Figure 4.

Fluorescence Stokes shift for isomer 1. a) Linear response theory estimate for the total Stokes shift, and the contributions from indole-water and indole-protein interactions. The time interval used to calculate the linear response correlation functions, Eqs. (3) and(4), and sampled for initial conditions of the non-equilibrium trajectories is indicated in Fig. 2a. b) Total Stokes shift, and the contributions from indole-water and indole-protein interactions calculated from 360 non-equilibrium molecular dynamics trajectories. Error bars represent one standard deviation as estimated from block averages obtained by breaking the total data set into three parts.⁶⁹ c) Comparison of the Stokes shift calculated with full protein dynamics, as in (b), or from 120 trajectories propagated with the protein coordinates frozen following photo-excitation. When the protein is frozen, the water response is the total response. d) Contribution of the loop region (residues 77–86) to the Stokes shift, and the contribution that arises from the backbone atoms of the loop.