title: Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture.
abstract: Solvent molecules play an important role for the structural and dynamical properties of proteins. A major focus of current protein engineering is the development of enzymes that are catalytically active in the presence of organic solvents. The monooxygenase P450 BM-3 is one of the best-studied enzymes and promising for industrial applications but with limited activity in the presence of organic solvents or cosolvents. To gain insights into the structural and dynamical properties of the heme domain of this enzyme in solution, molecular dynamics simulations in pure water and in a 14% DMSO/water mixture were performed. The results of the simulations show overall similar structural fluctuations in both solvent systems, with no indication of partial or global unfolding. In 14% DMSO, the regions comprising the helices E, F, and the EF loop (implicated in controlling the entry to the active site channel) undergo a large shift. Significant changes were also observed near the active site access channel at the residue R47. During the simulation, no DMSO molecule penetrated the active site. However, a significant accumulation of DMSO molecules close to the substrate-binding site and to the Flavin Mononucleotide (FMN) reductase domain interface was observed.
authors.affiliation: School of Engineering and Science, International University Bremen, Campus Ring 1, D-28725, 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; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry*; D004121:Dimethyl Sulfoxide / Q000737:chemistry*; D006418:Heme / Q000737:chemistry; D006899:Mixed Function Oxygenases / Q000737:chemistry*; D009251:NADPH-Ferrihemoprotein Reductase; D011487:Protein Conformation; D017510:Protein Folding; D012996:Solutions / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D012996:Solutions; D012997:Solvents; D014867:Water; D006418:Heme; D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; D009251:NADPH-Ferrihemoprotein Reductase; C052423:flavocytochrome P450 BM3 monoxygenases; D004121:Dimethyl Sulfoxide