Deriving reaction mechanisms from kinetic spectroscopy. Application to late rhodopsin intermediates

A general algebraic approach to the kinetic analysis of time-dependent absorption data is presented that allows the calculation of possible kinetic schemes. The kinetic matrices of all possible reaction mechanisms are calculated from experimental eigenvalues and eigenvectors derived from the decay constants and amplitude spectra (b-spectra) of the global exponential fit to the time-dependence of the absorption data. The eigenvalues are directly related to the decay constants, and the eigenvectors are obtained by decomposing the b-spectra into spectral components representing the intermediates. The analysis method is applied to the late intermediates (lumi, meta I, meta I-380, and meta II) of the rhodopsin photoreaction. The b-spectra are decomposed into lumi, meta I, meta-380, and rhodopsin spectra. The meta-380 component is partitioned into isospectral meta I-380 and meta II components based on physical criteria. The calculated kinetic matrices yield a number of reaction mechanisms (linear scheme with back reactions, branched schemes with equilibrium steps, and a variety of square models) consistent with the photolysis data at 25 degrees C. The problems associated with isospectral intermediates (meta I-380 and meta II) are treated successfully with this method.