The required shift of the backbone to put the plus and minus side chains in the same position is more likely for linear motifs than for extensive interfaces between two folded proteins, since the latter are constrained by many additional contacts outside of the helix-binding groove.
A two-dimensional C−C dipolar-assisted rotational resonance (DARR(10)) spectrum, which can be considered the "fingerprint" of the protein, differentiates between peaks arising from α-helical residues and those from the β-barrel, based on C chemical shift of the backbone and side-chain carbon atoms.
Although we did not see a chemical shift perturbation of the backbone amide resonances of V351, close contact does not necessarily produce shift changes.
For example, for residue i of a target protein, a peak for N-HSQC at position (Ni, HNi) and a peak for HNCO at positions (Ni, HNi, Ci−1) are generated, where Ni, HNi and Ci−1 are experimentally assigned chemical shift values of backbone N and HN atoms for residues i, and a chemical shift value of the backbone C atom for residue i − 1, respectively.
Chemical shift assignments of the backbone amide 1H and 15N resonances were obtained for each titration point (Fig. 2B).
The random coil shift values of the backbone NH protons in AST3-88 and AMW3-130, especially in the His, DPhe, Arg, and Trp region, have negative random coil shift values between 0.2 and 0.3 ppm.
Recent chemical shift assignments of the backbone nitrogens, α and β carbons, and amide protons of the polymerase core and the LF domain of Dpo4 will likely facilitate future investigations of this nature at atomic resolution.
Chemical shift analysis of the backbone resonances with the TALOS+ algorithm [ 60] predicts Φ and Ψ torsion angles of (88, −7) for Gly in the major slow exchange state {X-ray structure [ 30] yields (103, −28)}, while torsion angles of (−59, −27) are predicted for the minor slow exchange state.
The chemical shift of the PHD1KDM5B backbone atoms amide 1H and 15N after H3K4me0 peptide binding was calculated using the following equation: Δ δ av = 0.5 × Δ δ ( NH) 2 + 0.2 × Δ δ 15 N 2 1 / 2. (B) Ribbon representation of free PHD1KDM5B.
Chemical shift-based prediction of the backbone torsion angles for the minor slow exchange state yielded a negative ϕ torsion angle for Gly as compared with a value of +103° reported in the 0.92 Å resolution structure of FKBP12 [ 31] (PDB code 2PPN).
This zinc binding is accompanied by a large shift in the backbone conformation of the 99-loop and by large movements of both His side-chains.
