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However, careful analysis of the various conformers shows that one particular conformation exhibits appropriate intermolecular distances with the methyl groups arranged eclipsed to each other (see the Supporting Information).
If the average shape is not what is recognized, then a particular conformation must somehow be selected from the conformational ensemble.
For a metabolic enzyme with an "ordered" structure, the particular conformation required for "induced fit" may have a very high negative conformational free energy chosen by evolutionary selection pressure over time and thus the issue of "context" may appear to be irrelevant in these cases.
Rotamer propensity score (Eq. 2) leverages the statistics on the rotamer of a particular fragment to estimate the likelihood of a particular conformation.
This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation.
The structure derives from a particular conformation of the glutaric units and appears to be independent of the number of methylene groups present in the diamine residue.
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A central challenge for the structural enzymologist is to define how individual terpene synthases statically or dynamically discriminate between alternative polyprenyl cation conformational modes or selectively favor particular conformations to shepherd reactive intermediates along distinct cyclization cascades.
JAK2 wild-type, on the other hand, was activated only in the presence of the particular conformations corresponding to an activated EpoR dimer.
Values of J for particular conformations and corresponding values of the looping free energy are also given in Figure 2. Remarkably, the LB conformation has the largest J value among the three classes of v-shaped protein structures and dominates the distribution (Figure 3A).
By targeting particular conformations of env it also inhibited late fusion steps [ 72].
Since E3 enzymes require flexibility during their catalytic cycle, they can be regulated by processes that restrict their flexibility and lock them in particular conformations.
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