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We find that the two-node transcriptional networks are fragile; very few parameter sets allow these motifs to function in a noise-resistant way.
Importantly, both monomers of the dimer require intact tyrosine motifs to function.
The capacity of Alu-DR2 motifs to function as RAREs is supported by several lines of evidence.
We believe that these attempts to link structure (of motifs) to function in terms of mathematical models raise a number of interesting questions and problems.
Furthermore, the Dorsal protein, when itself acting as a long-range repressor, is dependent on neighboring Cut and Dri transcription factor motifs to function, indicating that long-range repression complexes may require specific cis-regulatory grammar (Cai et al., 1996; Nibu et al., 2001).
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Furthermore, p22 seems to depend on the MERES motif to function as a secretory pathway inhibitor; however this motif alone is not responsible for antagonism, as replacement of the ER export signal from VSV G with the MERES motif functionally restored ER export efficiency without any obvious impediment.
However, signaling via SIRPα is primarily inhibitory (the cytoplasmic portion of SIRPα contains four immunoreceptor tyrosine-based inhibititory motifs) to cell function, including phagocytosis [27], [30].
These motifs appear to function synergistically to provide maximal induction of Cyp26a1 in response to AtRA [33], [34].
Characterized protein motifs known to function in this manner are largely involved with protein sorting and lipidation [ 1].
These differences are reflected at the sequence level as well: only the N-terminal domain appears to be conserved, although the double arginine motifs thought to function as a phosphorylation sensor in yeast Atg13 are missing in higher eukaryotes (Fig. S5).
We used the structural motifs to infer functions of 13 novel PKs/NRPs clusters produced by Pseudomonas spp. and Burkholderia spp. and found a putative virulence factor.
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