Figure 5 shows the geometric average backbone structure from the 20 NMR kurtoxin models superimposed on the backbones of AaH II (antimammal α-toxin), LqhαIT (anti-insect α-toxin), and BmK M1 (α-like toxin).
One basic idea of my current project is to apply the rotamer library, the geometry relationship, and the backbone structure computed from the RDC-EXACT method to help NOE assignment.
Overlaying the backbone structures of the four binding helices from both complexes – based on a pair-wise alignment of the complete domains – shows only minor variability in conformation, with the most occurring at the helix spanning residues 216 to 228.
The important points in collagen biosynthesis are thus the positioning of the hydroxylproline residues in the triple backbone structure, the knipping off of the propeptides from procollagen to form collagen as it leaves the cell and finally the cross-linking to form fibers.
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.
A shift in the position of a characteristic Raman band, initially located at ∼1095 cm−1, emanating from the backbone structure of the cellulose polymer chains was followed under tensile deformation.
MOTIF-EM also gives relative geometric rigid body transformation matrices needed to dock/fit the extracted conserved domains from the Cα backbone structure into the cryoEM map.
However, these tools does not perform well when predicting side-chain structures from predicted backbone structures.
Several side-chain prediction tools have been proven to predict accurate side-chain structures from native backbone structures [ 8, 9, 25, 26].
For an idealized protein backbone structure, the coordinates of O, H and C β backbone atoms can be calculated from the coordinates of n, C α and C backbone atoms.
