For example, the best results were obtained on the 4state dataset, where decoys are obtained through enumeration of conformations surrounding the native structure and further selection of low-RMSD decoys.
The conformation and surrounding network of Tyr402 of RXR which plays an important role for dimerization [22] are also conserved.
The membrane-inserting domains of α-PFTs are composed of a hydrophobic, central, helical hairpin which, in the native conformation, is surrounded by amphipathic helices.
Kinases undergo conformational changes between active and inactive conformation and thus an additional hydrophobic pocket is created in the inactive conformation where the surrounding amino acids are less conserved [2].
The structure shows that the dodecameric APY efficiently occupies the ephrin ligand-binding pocket of EphA4 and promotes a "closed" conformation of the surrounding loops.
DNA methylation controls gene expression by directly inhibiting the binding of transcription factors (TFs), by recruiting methyl-binding proteins that prevent TFs from binding to DNA [ 14], or by affecting the conformation of the surrounding chromatin [ 15].
This implies that the Cα atoms of the unrelated octapeptides and identical reverse octapeptides may not be accurately superimposed on their pair, probably due to the influence of several other factors such as conformation angle preferences, surrounding residues, position of the octapeptide in the sequence, etc. Chirality and symmetry are treated as key descriptors of molecules.
This is expected because there is a distribution of water molecule conformations that surround the bond; each polarizes the C2=O bond differently.
One possibility is that the mutation changed the local polarity and consequently the conformations of its surrounding BRI1-interacting residues, which in turn facilitates BRI1-BAK1 interaction.
The slower rates of structural change in Region3 could be due to RNA conformational changes, or adjustment of Rev conformation as influenced by surrounding RNA and proteins to allow additional Rev oligomerization, or a combination of both effects.
The conformation of the atoms surrounding the dissociating hydrogens strongly influences the dissociation process, and also the atomic charges.
