It uses the local and global structural properties of the entire NOE network in comparison to the available tridimensional protein structure, to obtain assignment constraints.
Using standard 2D ssNMR spectra (e.g., Figure 1a,b), we obtained assignments for the labeled residues.
The obtained assignments validated and reproduced several previous assignments, and in all cases, the chemical shifts of the labeled httNT sites are indicative of α-helical secondary structure.
This was done by first collapsing the obtained assignments (by a given method) at or below the desired taxonomic level of comparison and subsequently enumerating the same.
Given the joint probability density function outlined in Equation 1, our original problem reduces to obtaining assignments for the interaction variables and the parameters θ X and θ Y that maximize it.
Via 2D MAS ssNMR experiments on the mature aggregates, we obtained assignments for five httNT residues: L4, K6, L7, M8, and A10 (e.g., Figure S3 and Table S2 of the Supporting Information BMRBB entry 25146).
We obtained assignments for some of these cross-peaks using triple resonance experiments as described (Chen et al., 2002) and found that they generally were at similar positions to those observed for free H,N-Syb (e.g., for A67, A69, A72, A74, W89 and K91; compare Figure 5B, orange contours, with Figure 5 figure supplement 1A).
We start by rounding the entries (x^{(n)}_{i,j}) to the closest integer, and then we check if the obtained assignment matrix is part of the set (mathcal {X}).
NOE net employs a complete search algorithm, giving no guarantee for a limited runtime, but ensuring the correctness of the obtained assignment ensemble.
