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Surprisingly, we show that heteroclitic peptides designed with optimal MHC binding motifs do not always form pMHCs that are substantially more stable than their wildtype progenitors.
It is interesting that similarity of TF binding motifs do not always reflect similarity of DNA-binding domains, as demonstrated by a comparison of the groups of motifs with a phylogenetic tree based on DNA-binding domains (Fig. 2).
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Nonetheless, the presence of in silico predicted binding motifs does not guarantee a specific regulatory factor will bind that sequence.
Hepcidin promoter constructs mirrored the response of mRNA levels to interleukin-6 and bone morphogenetic proteins, but not consistently to hypoxia or HIF stabilizers, and deletion of the putative HIF binding motifs did not alter the response to different hypoxic stimuli.
Wang et al. reported that TLS bind to RNA in the length dependent manner, and the mutation in the known binding motifs did not show a dramatic decrease in the binding [ 13], supporting the low specificity of the RNA binding of TLS.
Because naturally occurring PTEN missense mutations outside the ATP-binding motifs do not result in abrogation of ATP binding nor nuclear mislocalization (Supplementary Material, Fig. S5 and S6), we believe that it may be both the presence of a mutation and the resulting nuclear mislocalization that are important.
Similarly, site-directed mutagenesis of the c-Rel binding motif did not significantly alter hres gene promoter activity.
The scramble peptide, as well as other peptides with single mutation within the PDZ binding motif, did not show significant binding to the TIP-1 protein (Fig. 1E).
In contrast, W179C, a mutant form of α-HL (which has a mutation in Cav-1 binding motif) did not affect the caveolae dynamics (Video S5).
As shown in figure 7, full-length Podocalyxin showed strong colocalization with endogenous NHERF-1 at the apical membrane, while ΔDTHL and Δtail mutants, both of which lack the C-terminal NHERF binding motif, did not.
The presence of a consensus binding motif did not have an impact on whether a target gene was repressed or activated.
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