I need the structure of different rotamers for a triexponential decay of HSA of Trp 214 in subdomain IIA ( tau 1= 1.1 ns, tau 2= 3.96 ns and tau 3= 7.32 ns), if there is any paper that has given the structure of rotamers of Trp 214, please provide
Check out the reference below, this might help---
On the origin of nonexponential fluorescence decay in tryptophan and its derivatives
J. W. Petrich , M. C. Chang , D. B. McDonald , G. R. Fleming
J. Am. Chem. Soc., 1983, 105 (12), pp 3824–3832
DOI: 10.1021/ja00350a014
I did my master thesis long time ago (2004) on HSA W214 fluorescence (in the Yves Engelborghs lab, KU Leuven, Belgium). I unfortunately do not have the pdf version with me here. Nevertheless, let me give you a small summary of what we found.
We used DEE (dead-end elimination) to computationally determine the different rotamers. For each of these rotamers we determined the distance to the carboxy carbon, and the solvent accessible area (ASA). The former value relates to the non-radiative decay rate constant via Markus theory (see also Hellings et al, Biophys J 2003). The latter parameter (ASA) was used to assign each rotamer to an experimentally found lifetime. As you mentioned, we found that the fluorescence decay was best fitted using 3 lifetimes. However, computationally we found 4 rotamers. The discrepancy was explained by the fact that two of those rotamers had quasi-identical distance to the carboxy carbon, and similar ASA.
In relation to the note by Dr. Van der Zwan on the rotational freedom and exchange between rotamers in proteins: From the computational results, we estimated the energy barriers between the different rotamers, and indeed found that such transition was very much unlikely. However, it is not unlikely that during protein folding, the different rotamers are “trapped” in different proteins, resulting in a conformational heterogeneous ensemble?
The data were never published. Given that the thesis was made ~ 12 years ago, and since I entered a different research area, I do not recall many of the details. However, if you are interested, I can try to retrieve the pdf of the thesis?
Let me know!
Best of luck with your research,
Willem
OK, I found the pdf of the thesis. Unfortunately, it is in Dutch, so probably of little use to you?
Again, if you are still interested in the data, let me know. We might figure out a way to share .
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