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The amino-terminal region of the peptide-binding site of HLA-DR1 was previously suggested to be more flexible upon peptide-removal in a normal mode analysis [33] as well as in another molecular dynamics calculation [34].
The results of the MD simulations show that as in the WT protein, F97Y HbI also becomes more flexible upon binding CO but to a smaller degree than the WT protein.
This tendency is more evident in the WT where, for example, the backbone amide groups of helices E and F that become more flexible upon CO binding are located on the heme-facing side of the helix.
The backbone amide groups of both WT and F97Y HbI become globally more flexible upon binding CO, but this effect is more pronounced in the WT protein than in the F97Y mutant (Table 2).
In general, we observed that the backbone NH groups of residues surrounding the heme group become more flexible upon ligand binding, particularly in the WT where, for example, the largest increase in flexibility is observed for the residues of helices E and F that face the heme group.
In the WT protein, the largest differences are observed in the pre-A, B, F, and G helices, while the F97Y internal dynamics are most affected by binding in helices E and F. From Figure 4, one can make the qualitative observation that the residues surrounding the heme group become more flexible upon ligand binding.
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These data indicate that the mutation has resulted in a structural reorganization of the protein and that it has formed a more flexible layer upon binding to the SLB (DOPC/DOPE/POPC/DOPS).
Each approach comes with trade-offs - the MANOVA approach is conceptually more simple and computationally less expensive while the BNN approach is more flexible and built upon fewer assumptions.
By contrast, the U.S. Navy had developed the World War II Thach weave into the loose deuce, a more flexible formation either pilot, depending upon the combat situation, could adopt the role of lead fighter while the other covered as wingman and, as experience over Vietnam would show, one better suited for the jet age.
Similarly, ADAM17 has been shown to have a more flexible active site than MMP-2 upon binding to a non-competitive inhibitor [ 45].
In general these more flexible models could not be relied upon to consistently find a threshold which could be said to differentiate protected from susceptible individuals.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com