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A de novo drug design methodology was used to generate an initial set of structures that could potentially bind to a putative binding site.
The ability of ZNF9 to bind to a putative IRES element in the absence of other proteins suggests that it may act as an ITAF through direct recognition of the IRES sequence.
SREBP1 has been shown to bind to a putative E-box motif at -1535 bp of the PPARγ1 promoter, and mutation of this motif inhibits SREBP1 binding [ 66].
Chromatin immunoprecipitation assay further revealed that ER α could bind to a putative estrogen response element region of the INPP4B promoter in bladder cancer cells.
dRFX was identified through a homology search for the RFX DNA binding domain (DBD) and dRFX2 was identified through yeast-one-hybrid (Y1H) screening for transcription factors that bind to a putative promoter sequence [ 13, 14].
We then evaluated in MCF7 3-D spheroids and in MCF7 hypoxic cells whether HIF-1α may bind to a putative HRE within the promoter region of the MDR-1 gene, increasing Pgp transcription, by a ChIP assay.
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In adipocytes, STAT5A binds to a putative STAT site in the PDK4 promoter in response to PRL stimulation [ 35].
Potentially related is the observation that S1P bound to a putative TRPC3-PLCγ1 intermolecular domain that also interacted with PI phosphates, although the functional relevance of this binding was not determined (van Rossum et al. 2005).
Using highly purified polysaccharides, we were able to show that opsonic antibodies are directed against only two of these antigens: In acapsular strains, LTA is the major opsonic epitope and in encapsulated strains opsonic antibodies bind to a novel diheteroglycan, the putative capsular polysaccharide of E. faecalis in CPS-C and CPS-D strains.
We herein also adopted a similar approach to test whether and how CupB2/CupB4 bind to their putative binding partners.
The PLU-1/JARID1B ARID domain preferentially binds to a GCACA motif, a putative consensus sequence that is abundant in MT promoters.
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