Comment 4: An important point when it comes to comparisons with experiment concerns the fact that most of the peptides are quite flexible, with the experimental NMR bundles in many cases exhibiting significant structural diversity.
Finally, an important point when it comes to comparisons with experiment concerns the fact that many peptides are quite flexible, with the experimental NMR bundles in many cases exhibiting significant structural diversity.
Furthermore, some standard measures of quality for one method cannot be calculated for other experimental methods, e.g. crystal resolution or NMR bundle RMSD.
We find excellent agreement between the methyl C chemical shifts and the side chain rotamers that are present in the solution structures of both complexes (binary KIX·MLL and ternary KIX·MLL·pKID), suggesting the conformation that is present in the NMR structural bundles represents the most populated rotameric state of isoleucine, leucine, and valine residues in all cases.
These spectra (shown in Figure S4) demonstrate the structures are predominantly alpha-helical, and similar to the spectra of designed 4-helix bundles solved previously by NMR [19], [20].
Samples displaying the bundled untwisted morphology gave less optimal NMR spectra, suggestive of increased disorder and significant sample heterogeneity, thus inhibiting detailed analysis.
For simulations of structures derived from NMR studies, the top ranked structure from the deposited bundle, representing the lowest energy structure, was selected.
Using high resolution NMR, we solved the structure (Protein Data Bank ID: 2I7U) of a prototypical dimeric four-α-helix bundle, (Aα2-L1M/L38M 2, with designed specific binding pockets for volatile anesthetics.
A structural investigation by NMR of the BD from one such coactivator, the acetyltransferase P/CAF, revealed a 4-helix-bundle fold with a prominent hydrophobic pocket.
Initial indications that this might be the case came from E.M. (Molony et al., 1987; Winkler et al., 1997), and recent NMR studies have shown that the talin F3 FERM domain binds to a 5-helix bundle (residues 1655 1822) in the talin rod masking the integrin-binding site in F3 in the process (Goksoy et al., 2008; Goult et al., 2009a).
Here, we have conducted a systematic measurement of inner gate fluctuations in KcsA using electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), and molecular dynamics (MD) simulations to evaluate the conformational space of the inner helical bundle during pH-induced gating.
