While in vitro data provides important information regarding binding specificities, such data is context independent.
Whereas it is possible that more sensitive methods could, in the future, be used to further subdivide ETS-domain DNA-binding specificities, such differences would necessarily be even smaller than those reported here.
Finally, Kumar and colleagues30 found that the mobility of soluble transcription factors depends on their binding specificity: those that make less specific contacts move faster.
The advantages of using synthetic CBMs -which is novel for this study- over native CBMs is related to their molecular properties such as stability and binding specificity that can be targeted by engineering.
Information gained from such studies may enable the design of Evasins with defined chemokine binding specificity that could be therapeutically useful in inflammatory and infectious diseases, and cancer.
How is it that lectins are able to display such broad binding specificities for structurally distinct carbohydrate epitopes?
The specifications of the DREAM4 challenge and public availability of ERBB2IP-1 single-mutant phage-display data have allowed us to design a method that uses such data in predicting binding specificities of multi-mutant domains.
Representing transcription factor binding specificities in this form means that no data is stored on the interaction of binding specificity between different base positions in the binding sites.
The very molecular features that confer binding potency and specificity, such as stereochemistry, regiochemistry, and scaffold rigidity, are conspicuously absent from most libraries because isomerism introduces mass redundancy and diverse scaffolds yield uninterpretable MS fragmentation.
Such TFs often have highly similar DNA binding specificities (Badis et al., 2009; Jolma et al., 2013), despite the fact that they are observed to interact with different sets of genomic sites in vivo (ENCODE Project Consortium, 2012).
