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The CC domain is organized in five β-strands surrounded by six α helices (α1 to α6), and contains a highly conserved catalytic D, DX35E motif embedded in a protein RNase H fold [17], [20], [21].
To evaluate the positional specificity of YY1 motifs within CpG islands, we used a position frequency matrix (PFM), which allow us to calculate the nucleotide frequencies at each position of the YY1 motif embedded in promoter sequences [44].
The hairpin ribozyme motif is a self-cleaving RNA motif embedded in the satellite tobacco ringspot virus.
Looking forward, we need to understand how NTCP interacts with both HBV envelope proteins and with other cellular proteins, especially through the motif embedded in the cell membrane.
APPL1 is a 79 kDa protein, which contains several distinct domains, including a pleckstrin homology domain, a phosphotyrosine-binding domain and a leucine zipper motif embedded in the coiled-coil region [ 19].
As in some CXC chemokines, such as IL-8, an Glu-Leu-Arg motif embedded in the sequence of mini-TyrRS was shown by mutational analysis to be critical for its cytokine activity [ 9- 11].
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Then he enthusiastically deconstructed Ives's "Concord" Sonata, untangling and explaining the themes and motifs embedded in the complex textures of this fascinating score.
At high temperatures, it is probably too weak binding that makes short motifs embedded in disordered regions non-functional.
Both PrPC and the above ZIPs belong to a small group of proteins known to be able to concomitantly bind multiple divalent metal ions through histidine-containing motifs embedded in N-terminal repeat sequences [19], [27].
Moreover, we implemented an algorithm for the detection of RNA motifs as well as protein RNA binding domains, which will help to retrieve recognition motifs embedded in sequences.
Future work should be devoted to analyzing how the coexistence of different motifs embedded in a large network affects their dynamics and abundance compared to the single motif analysis performed in this work.
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