Fig. 2: Structure of a Gln-based single α-helix.
From: A glutamine-based single α-helix scaffold to target globular proteins
a 15N NMR relaxation data for main chain (NH) and Gln side chain (Nε) amide groups of peptide (P3-7)2, measured at 14.1 and 18.8 T at 278 K in 10% D2O (main chain) and 50% D2O (side chain). Left: 15N R2/R1 ratios, error bars represent the error-propagated SD of both exponential decay fits to R1 and R2 data and solid horizontal lines represent the theoretical R2/R1 ratio of a rigid body in isotropic motion with τc = 4.5 ns, whose field dependency agrees well with the experimental data. Right: 15N{1H} heteronuclear NOE, where the error bars correspond to the NOE SD71 and the shade corresponds to the region with the highest degree of structuration. b Spectral densities derived by reduced spectral density mapping of all 15N relaxation data: the dashed line corresponds to the behavior expected for a polypeptide. c Strips from a 3D 15N-edited TOCSY-HSQC spectrum showing the Hβ and Hγ resonances of all four Gln residues in (P3-7)2. d Residue-specific CoMAND fitting of NOE signal intensities from the 3D CNH-NOESY spectrum of (P3-7)2. Top: example measured and back-calculated 1D 13C traces (Gln14 main chain N, a99sb-disp frame pool). Bottom: average R-factors obtained from 100 CoMAND iterations using either frame pool. e Density plots and mean values of the fraction of mt rotamer found in the 100 fitting iterations for all four Gln residues. The fraction of helical glutamines in mt configuration in the BBDep dataset25 is shown in blue f Probability density for Gln14 χ1 and χ2 derived using the Gaussian mixture model (GMM). g Structural ensemble of (P3-7)2, with main chain conformations selected by CoMAND from both trajectory pools and side chain conformations generated by GMM sampling. Top: one of 20 global ensemble calculations aligned for the Leu10-Gln14 pair. Bottom: same iteration aligned for the Leu13-Gln17 pair. h Residual dipolar couplings (RDCs) for the main chain 1H-15N moieties and relaxation-derived main chain spectral density at zero frequency, J(0). i Correlation between experimental and back-calculated RDCs.
