Chemistry Reference
In-Depth Information
The group fit may be performed for (1) a group of residues and/or (2) for a set of
R
2
dispersion data recorded by observing different nuclei [
47
,
139
,
140
]. The fit using a
group of residues will be advantageous to identify regions that undergo conforma-
tional equilibrium in the same time scale and population, presumably indicating
cooperative dynamics. Selection of the group of residues may not be straightforward
because uncertainty of the optimized parameters at each residue is not necessarily
Gaussian distributed [
47
]. In the fits of data of different types of nuclei, there may be
systematic errors in individual experiments so that contour maps of the
w
2
values (5)
consistent with data acquired for all types of nuclei may not be obtained [
139
].
Finally, a practical aspect of evaluation of regions that undergo conformational
exchange is described. General technical limitation of spectroscopies, such as NMR
relaxation, is that information of only a limited frequency range is obtained.
R
2
dispersion experiment detects chemical (conformational) exchange on or around the
n
CP
range. In the CT-CPMG
R
2
dispersion studies of Human Immunodeficiency
Virus-1 (HIV-1) protease (as depicted in Fig.
5
), significant
R
2
dispersion profiles
were detected to optimize the exchange parameters only in the terminal
-sheet region
[
137
]. Although the flap region exhibited very high
R
2
values, the data did not have the
sensitivity to be fit, presumably because the time scale of motion is much faster than
the studied
b
n
CP
) of the HIV-1
protease has previously been characterized by the model-free analysis and amide
1
H
R
1
r
experiments [
141
,
142
]. Thus, application of the
R
2
dispersion with other
experiments will be important to avoid misinterpretation of data.
n
CP
range. Such fast dynamics (comparing to the
Acknowledgments This study was supported by grants from the National Institutes of Health
(AI077424 and GM066524), the National Science Foundation (MCB 0814905), and funds from
the University of Pittsburgh. We thank Dennis Torchia and Robert Bryant for discussion and
critical reading.
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