The putative signal of secretion, the structural similarities with these different proteins sharing the DC-SIGN domain and its mannose binding specificity suggest that PdC-Lectin could interact with zooxanthellae mannose ligands to mediate symbiont acquisition as it was described for the F. scutaria/ Symbiodinium model [ 64].
DOI: http://dx.doi.org/10.7554/eLife.00173.005 Such dramatic site-specificity suggested that sequence binding positions Spitz in the active site, as occurs with soluble proteases.
Interestingly, optimization of zinc finger protein amino acid sequences for high-affinity binding to specific DNA sequences results in proteins with little or no predicted specificity, suggesting that naturally occurring DNA-binding proteins are optimized for specificity rather than affinity.
We do not observe significant differences between Elk1 and Elk4 DNA-binding specificity in either of the independently performed DNA-binding specificity assays, suggesting that the differences in binding observed earlier were related to changes in overall affinity of the ETS factors to DNA as opposed to effect on specificity of binding to different sequences.
These, together with measured binding-specificity differences, suggest that there is a potential for the design of molecules that might selectively block the acyl-CoA binding site.
This result further demonstrates the binding specificity of the RBFOX1/2 binding motif and suggests that the SRSF1 motif would not efficiently interact with RBFOX1/2 proteins.
This study defines the domain requirements for SYG-1/SYG-2 heterophilic binding and suggests that unknown SYG-1 extracellular interactors may play a role in SYG-1-mediated synaptic specificity.
We have observed that docking heparin/heparan sulfate disaccharides to the IL-8 heparin-binding site (Kuschert et al. 1998) does not reveal binding specificity that could help suggesting a most probable binding pose for longer GAGs (data not shown).
This suggested that structural details on the ligand are driving the small differences in binding specificity toward either TIR1 or AFB5 and that these details may be uncovered by the second factor (Factor 2 = Specificity).
Because the C-terminal domain is thought to act as a DNA-binding domain, our finding suggests that plasmid specificity is governed at the level of protein DNA interactions, whereas the PAS domain might be dedicated to regulatory functions, possibly in response to cellular signals, as signal sensing is a common feature in many known PAS domains.
