Computation of tryptophan fluorescence quenching by amide and histidine
Tusell, Jose Ramon.
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Tryptophan fluorescence quantum yield is widely used to follow protein folding for the villin headpiece subdomain (HP-35) and a synthetic peptide Ac-W-(A) ₃ -H + -NH ₂ (WH5). These biopolymers have a histidine residue, which is a potent quencher of tryptophan fluorescence, positioned four amino acids away from tryptophan. Experiments assumed that when folding occurs the fluorescence of tryptophan will be quenched by histidine due to the formation of an alpha helix. The reliability of folding and unfolding rate constants determined by tryptophan fluorescence has been called into question by several computational studies. A method to calculate the electron transfer matrix element was developed for different donor/acceptor systems. This method shows that the electron transfer matrix element is sensitive to orientation at close distances and that it does not follow a simple exponential decay with distance. This thesis improved the methods developed by Callis and coworker by conducting 100 ns long simulations for single tryptophan proteins and by modifying the calculation of the fluorescence quantum yield to account for heterogeneity in the calculated electron transfer rates. In addition the method was extended to calculate electron transfer rate constants for histidine quenching by conducting 1 microsecond long simulations of HP-35 and WH5. Calculated tryptophan fluorescence quantum yields for the single tryptophan proteins show better agreement with experiment than was previously reported. Simulations for HP-35 and WH5 indicate that the ability of histidine to quench the fluorescence of tryptophan is surprisingly controlled by the energy gap dependence on the distance that separates them. The energy gap dependence on this distance arises from water solvation around histidine. At large distances this solvation decreases the ability of histidine to accept an electron from tryptophan. Different tryptophan/histidine rotamers control this distance. Even when HP-35 is completely folded much of the time histidine does not quench tryptophan fluorescence contrary to the idea that histidine is only close when HP-35 is folded. The calculated fluorescence quantum yield is sensitive to the distribution of close and far conformations and the rate of exchange between these two conformations. This sensitivity gives credibility to the folding/unfolding rates derived from tryptophan fluorescence quantum yields.