title: Examination of the solvent perturbation technique as a method to identify enzyme catalytic groups.
abstract: The present study was undertaken for the purpose of evaluating the solvent perturbation technique as a method to identify enzyme catalytic residues. For establishment of expected directions and sizes of pKa perturbations for different types of acids in different classes of solvents, a study of the pKa of a series of acids in mixed solvent systems was carried out. Consistent with previous findings, the presence of organic solvents (25% v/v) increased the pKa values of neutral acids while it decreased or did not change the pKa values of cationic acids. The size of the perturbation observed was dependent on the nature of the organic solvent and on the polarity of the neutral form of the acid. The solvent perturbation studies were then extended to the catalytic aspartate residue of yeast hexokinase. The pKa of this residue was determined from the MgATP V/K profile measured in the presence and absence of organic solvents (25% v/v). While dimethylformamide and methanol induced small but perhaps significant increases in the observed pKa, dimethyl sulfoxide and propylene glycol did not. The pKa values, from the MgATP V/K profiles measured in the presence of fully saturating glucose, were not significantly increased by the organic solvents. The pKi vs. pH profile for the competitive inhibitor lyxose was also measured in the presence and absence of organic solvents. While methanol (25% v/v), dimethylformamide (25% v/v), and dioxane (17.5% v/v) induced a large increase in the pKa, propylene glycol and dimethyl sulfoxide (25% v/v) did not. The results from this investigation indicate that the solvent perturbation technique should not be relied upon indiscriminately.
mesh_terms: D000255:Adenosine Triphosphate; D001665:Binding Sites; D004798:Enzymes / Q000378:metabolism*; D005954:Glucosephosphate Dehydrogenase / Q000378:metabolism; D006593:Hexokinase / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008433:Mathematics; D009994:Osmolar Concentration; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D012997:Solvents
chemical_list: D004798:Enzymes; D012997:Solvents; D000255:Adenosine Triphosphate; D005954:Glucosephosphate Dehydrogenase; D006593:Hexokinase