Density functional calculations of chemical shielding of backbone 15N in helical residues of protein G

Abstract

Summary We performed density functional calculations of backbone 15N chemical shielding tensors in selected helical residues of protein G. Here we describe a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone 15N. We analyzed the role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field. Our results show that the dipole moment of the α-helix can cause significant deshielding of 15N; therefore, it needs to be considered when calculating 15N chemical shielding. We found that it is important to include interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. Chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data.

Ultrahigh resolution protein structures using NMR chemical shift tensors

“…5C), δ 22 is approximately 97°AE 12°f rom the 1 H-15 N vector and δ 33 is oriented near the N-Cα bond, in or within 10°of the peptide plane (approximately 75°AE 12°f rom the 1 H-15 N bond). All CST orientations are shown in Table S2 and are in good accord with recent ab initio studies (45). Of particular interest is the observation that our tensor measurements indicate the 15 N tensor deviates from ideal prolate symmetry, with η ranging from 0.15 to 0.32.…”

“…Overall, the greatest deviations between theory and experiment are for angles near 90°, a known weak region for tensor correlation experiments, and a disproportionate number of these angles are in the α-helix. It is possible that some effects not included in the ab initio calculations, such as the helix dipole, might make a contribution to the 13 Cα shielding in this region, and such effects are indeed important in computing helical 15 N shifts (45). This issue might be addressed in the future by implementing even stronger 13 C (CST)-( 15 N-13 C) correlations, by using ROCSA-REDOR type correlations.…”

Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation

“…GB3 and its close homolog GB1 have played a central role in the efforts to determine amide 15 N chemical shift tensors by solution phase relaxation, liquid crystal and cross-correlated relaxation, and solid state magicangle measurements as well as quantum mechanics predictions [24][25][26]. The magnetic field dependent 15 N relaxation measurements of Hall and Fushman [20] deduced a range of residue-specific CSA values from 111.3 to 240.8 ppm for GB3.…”

“…Thus in contrast to larger proteins for which the T 1 values of the well-ordered amides increases proportionate to τ c , the T 1 values of such residues in GB3 are less sensitive to the effective τ c than are the T 2 values. This relaxation behavior has also contributed to GB3 and its close homolog GB1 having become the favorite system for analyzing residue-dependent variations in the amide 15 N chemical shift tensor by magnetic field dependent solution phase relaxation measurements [20], liquid crystal and cross-correlated relaxation measurements [21], and solid state magic-angle measurements [22,23] as well as quantum mechanics predictions [24][25][26]. The present analysis provides an effective basis for assessing the utility of the sitespecific 15 N chemical shift anisotropy (CSA) values obtained by these various experimental techniques in providing NMR relaxation predictions.…”

Calculation of chemical shift anisotropy in proteins

“…More recently, Czinki and coworkers mapped the 15 N and 13 C CSA surface using L-Ala-NH 2 as a model for peptides and proteins (Czinki et al, 2007). Cai et al (2009; 2011) also calculated the 15 N chemical shift tensors of the selected residues in GB3 protein using a variety of peptide models. While these recent studies provide some understanding to the influence of protein geometry on chemical shift tensors, the effects of the complete protein environment remains to be assessed quantitatively.…”