Estimation of the free energy change of substrate binding lysozyme-catalyzed reactions

The binding constant and binding free energy of each subsite of lysozyme upon substrate binding have been customarily estimated from the experimental data with assumptions regarding the binding mode of substrate and the additivity of binding free energy of each subsite. In the present study, the binding constants and binding free energy of subsites were estimated from experimentally obtained overall binding constants on native and Trp 62-modified lysozymes. The estimations of binding constants and binding free energy were carried out by an optimization method, the modified Powell method, without assuming the binding mode for substrate. First the binding free energies of subsites A, B, and C were estimated from the experimental binding constants of (GlcNAc)1 to (GlcNAc)3, and the binding free energies of subsites D, E, and F were determined from the estimated free energies of subsites A, B, and C, and the experimentally obtained reaction time-courses of substrate (GlcNAc)5. Finally, the values of three rate constants in the lysozyme-catalyzed reaction of chitooligosaccharide were estimated from the experimental time-course by using the binding free energies obtained by the modified Powell method.