Tryptophan relative position change

A change in the relative position of a tryptophan residue towards internal protein quenchers, such as aspartate residues and disulfide bonds, which may occur as a result of processes of folding/unfolding. 

Figure 8.20 Schematic diagrams of docking the trp repressor to DNA in its inactive (a) and active (b) forms. When L-tryptophan, which is a corepressor, hinds to the repressor, the "heads" change their positions relative to the core to produce the active form of the repressor, which hinds to DNA. The structures of DNA and the trp repressor are outlined.

Figure 19 shows the typical fluorescence transients of TBE from more than 10 gated emission wavelengths from the blue to the red side. At the blue side of the emission maximum, all transients obtained from four Trp-probes in the cubic phase aqueous channels drastically slow down compared with that of tryptophan in bulk water. The transients show significant solvation dynamics that cover three orders of magnitude on time scales from sub-picosecond to a hundred picoseconds. These solvation dynamics can be represented by three distinct decay components The first component occurs in about one picosecond, the second decays in tens of picoseconds, and the third takes a hundred picoseconds. The constmcted hydration correlation functions are shown in Fig. 20a with anisotropy dynamics in Fig. 20b. Surprisingly, three similar time scales (0.56-1.431 ps, 9.2-15 ps, and 108-140 ps) are obtained for all four Trp-probes, but their relative amplitudes systematically change with the probe positions in the channel. Thus, for the four Trp-probes studied here, we observed a correlation between their local hydrophobicity and the relative contributions of the first and third components from Trp, melittin, TME to TBE, the first components have contributions of 40%, 35%, 26%, and 17%, and the third components vary from 32%, to 38%, 43%, and 53%, respectively. The...

In addition to the complicated response of the fluorophore to various stimuli, one more aspect should be home in mind. Only a small number of systems contain intrinsic fluorophores and are inherently fluorescent. Such systems (e.g., tryptophan-containing proteins) can be studied directly and reliable information on the positions, mobility, and accessibility of tryptophan residues for different molecules can be relatively easily obtained. In a majority of cases, a successful fluorescence study requires the addition of a low content of an extrinsic fluorescent probe, which modifies not only optical but also other properties of the studied system. An extrinsic probe feels only the effect of its immediate microenvironment, which has undoubtedly been altered by its insertion. Even though the change in the system is negligible at a macroscopic level, most fluorescence methods report the behavior of the tiny perturbed part of the system. Therefore, the extent and nature of possible perturbation of the system must also be investigated to enable description of the behavior of the unperturbed system. 

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