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Naturally, a question of whether binding specificity can be predicted from the PDZ domain's primary sequence, arises.
DNA binding specificity can be increased by interactions with cofactors, such as the homeodomain proteins Extradenticle (Exd; [14] [16]) and Homothorax (Hth; [17]) but the in vivo roles of these cofactors have been controversial.
Thus, TRAPs with novel binding specificity can be generated by mixing-and-matching TRAP pockets that have been selected to bind particular amino acids rather than performing new selections for every peptide target.
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The display of HA on yeast cell surfaces, on the other hand, may represent a convenient approach by which HA binding specificities can be confirmed.
However, the use of the DNA duplex stability data is limited because little verified information about TF binding specificities can be found from the literature and, therefore, binding specificities need to be learned from the data as well which currently requires that a set of verified binding sites is known.
The isolation of recombinant antibody fragments with unique binding specificities can be readily accomplished using antibody display methods such as phage display or ribosome display.
We also show that alterations of DNA-protein binding specificities can be achieved by supplementing the growth media with different sera.
Glycan microarray technology has since accelerated studies in glycomics since glycan binding specificities can be analyzed quantitatively in a short period of time using much smaller amounts of sample material [ 91].
Since at the lowest classification level, the DBDs are usually extremely similar, the DNA-binding specificities can be assumed to be nearly identical as well.
Based on these models, the amino acids relevant for substrate binding and specificity can be postulated.
In the simplest case, this includes an on/off switching of the binding affinity for a certain guest, but more sophisticated consequences such as fine-tuning of the binding kinetics or regulation of guest specificity can be achieved.
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