The RBC binding motif, defined by the F I N residues, served as the basis for designing a single peptide bond site-directed substitution by the ψ [CH2 NH] isostere bond, producing ψ-128 (F I) and ψ-130 (I N) pseudopeptides and their corresponding polymeric forms, ψ-129 and ψ-131, respectively as shown in Fig. 2.
An AT-hook is a small DNA-binding motif defined by a glycine-arginine-proline (GRP) tripeptide in which the central arginine is essential for DNA minor groove binding (DKPKGRPPKNLKEW in CbfA; underlined residues identical to the most frequent amino acids in these positions in other AT-hook proteins).
For example, the DNA-binding motif defined by deletion experiments (Zhou et al., 2005) was identified as spanning residues 86 118 in human PLSCR1.
Motif enrichment analysis of known splicing factor binding sites identified the top ranked Esrp1 (UGGUGG) binding site motif defined by SELEX in the upstream intron of Esrp silenced SE events in all three pairwise comparisons, and the Esrp1 motif was also enriched in the exon body of Esrp1 KO splicing targets (Dittmar et al., 2012).
Since zinc binding motifs are defined by coordinating residue type and position but typically not by specifics in connecting sequence, they can be difficult to define by algorithm.
In RNAMotifModeler, the consensus of each binding motif is defined by the following components: 1) The reference motif, a k-base RNA sequence on which the protein preferably binds; 2) Retained binding affinity despite of a one-nucleotide deviation from reference motif to the sequence of one binding sites.
The STAT1 binding motif as defined by the JASPAR CORE database [37] is shown in FIGURE S7A.
In case of BsuL-CTD, the metal binding motif is defined by the stretch DQHAAQERIKYEY extending from residues.
Using the twenty eight time course gene expression arrays, the upstream sequence data, and the binding motif TRTTTAC defined by Murphy et al.[32], TRANSMODIS was run twice to the same data set with signs inverted in the second run, giving two classes of genes.
