It was thus of interest to examine the possibility of differential hydrogen bonding patterns between the stereoisomeric hydroxyl groups and the DNA.
However, the structural data does not support the notion that the R, R- and S, S-DHB-dA adducts exhibit differential hydrogen bonding patterns between the stereoisomeric hydroxyls and the DNA.
Inspection of the Pikp-HMA/AVR-PikD complex, with the His-to-Asn mutated in silico, confirms a very different predicted hydrogen-bonding pattern between the proteins.
After removal of the protection groups and cleavage from the resin, the linear peptide needs to be refolded to generate the correct secondary and tertiary structure including the formation of the correct disulfide bond pattern between the cysteine residues present in the polypeptide chain.
As a potential component of the conformational transition that underlies this line-broadening behaviour, it may be noted that the canonical antiparallel hydrogen-bonding pattern between the β2 and β3a strands is disrupted by the amides of both Phe and Asp being oriented towards the carbonyl oxygen of Gly with the Asp amide being just beyond hydrogen-bonding distance.
Cellulose-urea interaction energy and hydrogen bond number were also calculated as a function of temperature and the result of calculation further proved the hypothesis that there exists a dominative hydrogen bonding pattern between cellulose and urea, in which oxygen atoms of urea as proton-acceptors and hydroxyl hydrogen atoms of cellulose as proton-donors.
Ly-6 superfamily members have a conserved Ly-6 domain that is defined by a distinct disulfide bonding pattern between eight or ten cysteine residues.
The more prevalent residues at this position on C. elegans are Glutamine (25.7 %), Serine (12.5 %) and Glutamate (11.0 %), ranging, so, significantly, in chain size, charge and hydrogen bonding pattern even between the three more representative residues.
Indeed, PubChem standardization protocols can "correct" the nitrogen atom type as highlighted in these cases, however, it is worth mentioning that such fixes consider the larger atom environment (r > 0) and often modify several atom types and respective bonding patterns between them, as opposed to a systemic fix considering only a single atom type (r = 0).
The hydrogen bond patterns between mainchain atoms in protein structures not only give rise to regular secondary structures but also satisfy mainchain hydrogen bond potential.
