Interference between cross-correlated relaxation and the measurement of scalar and dipolar couplings by Quantitative J

More accurate 1J(CH) coupling measurement in the presence of 3J(HH) strong coupling in natural abundance

J couplings are essential for measuring RDCs (residual dipolar couplings), now routinely used to deduce molecular structure and dynamics of glycans and proteins. Accurate measurement of (1)J(CH) is critical for RDCs to reflect the true structure and dynamics in the molecule of interest. We report noticeable discrepancies between (1)J(CH) values measured with HSQC type pulse sequences in the (1)H dimension from those measured in the (13)C dimension for 17 sugars and show that these discrepancies arise from strong scalar coupling. In order to determine how to minimize errors in measuring (1)J(CH), we analyze the strong coupling effects in detail using the product operator-formalism and spectral simulations based on the solution of the Liouville equation (not considering relaxation effects) in the presence of strong coupling. We report that the apparent (1)J(CH) measured with 2D HSQC-based sequences in either dimension can be in error by up to 4 Hz and that the values measured in the (1)H dimension can disagree with those in the (13)C dimension by up to 7 Hz. We demonstrate that spectral simulations can reproduce the errors induced by strong coupling and that these can be used to extract true (1)J(CH) values. We find that the (1)J(CH) values measured using a modified Z-filtered coupled HSQC are still affected by strong coupling. We conclude that spectral simulation yields accurate (1)J(CH) with errors as low as 1% in the presence of strong coupling.

Measurement of (1)H-(15)N and (1)H-(13)C residual dipolar couplings in nucleic acids from TROSY intensities

Analogous to the recently introduced ARTSY method for measurement of one-bond (1)H-(15)N residual dipolar couplings (RDCs) in large perdeuterated proteins, we introduce methods for measurement of base (13)C-(1)H and (15)N-(1)H RDCs in protonated nucleic acids. Measurements are based on quantitative analysis of intensities in (1)H-(15)N and (13)C-(1)H TROSY-HSQC spectra, and are illustrated for a 71-nucleotide adenine riboswitch. Results compare favorably with those of conventional frequency-based measurements in terms of completeness and convenience of use. The ARTSY method derives the size of the coupling from the ratio of intensities observed in two TROSY-HSQC spectra recorded with different dephasing delays, thereby minimizing potential resonance overlap problems. Precision of the RDC measurements is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC reference spectrum, and is approximately given by 30/(S/N) Hz for (15)N-(1)H and 65/(S/N) Hz for (13)C-(1)H. The signal-to-noise ratio of both (1)H-(15)N and (1)H-(13)C spectra greatly benefits when water magnetization during the experiments is not perturbed, such that rapid magnetization transfer from bulk water to the nucleic acid, mediated by rapid amino and hydroxyl hydrogen exchange coupled with (1)H-(1)H NOE transfer, allows for fast repetition of the experiment. RDCs in the mutated helix 1 of the riboswitch are compatible with nucleotide-specifically modeled, idealized A-form geometry and a static orientation relative to the helix 2/3 pair, which differs by ca 6° relative to the X-ray structure of the native riboswitch.

15N-1H scalar coupling perturbation: an additional probe for measuring structural changes due to ligand binding

Chemical shift perturbation mapping of backbone amides is one of the most widely employed techniques in biomolecular NMR, providing residue-by-residue information on interaction interfaces, ligand binding, and chemical modification sites, even for samples where poor solubility, short lifetime, or large size precludes more sophisticated experimental approaches. Significant changes can also occur in the amide one-bond (15)N-(1)H scalar coupling constants for glutamine binding protein (GlnBP) due to ligand binding. Like chemical shift perturbations, large changes (>1 Hz) are seen near the site of glutamine binding, though perturbations also occur distant to the site. The coupling constant perturbations correlate with significant structural changes, especially changes in backbone hydrogen bonding. Thus, amide scalar coupling perturbation can serve as an adjunct to chemical shift perturbation, providing additional information on both short-range and longer-range, allosteric structural changes.

Improved accuracy of 15N-1H scalar and residual dipolar couplings from gradient-enhanced IPAP-HSQC experiments on protonated proteins

The presence of dipole-dipole cross-correlated relaxation as well as unresolved E.COSY effects adversely impacts the accuracy of (1)J(NH) splittings measured from gradient-enhanced IPAP-HSQC spectra. For isotropic samples, the size of the systematic errors caused by these effects depends on the values of (2)J(NHalpha), (3)J(NHbeta) and (3)J(HNHalpha). Insertion of band-selective (1)H decoupling pulses in the IPAP-HSQC experiment eliminates these systematic errors and for the protein GB3 yields (1)J(NH) splittings that agree to within a root-mean-square difference of 0.04 Hz with values measured for perdeuterated GB3. Accuracy of the method is also highlighted by a good fit to the GB3 structure of the (1)H-(15)N RDCs extracted from the minute differences in (1)J(NH) splitting measured at 500 and 750 MHz (1)H frequencies, resulting from magnetic susceptibility anisotropy. A nearly complete set of (2)J(NHalpha) couplings was measured in GB3 in order to evaluate whether the impact of cross-correlated relaxation is dominated by the (15)N-(1)H(alpha) or (15)N-(1)H(beta) dipolar interaction. As expected, we find that (2)J(NHalpha) < or = 2 Hz, with values in the alpha-helix (0.86 +/- 0.52 Hz) slightly larger than in beta-sheet (0.66 +/- 0.26 Hz). Results indicate that under isotropic conditions, N-H(N)/N-H(beta) cross-correlated relaxation often dominates. Unresolved E.COSY effects under isotropic conditions involve (3)J(HNHalpha) and J(NHalpha), but when weakly aligned any aliphatic proton proximate to both N and H(N) can contribute.

On the accurate measurement of amide one-bond 15N-1H couplings in proteins: effects of cross-correlated relaxation, selective pulses and dynamic frequency shifts

Amide one-bond 15N-1H scalar couplings of 15N- and [15N,2H]-isotopically enriched ubiquitin have been measured with the Quantitative J approach by monitoring NMR signal intensity modulation. Scalar couplings of the non-deuterated protein are in average approximately 0.6 Hz larger than values of deuterated ubiquitin. This deviation is 30 times the error derived from experiment reproducibility. Refocusing dipole/dipole cross-correlated relaxation decreases the discrepancy to approximately 0.1 Hz, suggesting that it likely originates from relaxation interference. Alternatively, the subtraction of J values obtained at different magnetic fields largely reduces the relaxation effects. In contrast, the dynamic frequency shift whose main contribution to 1J(15N-1H) arises from 15N chemical shielding anisotropy/NH dipole cross-correlation, is not eliminated by refocusing spin evolution under this interaction. Furthermore, the average difference of 1J(15N-1H) values at two magnetic fields closely agrees with the theoretical expected difference in the dynamic frequency shift.