How Does an Amide-¹⁵N Chemical Shift Tensor Vary in Peptides?

Abstract

This study addresses a void in the existing literature on the amide-15 N chemical shift anisotropy (CSA) tensor of peptides: a systematic investigation of how the tensor varies in different peptides. Amide-15 N CSA tensors for several dipeptides are obtained using quantum chemical calculations, as well as for a series of model Ala-X and X-Ala sequences in both α-helical and β-sheet conformations (where X is one of the naturally occurring amino acids). The calculated values show a significant variation in both isolated and extended peptide structures. Hydrogen bonding at both the carbonyl group and the N-H bond of the peptide plane is shown to affect the principal values of the tensor. Calculations on model peptides indicate that the amide-15 N CSA tensor is dependent on atoms located within a distance of five bonds. Consequently, the tensor of a given peptide residue is unaffected by residues other than those adjacent to it, which implies that the amide-15 N CSA tensor should be considered in the context of tripeptide sequences. This further suggests that the amide-15 N CSA tensor of the second residue of a given tripeptide sequence may be extrapolated to the same sequence in any other polypeptide or protein, given the same backbone conformation and intermolecular environment. These conclusions will facilitate future NMR structural studies of proteins.

Density functional calculations of 15N chemical shifts in solvated dipeptides

“…This discrepancy may be well due to the fact that side-chain configuration averaging is not considered in our calculation. Figure 4c demonstrates that by applying the continuumonly model the magnitude of is reduced by ~13 ppm from that of Poon et al (Poon et al 2004). This reduction in the difference in shielding between the two secondary structures is due to the different deshielding effects the bulk water has for the two backbone conformations: the bulk water deshields 15 N by ~18 ppm in the α-helical conformation but only by ~5 ppm in the extended conformation of the β-sheet.…”

“…Comparison of the isotropic 15 N chemical shifts calculated in this study (red) with gas phase calculations (black) (Poon et al 2004) and statistically averaged experimental data (blue) (Wang and Jardetzky 2002) for each residue type. Panels (a) and (b) correspond to the α-helix and β-sheet conformations, respectively.…”

“…This difference in our calculation ranges from 0.76 ppm to 6.19 ppm with an average of 2.74 ppm. Now we would like to compare our results with the gas phase calculations of Poon et al (Poon et al 2004) who used the same dipeptide model but without structure optimization and solvent. Their gas phase calculations indicated that the difference in 15 N chemical shifts between the standard β-sheet and α-helix varies between 13.2 ppm and 24 ppm, with the average value of 15.8 ppm.…”

Variability of the 15N Chemical Shielding Tensors in the B3 Domain of Protein G from 15N Relaxation Measurements at Several Fields. Implications for Backbone Order Parameters

“…The 2η xy -η z method-This method utilizes a linear field dependence of the following combination of the cross-correlation rates: (13) which allows determination of the product, Δσ g ·J(0), directly from the slope m of the fitting line with zero intercept: (14) This approach has the advantage over the abovementioned methods in that (1) it is not affected by the possible conformational exchange contribution to R 2 and (2) it does not require correction for the high-frequency components of the spectral density (cf. Eqs.…”

Structure, Topology, and Tilt of Cell-Signaling Peptides Containing Nuclear Localization Sequences in Membrane Bilayers Determined by Solid-State NMR and Molecular Dynamics Simulation Studies

“…Errors on the reported tilt angles are estimated from the line widths observed in the chemical shift and dipolar coupling spectra. However, there could be additional contributions to the error from the variation of chemical shift tensors (57,64) from the model tensor used for these calculations and due to peptide dynamics that would have influenced the observed experimental parameters. Nevertheless, the reported tilt angles are in good agreement with results obtained from MD simulations, discussed below.…”