Photocycle kinetics: analysis of Raman data from bacteriorhodopsin

A recently developed algorithm for analyzing photocycle kinetics was applied to recently obtained Raman data for the time course of bacteriorhodopsin (bR) and its intermediates, L, M, N and O. The algorithm allows all possible transitions between any of the intermediates in the kinetic model. The best fit to all the Raman data required the transitions L in equilibrium with M in equilibrium with N----O----bR and also the branch L in equilibrium with N. The rates are moderately well determined and smooth as a function of pH. From the ratios of forward and backward rates the differences in free energy of the L, M and N states are no larger than 1.5 kcal. The possibility that only the sum of the L and N concentrations is well determined, but not the individual L and N concentrations, was investigated. The model L in equilibrium with M in equilibrium with N----O----bR satisfactorily fitted condensed L + N data and gave predicted individual L and N concentrations considerably different than those measured individually. The possibility of Raman invisible states, such as two Ms or two Ns was also investigated. Models with two Ns were not successful and it cannot yet confidently be concluded which model with two Ms is best. However, the model, L in equilibrium with M1----M2----N----O----bR plus the branch L----N, fits the data better with the same number of parameters as the best model with only one M intermediate. This provides strong support for two Ms in the bR photocycle.