Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase

Abstract

We have used a recently established quantum mechanics/molecular mechanics (QM/MM) method1 to calculate the optical absorption and emission spectra for NADH in liver alcohol dehydrogenase. The widths of these spectra are sensitive to the amplitude and time scale of protein fluctuations, while the Stokes shift is a direct measure of the extent of relaxation of the molecular system. Despite the very large Stokes shift in this system (∼0.9 eV), we find that the reorganization energy is recovered with 13% accuracy. Moreover, the spectral widths are within 6% of the experimental values. Our results demonstrate that our QM/MM approach to the calculation of free energy surfaces remains highly viable even for very large and very fast fluctuations and even for systems as complex as proteins. We also show that the quality of the results very much depend on the quality of the molecular dynamics trajectory and as such our method provides a way to validate molecular mechanics force field parameters for chromophores via direct comparison with experiment.