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In this fold of modeling of M ζ, an AP score is generated.
This residue is conserved in all mammalian PrP sequences, forms part of the α-fold mainstay Helix-3 and in this fold the side chain is in contact with hydrophobic residues located mainly on Helix-2 (Figure 1) [25].
In addition, we have compared these interactions in DTD with that in Pab-NTD to highlight the conservation of adenine recognition in this fold.
These structural features suggest that in precursors of the Nudix enzymes the β-GF domain most probably bound the substrate via the exposed face, as is common in this fold.
Proteins in this family adopt a fold that can be divided into four structurally distinct domains [ 31], and, of these, Domain IV is formed by the extreme C-terminal part of the protein and is the only domain in this fold that comprises a clear contiguous stretch of polypeptide chain (Supplementary Figure S2 at http://www.biochemj.org/bj/452/bj4520057add.htm).htm
In addition to the EndoU clade, our sequence comparisons indicated that several of the newly recovered BECR fold toxin domains from polymorphic toxin systems belong to other previously defined clades in this fold, such as barnase, colicin E5, and colicin D clades.
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In fact, this fold has been found in a wide range of proteins involved in very diverse cellular processes in which protein-protein interactions play an essential role.
Since the number of bonds in this folding is less than that of Figure 15, Algorithm 1 will choose the folding of Figure 15.
Cytosolic and signal transduction proteins show significant enrichment in this module (fold 5.07, P 1.25e-86; and fold 4.86, P 4.0e-55, respectively).
In fact this fold-change scenario has recently been shown to be the case.
Strikingly, it was found that mir-7, an up-regulated miRNA with high fold -change in this study (fold-change = 3.60) was not reported as a dysregulated miRNA in CRC in previous studies.
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