236
B. Czarnik-Matusewicz and Y.M. Jung
heterospectral correlation spectroscopy has also been used to establish the relationship between the information extracted from NmR and Raman spectroscopy
[104]. In this approach, the structural evolution of silk fibroin as the ph changed
from 6.8 to 4.8 was examined by two probes with different frequency scales
(10
5–9
hz for nuclear spin and 10
12–14
hz for molecular vibrations). With the two
spectroscopies, the changes that develop at different rates at different molecular
levels were probed. three different stages of the transition detected in the 2d NmR
homo-spectral correlation have been correlated with specific secondary structure
changes from the soluble helix state to the insoluble β-sheet state.
the concept of heterocorrelation has been expanded further to synchronous
sample–sample hybrid 2d correlation analysis [135]. this analysis concerns (1)
two systems under two different types of perturbations, (2) the same system under
related perturbations, (3) two systems under the same perturbation applied under
different conditions [76], or (4) two systems under the same perturbation [30]. this
hetero variant of 2dCoS is particularly useful for analyses aimed at the comparison
of responses to temperature, pressure, h/d exchange, or chemical denaturants by
mutants and genetic variants, by the holo- and apo-forms, or by proteins from two
different families. hetero 2dCoS in the different sample/perturbation configuration
opens a wide range of correlations, which, compared with the conventional homo
2dCoS, could help give additional insights into the studied systems.
8.4.2 Moving-Window 2D Correlation
A very promising variant form of 2dCoS in protein research is the moving-window
2d correlation introduced by Richardson et al. [136] for the analysis of transitions
in liquid crystal systems. Frequently, the interpretation of 2d correlation spectra
based on a large set of spectral data becomes difficult. this difficulty could arise if,
at different stages of the perturbation, unequal progress of many processes in the
studied protein system influence the spectral changes. the 2d analysis of these processes could be rationalized by the subdivision of the full data set into smaller sets;
next, these smaller sets can be separately analyzed with the synchronous component
of 2dCoS. Each window provides local information about the properties of the protein system. to obtain a global picture of the changes from the subsets of the data,
the autopower spectra of the subsets are plotted in a 2d layout. the moving-window
2d correlation approach is more effective when a large data set, covering a whole
perturbation, is segmented into a large number of small subsets chosen in a way that
ensures the presence of at least two measured spectra in each subset. If the subsets
include a large number of spectra, details of the transitional stages may be lost.
the application of moving windows aids in the observation of small, intermediate,
structural changes, which could not be detected in techniques that only apply to the
initial and final results of the conformational transitions in proteins. this approach
also allows the spectra from the entire perturbation range to be divided into groups
that contain more spectra specific to the intermediates.
B. Czarnik-Matusewicz and Y.M. Jung
heterospectral correlation spectroscopy has also been used to establish the relationship between the information extracted from NmR and Raman spectroscopy
[104]. In this approach, the structural evolution of silk fibroin as the ph changed
from 6.8 to 4.8 was examined by two probes with different frequency scales
(10
5–9
hz for nuclear spin and 10
12–14
hz for molecular vibrations). With the two
spectroscopies, the changes that develop at different rates at different molecular
levels were probed. three different stages of the transition detected in the 2d NmR
homo-spectral correlation have been correlated with specific secondary structure
changes from the soluble helix state to the insoluble β-sheet state.
the concept of heterocorrelation has been expanded further to synchronous
sample–sample hybrid 2d correlation analysis [135]. this analysis concerns (1)
two systems under two different types of perturbations, (2) the same system under
related perturbations, (3) two systems under the same perturbation applied under
different conditions [76], or (4) two systems under the same perturbation [30]. this
hetero variant of 2dCoS is particularly useful for analyses aimed at the comparison
of responses to temperature, pressure, h/d exchange, or chemical denaturants by
mutants and genetic variants, by the holo- and apo-forms, or by proteins from two
different families. hetero 2dCoS in the different sample/perturbation configuration
opens a wide range of correlations, which, compared with the conventional homo
2dCoS, could help give additional insights into the studied systems.
8.4.2 Moving-Window 2D Correlation
A very promising variant form of 2dCoS in protein research is the moving-window
2d correlation introduced by Richardson et al. [136] for the analysis of transitions
in liquid crystal systems. Frequently, the interpretation of 2d correlation spectra
based on a large set of spectral data becomes difficult. this difficulty could arise if,
at different stages of the perturbation, unequal progress of many processes in the
studied protein system influence the spectral changes. the 2d analysis of these processes could be rationalized by the subdivision of the full data set into smaller sets;
next, these smaller sets can be separately analyzed with the synchronous component
of 2dCoS. Each window provides local information about the properties of the protein system. to obtain a global picture of the changes from the subsets of the data,
the autopower spectra of the subsets are plotted in a 2d layout. the moving-window
2d correlation approach is more effective when a large data set, covering a whole
perturbation, is segmented into a large number of small subsets chosen in a way that
ensures the presence of at least two measured spectra in each subset. If the subsets
include a large number of spectra, details of the transitional stages may be lost.
the application of moving windows aids in the observation of small, intermediate,
structural changes, which could not be detected in techniques that only apply to the
initial and final results of the conformational transitions in proteins. this approach
also allows the spectra from the entire perturbation range to be divided into groups
that contain more spectra specific to the intermediates.