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Exact(3)
The most closed conformation is found in Prp28, which leaves no room for any ligand.
The representative structures were selected from each simulation (last 2 ns) and those were the most closed conformation to the average structure.
In order to compare the protein structures from the four different systems, their representative structures were selected from each simulation and those are the most closed conformation to the average structure for the last 2 ns snapshots.
Similar(56)
The most prevalent arrangement predicted by the MD simulations is the closed conformation (closely agreeing with the respective x-ray arrangement) or related geometries where, e.g., three bases are stacked and the fourth one samples mostly bulged-in geometries.
Glucokinase binds to GKRP in the wide-open state [44,45] and it binds to PFK2/FBPase2 most likely in the closed conformation [46].
The deviation of the 200s flap from the closed conformation is most evident near residues Pro206-Ala207.
Apo cNTnC was shown to adopt a "closed" conformation with most of its hydrophobic residues buried (4).
In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions.
Exploration of these motions with an explicit-solvent representation using molecular dynamics with excited normal modes confirmed that the closed conformation is the most stable for the CDK2/cyclin A complex, in agreement with their experimentally available structures.
This indicates that the conformation of TGF-β313 differs from TGF-β3, most likely because it adopts a closed conformation similar to TGF-β1.
Thus, the finding that TGF-β3H4 adopted the closed conformation and lost most of its activity in the migration assay provides strong, though not conclusive evidence, that the shift in the KCO equilibrium toward the closed state is caused by an increase in helical stability and that the activity in the migration assay is specifically due to the open conformation.
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CEO of Professional Science Editing for Scientists @ prosciediting.com