It seems possible that binding of a range of substrate conformations could be facilitated by the variety of orientations presented by the various R states.
For erlotinib, however, no significant difference in the binding affinity for inactive and active EGFR-TKD conformations could be detected using a range of computational approaches.
Particular protein domains in their native conformations could be responsible for non-specific binding, so their denaturation partly prevented this undesirable effect from occurring.
Besides, since the binding energy and conformation could be calculated precisely, a promising large-scale in silico design strategy could be applied to gain various enzymes with outstanding characteristics.
In addition, studies on the effect of phosphorylation on the autoinhibitory conformation of NHERF-1 by solution SAXS and binding assays suggest that this conformation could be disrupted by protein kinase C (PKC) phosphorylation at Ser-339 and Ser-340 in the C-terminal domain of NHERF-1.
To summarize, the behavior of the active site in presence of different modulators suggests that the difference in binding conformation of compounds could be attributed to structural differences in either the protein subunits or the compounds, and hence could possibly be a reason for their selective functional efficacy profiles.
These mutations did not cause significant structural changes in either the closed or open conformation of MBP, but rather removed interactions in the hinge that shifted the equilibrium of conformational states toward the closed conformation such that the binding affinity could be greatly increased.
In this way, binding pocket could be defined consistently across the same structural ensemble, varying in conformation but not in composition.
Since the conformation of these individual domains could be altered under physiological conditions, we evaluated the possibility that these binding interactions could be different in muscle expressing full-length dysferlin.
First, the interaction of BAX with a binding partner could be affected by low levels of BAX protein, especially if the binding partner had a reduced affinity for BAX in its globular conformation.
