title: Effect of protein dynamics upon reactions that occur in the heme pocket of horseradish peroxidase.
abstract: Free base and Pd porphyrin derivatives of horseradish peroxidase show long-lived excited states that are quenched by the presence of the peroxidase inhibitor, benzhydroxamic acid. The relaxation times of the excited-state luminescence and the rates of the quenching reaction for these derivatives of peroxidase were monitored as a function of pH, temperature, and viscosity with the view of examining how protein dynamics affect the quenching reaction. As solvent viscosity increases, the rate decreases, but at the limit of very high viscosity (i.e., high glycerol or sugar glass) the quenching still occurs. A model is presented that is consistent with the known structure of the enzyme-inhibitor complex. It is considered that the inhibitor is held at an established position but that solvent-dependent and independent motions allow a limited diffusion of the two reactants. Since there is a steep dependence upon distance and orientation, the diffusion toward the favorable position for reaction enhances the reaction rate. The solvent viscosity dependent and independent effects were separated and analyzed. The importance of internal reaction dynamics is demonstrated in the observation that rigidity of solvent imposed by incorporating the protein into glass at room temperature allows the reaction to occur, while the reaction is inhibited at low temperature. The results emphasize that protein dynamics plays a role in determining reaction rates.
authors.affiliation: Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Mazdak
authors.initials: M
authors.lastname: Khajehpour
authors.forename: Thomas
authors.initials: T
authors.lastname: Troxler
authors.forename: Jane M
authors.initials: JM
authors.lastname: Vanderkooi
mesh_terms: D001665:Binding Sites; D003903:Deuterium / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D006418:Heme / Q000737:chemistry*; D006735:Horseradish Peroxidase / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D006877:Hydroxamic Acids / Q000737:chemistry; D007700:Kinetics; D008652:Mesoporphyrins / Q000737:chemistry; D010777:Photochemistry / Q000379:methods; D012997:Solvents; D013696:Temperature; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D006877:Hydroxamic Acids; D008652:Mesoporphyrins; D012997:Solvents; D006418:Heme; C031468:mesoporphyrin IX; D003903:Deuterium; D006735:Horseradish Peroxidase; C006696:benzohydroxamic acid