Orientational constraints as three‐dimensional structural constraints from chemical shift anisotropy: The polypeptide backbone of gramicidin A in a lipid bilayer

Abstract

Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these constraints have been used to evaluate models for the channel conformation of gramicidin A. Of the three models used, the one experimentally derived model of gramicidin in sodium dodecyl sulfate micelles fits the data least well.

Density functional calculations of 15N chemical shifts in solvated dipeptides

“…A good agreement with the experimental data is also found for the angle β between the least shielded component (σ 11 ) of the 15 N shielding tensor and the NH bond. The values of β obtained here, from 13.5° to 19.8°, are well in the range of the experimental values (12°-24°) obtained by different NMR techniques, both solution and solid-state Oas et al 1987;Hiyama et al 1988;Shoji et al 1989;Mai et al 1993;Fushman et al 1998;Cornilescu and Bax 2000;Kurita et al 2003;Loth et al 2005;Hall and Fushman 2006;Vasos et al 2006). There seems to be a weak correlation between the β angle and secondary structure, with slightly smaller angles for the β-sheet than for the α-helix (mean β angles are 14.8° and 16.5°, respectively).…”

“…It is worth pointing out that in our data this difference arises primarily from σ 22 , which is systematically higher in α-helix (by 7.8 ppm on average), while the other two components of the 15 N shielding tensor (particularly σ 11 ) show a considerably smaller and less systematic difference between the β-sheet and α-helix conformations (see Tables 3, 4). The calculated 15 N CSA values also agree with the solid state NMR measurements in short peptides Oas et al 1987;Hiyama et al 1988;Shoji et al 1989;Mai et al 1993;Wu et al 1995). A good agreement with the experimental data is also found for the angle β between the least shielded component (σ 11 ) of the 15 N shielding tensor and the NH bond.…”

Continuity conditions and torsion angles from ssNMR orientational restraints

“…Using (6), (10) where (11) (12) Using (5), (13) The bond orientation cosines and the scalar triple products involving backbone bond vectors of a diplane with B 0 in (13) can be written in terms of the degeneracies using the peptide plane geometry and (8) as: (14) where (15) with (16) The equations in (15) and (16) were derived in [17] assuming ideal peptide plane geometry [26]. Here, (σ 11 , σ 22 , σ 33 ) are the principal values of the 15 N chemical shift tensor written in the order of increasing magnitude, β is the angle between the NH bond and the principal axis vector σ 33 (≈ 17° [17]), and ν ‖ is the NH dipolar coupling constant.…”

Protein structure in anisotropic environments: Development of orientational constraints

“…• smaller than for the rest of the amino acid residues (51,35,37). Ramamoorthy and co-workers have furthermore suggested the occurrence of nonzero values for glycine D (49).…”

“…With four valines, four leucines, and four tryptophans out of 15 amino acids in gramicidin A there are numerous identical dipeptide sequences for which the tensors can be compared. There are significant differences in the tensors for identical dipeptides even though the secondary structure is the same (51). Consequently subtle factors appear to have a significant influence on the tensor element magnitudes.…”