To shift the population of conformational states towards the energetically less-accessible states and detect new binding sites for low-affinity, less-soluble fragments, we suggest a dual strategy: collect both datasets, if possible.
Dissociation is fast and reproducible at binding sites of low stability.
The subunits can independently be modified, making it possible to create avidins with altered binding sites, for instance for low-affinity and high-affinity binding of a ligand within a single protein molecule [7].
SAL1 exhibits a classical structure of lipocalins characterized by a fully conserved N-terminal -G-X-W motypical the typical folding pattern of a nine-stranded antiparallel β-barrel forming an internal ligand binding site for small hydrophobic molecules [ 12], despite relatively low sequence similarity [ 13].
NikR has multiple types of metal binding sites: high-affinity nickel binding sites for stoichiometric nickel (low picomolar dissociation constant) (2, 6), potassium binding sites (4, 7, 8), and low-affinity nickel binding sites (dissociation constants from 30 μM to 30 nM) (1, 2).
It was shown that S-adenosyl L-homocysteine hydrolase from bovine kidney possesses two binding sites for adenosine: a low affinity binding site located in the catalytic domain and a high affinity binding site located in the NAD+/NADH binding domain of the enzyme [88].
This fortuitous binding site could later prove to be a useful binding site for other low molecular mass partners.
While tubulin possesses low affinity binding sites for zinc, they are likely not relevant under physiological conditions., These low affinity sites have historically been used to produce tubulin sheets with anti-parallel protofilaments, not the parallel orientation found endogenously.
Competition curves were biphasic and displayed a similar proportion (50 to 66%) of low-affinity binding sites for all agonists but different affinities for both high- and low-affinity binding sites (Table 2).
This model predicts that genes with few or low-affinity binding sites for the MR-TF would only be induced close to the morphogen source, where MR-TF concentration is at its highest.
It is noteworthy that binding sites for ArcA, the transcriptional regulator expressed under low oxygen conditions, were only detected in a single region, reflecting perhaps that we only screened TSSs from aerobic cultures.
