In the case of darunavir a decrease of more than 1000 in binding affinity was required to see a decrease in antiviral effect, which is more than two orders of magnitude higher than observed for other PIs.
First, the domain may act as a processivity factor, such that full DNA-binding affinity is required to maintain an association with the nucleosome so that sufficient cycles of remodelling can occur to complete the sliding reaction.
In our experience, sub-nanomolar, and often low picomolar, affinities are required for small molecules to compete with high-affinity endogenous ligands for binding to anti-apoptotic proteins, such as BCL-2 and BCL-XL.
While high-affinity ligand binding is sufficient for activation of most canonical signaling pathways, low-affinity binding is required for the activation of the Signal transducers and activators of transcription (Stats) and Phospholipase C-gamma 1 (PLCγ1).
Given our peptide-based approach, we did not investigate whether a second low-affinity binding site is required for WNK ubiquitylation.
This concentration of antigen was required for precise enthalpy measurements, but precludes determination of the KD in cases where the binding affinity was high.
HER2 binding affinity was determined in saturation radioligand binding assays using SKBR-3 cells (1.3 × 106 HER2/cell).
It has been shown that RAGE oligomerises on plasma membranes of human cells, and that this oligomerisation provides a mechanism to increase the number of binding sites and is required for high affinity binding of ligands (Xie et al. 2008).
Thus, neither arginine side chain is completely indispensable for binding, but each is required for high-affinity binding.
Often, affinity maturation is required to obtain high affinity binders.
