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Evolving a readily available helix-turn-helix protein into either PrgI or the Bcl-2 protein family seems like a simpler path than the conversion of a uniquely distinct fold to incorporate a core helix-turn-helix motif.
Different from the prion protein, which has a distinct fold, Tau protein is intrinsically disordered.
The macrodomain portion is made of a distinct fold containing a six stranded β-sheet between two α-helices.
Under both scenarios an exclusive monophyletic group or a distinct fold would have a unique conserved network of hydrophobic interactions.
These bacterial enzymes use CMP-NeuAc as a sugar donor and have a distinct fold that is also found in mammalian sialyltransferases.
In summary, the Dcr1 dsRBD is not only extended by C33 and zinc coordination but also adopts a very distinct fold compared with other dsRBDs.
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This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds.
We then test the performance of four different sequence representations of proteins (their native sequence, the sequence of their secondary-structure elements, and the local and global structural sequences based on our fragment library) with different classifiers in their ability to classify proteins that belong to five distinct folds of CATH.
The motivation was to have a method for superimposing protein structures independent of residue connectivity, thereby facilitating comparisons between proteins that have distinct folds and maximize side-chain as opposed to main-chain overlap.
It has recently been shown that two specific amino acid sequences with overwhelming identity (∼88%) adopt distinct folds, thus postulating that for the specific protein pair considered, only ∼12% of the amino acid sequence codes for sequence-to-structure mapping [47].
From that perspective, by considering solely distinct folds, we might be underestimating the total number of non-homologous enzyme pairs.
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