Why do eukaryotic CE peptidases show specificity distinct from their prokaryotic counterparts?
In conclusion, our regression-based approach for learning complex models of TF DNA binding specificity from custom PBM data can be easily extended and improved, and we anticipate that the proposed regression models will help explain, at least in part, how paralogous TFs with highly similar PWMs are able to interact with distinct genomic targets.
In order to test the transferability of the prediction method to different MHC proteins, we trained the scoring method on binding data for DRB1*0101 and used it to make predictions for multiple MHC allotypes with distinct peptide binding specificities including representatives from the other human class II MHC loci, HLA-DP and HLA-DQ, as well as for two murine allotypes.
A hybrid site is assembled from two half-sites, each harboring a distinct binding specificity.
Despite its high sequence homology with the other PDZ domains, only the PDZ1 domain of PTP-Bas showed distinct binding specificity for TAPP1/2.
Structural comparison with the PTP-Bas PDZ2/RA-GEF2 peptide complex revealed a structural basis for distinct binding specificity of PTP-Bas PDZ1 for TAPP1p/2p peptides.
Humans and mice possess four conserved FGFR genes, of which FGFR1-3, but not FGFR4, are alternatively spliced in the extracellular ligand binding domain to yield two principal isoforms, b and c, each exhibiting distinct ligand binding specificity [2].
This further affirms the distinct receptor binding specificity of avian and human HA proteins.
Binding to human BH3-like peptides showed that KSBcl-2 has similar specificity to Mcl-1, and BHRF1 has a restricted binding profile; M11 binding preferences are distinct from those of Bcl-xL, Bcl-2, and Bcl-w.
How is it that lectins are able to display such broad binding specificities for structurally distinct carbohydrate epitopes?
