title: Understanding of the Effects of Ionic Strength on the Bimolecular Rate Constant between Structurally Identified Redox Enzymes and Charged Substrates Using Numerical Simulations on the Basis of the Poisson-Boltzmann Equation.
abstract: To understand electrostatic interactions in biomolecules, the bimolecular rate constants (k) between redox enzymes and charged substrates (in this study, redox mediators in the electrode reaction) were evaluated at various ionic strengths (I) for the mediated bioelectrocatalytic reaction. The k value between bilirubin oxidase (BOD) and positively charged mediators increased with I, while that between BOD and negatively charged mediators decreased with I. The opposite trend was observed for the reaction of glucose oxidase (GOD). In the case of noncharged mediators, the k value was independent of I for both BOD and GOD. These results reflect the electrostatic interactions between the enzymes and the mediators. Furthermore, we estimated k/k° (k° being the thermodynamic rate constant) by numerical simulation (finite element method) based on the Poisson-Boltzmann (PB) equation. By considering the charges of individual atoms involved in the amino acids around the substrate binding sites in the enzymes, the simulated k/k° values well reproduced the experimental data. In conclusion, k/k° can be predicted by PB-based simulation as long as the crystal structure of the enzyme and the substrate binding site are known.
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Sugimoto
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kitazumi
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Shirai
authors.affiliation: Department of Chemistry, Konan University , 8-9-1 Okamoto, Higashi-Nada, Kobe, Hyogo 658-8501, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yamamoto
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Kano
mesh_terms: D005949:Glucose Oxidase / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009994:Osmolar Concentration; D010084:Oxidation-Reduction; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry* / Q000378:metabolism*; D016012:Poisson Distribution; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D005949:Glucose Oxidase; D044925:Oxidoreductases Acting on CH-CH Group Donors; C042401:bilirubin oxidase