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The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored.
In section The Combination Method for topology design, we propose a Combination Method (CM) that develops formulas and algorithms to construct a circulant graph with a relatively minimum average distance, based on the features and characteristics of the average distance fluctuation curves.
Figure 3b is the corresponding distance fluctuation correlation contour plot.
This group of residues is also observed in Figure 5b, the distance fluctuation matrix contour plot, to form a dark strip, implying that they are correlated with rest of the residues.
M185A displayed some distance fluctuation between Q192I−Q192II, but no significant difference was observed between the wild-type and the mutant M185A, primarily due to that short Met185 did not involve many interactions with its neighboring residues.
Other improvements in the graphical user interfaces, such as the more convenient navigation in the correlation maps and the inter-residue distance fluctuation maps permit a direct assessment of structural regions subject to distinctive cross-correlations as well as those that are highly decoupled.
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tFCS measures the distance fluctuations between two fluorescently labeled sites within an untethered, freely diffusing biomolecule.
Obtained via matching distance fluctuations, these force constants represent strengths of mechanical coupling between CG beads.
Moreover, active modes 2 and 3 additionally shows distinct efflux-like motions, characterized by NBDA NBDB distance fluctuations (active mode 2) and rotation of the TM helical bundle (active mode 3, Fig. 8B), similar to that observed for P-gp36 or G5G8 heterodimer (unpublished data).
We found that, in general, shorter Cys-His distance fluctuations led to a higher deacylation rate constant, implying that greater confinement of the two residues will allow a higher frequency of the acetyl exchange between the cysteine thiol and histidine imidazole R-groups.
Figure 7b is the contour plot of the distance fluctuations.
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