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It was later refined by using C,N double quantum spectroscopy [137] and by modeling of the backbone structure in the vicinity of the metal ion based on the crystal structure of mouse ARD (PDB: 1VR3), which had become available and shows 23% sequence identity with ARD from K. oxytoca.
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We reasoned that if α-sheet is the novel backbone structure in toxic oligomers, then α−sheet peptides designed to be complementary to the structure in the oligomer should bind to the toxic oligomer and inhibit amyloidosis.
HA molecules are also present in cartilage matrix as the backbone structure in proteoglycan aggregates.
Firstly, it facilitates the representation of protein backbone structure in a summarized 1D-sequence making an economic pre-calculated database of the structural information.
This segment, however, adopts a different backbone structure in eNOS compared to iNOS and nNOS, and despite the relatively high mobility of this region, the polypeptide is closer to the conserved Tyr in eNOS, thus presenting a greater energy barrier to the conserved Tyr adopting the out-rotamer conformation.
The rule used to differentiate these resembles the distinction between regular and irregular backbone structure in proteins, in that both depend only on local chain conformation.
In summary, we have presented a novel NMR pulse sequence for probing local backbone structure in IDPs.
For the SH3 domain, the backbone structure variation in the family is also better recapitulated than in randomly perturbed backbones.
A negative amide II band is identified in the retinal ethylenic stretch region of CaChR1, which reflects along with amide I bands alterations in protein backbone structure early in the photocycle.
To address this, we compared the predicted side-chain structures given the native backbone structures and those given the predicted backbone structures in terms of free energy.
This is shown by checking the free energy differences between the idealized and the target protein backbone structures in Figure 6.
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