Fig. 4.

Visualization of the chromophore in protein and its fluctuation correlation. (A) The protein structure of Fre/FAD complex. The tyrosine residue Tyr³⁵ and the FAD substrate, which are responsible for the fluorescence quenching, are shown in the dash circles. (B) The autocorrelation function of fluorescence lifetime fluctuation 〈δγ⁻¹ (t)δγ⁻¹ (0)〉 evaluated by Eq. 6 with the transition time of 2ⁿ (n = 3, 4, …, 8) (denoted by the circles) in linear-logarithmic plot. For comparison, the previous numerical result from a photon-by-photon-based calculation is also depicted (the solid line) together with the normal Brownian diffusion model (gray dashed line) represented by the overdamped Langevin equation on a harmonic potential well presented in Fig. 2. θ and λ are set to be 0.19 Ų and 1.73 s⁻¹, respectively, with β = 1.4 Å⁻¹ (15). The arrows indicate the time scales at which 〈δγ⁻¹ (t)δγ⁻¹ (0)〉 is evaluated according to the multiscale SSNs shown in Fig. 5. The results indicate that the SSN indeed captures the system's multiscale dynamics.