It looks like the conformations in comb1-2µs (red) and comb2-2µs (greenotnonlynly cover the most of conformational space sampled by single-2µs (black), but also reach a large portion of other regions in the essential subspace.
Surprisingly, our Aurelia RS strain did not contain the same small suggested peptide fragment sequence, but it is possible that other changes occurring in the Aurelia RS CL390-like sequence provide the conformation needed for its biological activity.
We speculate that Q47 might feature a PPII-like structure that resembles the conformation of the oligoPro-flanked polyQ tail prior to β-nucleation.
In the absence of the antibody, all complexes were shifted to the inactive-like conformation of the receptor, restoring the known contacts of the inactive state, that is, the inward position of F2826.44, the ionic interaction between R1313.50 and E2686.30, and the water clusters.
Aib was selected for the rational induction of the R-like helical conformation of the B1 B8 segment, as the amino acid with a high helical propensity that often facilitates folding into the right- or left-handed α-helices.
The reason the B-like conformation scores slightly better than the A-like is likely due to the fact that the deposited alternate A has a modest steric clash with Tyr b25 of the preceding helical turn.
We discovered that in addition to the ring-like conformation, the Z-ring of E. coli may adopt a variety of compressed helical conformations with tight pitches and variable lengths.
Similarly, the strength of the fit of geometric random graphs to the RIG of a predicted conformation might indicate how native-like the specific protein conformation is.
By contrast, in the ornithodorin-like conformation only the N-terminal peptide of the inhibitor interacts with thrombin active site, which is essentially unmodified compared to the free enzyme.
The hallmark LRR domain, responsible for the horseshoe-like conformation of the protein, is found in a functionally diverse set of proteins, and is typically involved in protein-protein interactions [55].
