There is great interest in characterizing the dynamic properties of multidomain systems, and moving beyond conventional descriptions in terms of static structures, toward the characterization of population-weighted ensembles describing a distribution of many conformations sampled in solution.
Similarly to predictive tasks, in molecular dynamics simulations typically many conformations are generated, in the range of thousands, by taking snapshots of the trajectory at given time intervals.
Many conformations will vanish in the process of deformation.
Thus small ligands binding to the AcrB site derive an affinity benefit from the ability to bind weakly in many conformations, while larger ligands benefit by binding in only a few conformations, but making more receptor/ligand contacts in each conformation.
In some cases, there is too much residual disorder in those atoms, and the resulting electron density for atoms existing in many conformations is smeared to such an extent that it is no longer detectable in the electron density map.
Overall, there is no consensus on the effects of the size of the conformer models upon ligand-based 3-D virtual screening and biological activity analysis and how many conformations should be considered in general.
The cavity is large enough that all known ligands can, in principle, adopt many conformations within the cavity.
In order to overcome this limitation, time-resolved X-ray crystallography allows determination of many conformations at 1 picosecond intervals.
As single-stranded oligonucleotides, the ability of DNAs to change conformation remains limited, even though functional DNAs, including aptamers and DNAzymes, require the presentation of many different conformations in order to generate signals that can be controlled and monitored.
Exhaustive structural studies of protein kinases have established that the kinase/pseudokinase domain is plastic, and attains many different conformations in response to binding of micromolecular and macromolecular ligands.
