MD Simulations of the Time-Dependent Red Shift in the Fluorescence of Trp in Protein GB1

Abstract

Time-dependent red shift (TDRS) in the emission of Trp after impulse excitation reports the dynamics of solvent and protein relaxation. TDRS of the single Trp in the B1 domain of streptococcal protein G (GB1) has been measured experimentally [Toptygin, Gronenborn and Brand, J. Phys. Chem. B 2006, 110, 26292]. The present work compares the results of Charmm MD simulations with the experimental data. The protein in a box of explicit TIP3P water was equilibrated with the ground-state charges on Trp atoms. At t=0 the charges on Trp atoms were changed to those characteristic of the excited state 1La. TDRS was calculated from a series of 2000ps excited-state MD trajectories using first-order QM perturbation theory. TDRS from a single trajectory is overwhelmed by random noise. Averaging over 100 trajectories produced a result qualitatively consistent with the experimental data. The amplitudes of the calculated and measured TDRS during the time interval from 200ps to 2000ps are in good agreement. However, at t - 2 of random fluctuations in the ground-excited state energy gap ΔE and the relation hν(t)-hν(infinity)=C(t)/(kBT) [Nilsson and Halle, PNAS 2005, 102, 13867]. This produced a TDRS curve containing less high-frequency noise, but more low-frequency noise as compared to the result of averaging over 100 short nonequilibrium trajectories. We thank Patrick R. Callis for accurate excited-state Trp atom charges. Supported by NSF grants MCB-0416965, MCB-0719248.