In general, residues that photo-cross-link are likely to be involved in binding interactions that are at the periphery of the protein protein binding interface and are therefore weaker than those in the core hot spot.
Gly70 is not involved in the DNA-binding interface and is in loop region (L2) between helices 2 and 3 (Fig. 4B).
Last but not least, DARPins have a relatively large binding interface and have been engineered, mostly via phage display and ribosome display, to bind a wide range of targets with pmol/L nmol/L affinities (Pluckthun, 2015).
As noted in our previous study, the RPA32C binding interface is devoid of hydrophobic pockets typically found at protein binding interfaces and, rather, is relatively flat.
On the other hand, the acquisition of the common function of binding to HBGAs by distinct binding interfaces and modes is consistent with functional convergence as a result of adaptation to and selection by the same niche of human HBGAs.
Three dimensional structural studies of ZFPs have given insights on the ZFP-DNA- binding interface and it can be compared with respect to a 'canonical binding model' where each finger interacts with DNA in an anti-parallel mode.
Although this observation at first seems paradoxical, in fact, it provides strong support for recent hypotheses that structural plasticity and conformational changes are involved in the arrestin rhodopsin binding interface and that the two proteins may be able to interact through multiple docking modes, with arrestin binding to both monomeric and dimeric rhodopsin.
In GI.2 FUV the much longer P-loop reaches the HBGA binding interface and two residues (G343′ and G245′) are involved in the formation of the Le epitope binding site (Kubota et al., 2012).
The binding site is at the heterodimer interface and is composed of residues from both ChsE4 and ChsE5, as previously predicted.
Relatedly, how easily does orthologous neofunctionalization occur and how dependent upon protein fold and binding interface size is it?
