; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D006899:Mixed Function Oxygenases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D008958:Models, Molecular; D009154:Mutation; D009930:Organic Chemicals / Q000737:chemistry*; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D009930:Organic Chemicals; D012997:Solvents; D014867:Water; D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; D004121:Dimethyl Sulfoxide