title: Numerical method to analyze pH-profile from initial velocity data and semi-empirical procedure to identify catalytic residues of enzymes using pK and heat of ionization.
abstract: A numerical computing method to estimate pK and heat of ionization directly from initial velocity data was developed for systematic analysis of rate parameters. Values of rate and thermodynamic parameters were determined together with standard deviations, without using Arrhenius and van't Hoff plots. Distributions of pK and heat of ionization of small-molecular derivatives of aliphatic carboxylates, imidazoles, thiols, and aliphatic amines as possible models for catalytic residues of enzymes were analyzed from a thermodynamic point of view. Each group was classified in a parallelogram without overlapping, except for a part of the imidazole and thiol groups. It was shown that values of pK and heat of ionization of carboxylates and histidine residues involved in the catalytic activity of enzymes determined from pH-profile experiments can be classified into similar, though somewhat extended, areas to those of the corresponding small-molecular derivatives. Identification of catalytic residues using values of pK and heat of ionization is proved to be a reliable method when the procedure is properly used.
authors.affiliation: Department of Food Science and Technology, Faculty of Agriculture, Kyoto University.
authors.forename: H
authors.initials: H
authors.lastname: Nakatani
authors.forename: K
authors.initials: K
authors.lastname: Ishikawa
mesh_terms: D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D007093:Imidazoles / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D015203:Reproducibility of Results; D013438:Sulfhydryl Compounds / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D004798:Enzymes; D007093:Imidazoles; D013438:Sulfhydryl Compounds