Magnetization Transfer via Residual Dipolar Couplings: Application to Proton–Proton Correlations in Partially Aligned Proteins

A novel three-dimensional NMR experiment is reported that allows the observation of correlations between amide and other protons via residual dipolar couplings in partially oriented proteins. The experiment is designed to permit quantitative measurement of the magnitude of proton–proton residual dipolar couplings in larger molecules and at higher degree of alignments. The observed couplings contain data valuable for protein resonance assignment, local protein structure refinement, and determination of low-resolution protein folds.     

Measurement of Dipolar Couplings for Methylene and Methyl Sites in Weakly Oriented Macromolecules and Their Use in Structure Determination

A simple and effective method is described for simultaneously measuring dipolar couplings for methine, methylene, and methyl groups in weakly oriented macromolecules. The method is aJ-modulated 3D version of the well-known [¹H-¹³C] CT-HSQC experiment, from which theJand dipolar information are most accurately extracted by using time-domain fitting in the third, constant-time dimension. For CH₂-sites, the method generally yields only the sum of the two individual¹³C-¹H couplings. Structure calculations are carried out by minimizing the deviation between the measured sum, and the sum predicted for each methylene on the basis of the structure. For rapidly spinning methyl groups the dipolar contribution to the splitting of the outer¹³C quartet components can be used directly to constrain the orientation of the C-CH₃bond. Measured sidechain dipolar couplings are in good agreement with an ensemble of NMR structures calculated without use of these couplings.     

Accurate Measurement of Small Spin–Spin Couplings in Partially Aligned Molecules Using a Novel J-Mismatch Compensated Spin-State-Selection Filter

The accurate measurement of small spin–spin coupling constants in macromolecules dissolved in a liquid crystalline phase is important in the context of molecular structure investigation by modern liquid state NMR. A new spin-state-selection filter, DIPSAP, is presented with significantly reduced sensitivity to J-mismatch of the filter delays compared to previously proposed pulse sequences. DIPSAP presents an attractive new approach for the accurate measurement of small spin–spin coupling constants in molecules dissolved in anisotropic solution. Application to the measurement of ¹⁵N–¹³C′ and ¹H^N–¹³C′ coupling constants in the peptide planes of ¹³C, ¹⁵N labeled proteins demonstrates the high accuracy obtained by a DIPSAP-based experiment.     

Measurement of Cross Correlation between Dipolar Coupling and Chemical Shift Anisotropy in the Spin Relaxation ofC,N-Labeled Proteins

We present a simple method for extracting interference effects between chemical shift anisotropy (CSA) and dipolar coupling from spin relaxation measurements in macromolecules, and we apply this method to extracting cross-correlation rates involving interference of amide¹⁵N CSA and¹⁵N–¹H dipolar coupling and interference of carbonyl¹³C′ CSA and¹⁵N–¹³C′ dipolar coupling, in a small protein. A theoretical basis for the interpretation of these rates is presented. While it proves difficult to quantitatively separate the structural and dynamic contributions to these cross-correlation rates in the presence of anisotropic overall tumbling and a nonaxially symmetric chemical shift tensor, some useful qualitative correlations of data with protein structure can be seen when simplifying assumptions are made.     

Anisotropic Orientation of Lactate in Skeletal Muscle Observed by Dipolar Coupling in H NMR Spectroscopy

Double quantum (DQ), J-resolved (1)H NMR spectra from rat and bovine skeletal muscle showed a splitting frequency ( approximately 24 Hz) for the lactate methyl protons that varied with the orientation of the muscle fibers relative to the magnetic field. In contrast, spectra of lactate in solution consist of a J-coupled methyl doublet and a J-coupled methine quartet (J(HH) = 7 Hz) with no sensitivity to sample orientation. Spectra acquired in magnetic fields of 4.7, 7, and 11 T showed that the splitting was not due to inhomogeneities in magnetic susceptibility within the muscle, because the magnitude of the splitting did not scale with the strength of B(0) fields. Triple quantum coherence (TQC) spectra revealed two distinct transition frequencies on the methyl resonance. These frequencies resulted from intra-methyl and methine-methyl couplings in this four spin system (A(3)X). Decoupling experiments on the triple quantum coherence showed that the observed frequency splitting was due mainly to the dipolar interactions between the methine and methyl protons of the lactate molecule. Thus, all the proton resonances of the lactate molecules in muscle behave anisotropically in the magnetic field. Adequate design and interpretation of spectroscopic experiments to measure lactate in muscle, and possibly in any cell and organ which contain asymmetric structures, require that both the dipolar coupling described here and the well-known scalar coupling be taken into account.     

Measurement of Small One-Bond Proton–Carbon Residual Dipolar Coupling Constants in Partially Oriented C Natural Abundance Oligosaccharide Samples: Analysis of Heteronuclear JCH-Modulated Spectra with the BIRD Inversion Pulse

Two 2D J-modulated HSQC-based experiments were designed for precise determination of small residual dipolar one-bond carbon–proton coupling constants in ¹³C natural abundance carbohydrates. Crucial to the precision of a few hundredths of Hz achieved by these methods was the use of long modulation intervals and BIRD pulses, which acted as semiselective inversion pulses. The BIRD pulses eliminated effective evolution of all but ¹J_CH couplings, resulting in signal modulation that can be described by simple modulation functions. A thorough analysis of such modulation functions for a typical four-spin carbohydrate spin system was performed for both experiments. The results showed that the evolution of the ¹H–¹H and long-range ¹H–¹³C couplings during the BIRD pulses did not necessitate the introduction of more complicated modulation functions. The effects of pulse imperfections were also inspected. While weakly coupled spin systems can be analyzed by simple fitting of cross peak intensities, in strongly coupled spin systems the evolution of the density matrix needs to be considered in order to analyse data accurately. However, if strong coupling effects are modest the errors in coupling constants determined by the “weak coupling” analysis are of similar magnitudes in oriented and isotropic samples and are partially cancelled during dipolar coupling calculation. Simple criteria have been established as to when the strong coupling treatment needs to be invoked.     

Direct Refinement against Proton–Proton Dipolar Couplings in NMR Structure Determination of Macromolecules

The computational tools necessary for making use of ¹H–¹H dipolar couplings in macromolecular structure refinement are presented. Potentials are described for direct refinement against ¹H–¹H dipolar couplings of known sign as well as of unknown sign. In addition, a multiple potential is developed for prochiral protons whose stereospecific assignments are unknown. The utility of direct ¹H–¹H dipolar coupling refinement is illustrated using the small protein ubiquitin. It is shown that direct ¹H–¹H dipolar coupling refinement leads to improvements in the precision, accuracy, and quality of the resulting structures.     

Improved Estimation of CSA–Dipolar Coupling Cross-Correlation Rates from Laboratory-Frame Relaxation Experiments

We have investigated the underlying assumptions in estimating cross-correlation rates between chemical shift anisotropy (CSA) and dipolar coupling mechanisms in a scalar-coupled two-spin IS system, from laboratory frame relaxation experiments. It has been shown that for an arbitrary relaxation delay, the difference in relaxation rates of the individual components of an in-phase (or antiphase) doublet is not related to the CSA–dipolar coupling cross-correlation rate in a simple way. This is especially true in the case where the difference in the decay rates of the in-phase and antiphase terms of the density matrix becomes comparable to the magnitude of the scalar coupling between the two spins. Improved means of extracting cross-correlation rates in these cases are presented.     

H NMR Imaging of Residual Dipolar Couplings in Cross-Linked Elastomers: Dipolar-Encoded Longitudinal Magnetization, Double-Quantum, and Triple-Quantum Filters

Contrastfilters for NMR imaging of residual ¹H dipolar couplings of elastomers are introduced based on dipolar-encoded longitudinal magnetization, as well as double- and triple-quantum coherences. The spin response is discussed in the initial excitation time regime for methylene, methyl, and methine protons applicable to poly(isoprene) and other elastomers, taking into account the hierarchy of dipolar couplings and the associated editing features of multiple-quantum experiments. The efficiency of these filters is investigated for a series of cross-linked poly(isoprene) samples. Spatially resolved dipolar-encoded longitudinal magnetization decays and double-quantum and triple-quantum buildup curves are presented for a phantom made of poly(isoprene) with different cross-link densities. Two-dimensional images representing residual dipolar couplings are presented using dipolar-encoded longitudinal magnetization, double-quantum, and triple-quantum contrast filters. Images from dipolar-encoded longitudinal magnetization and triple-quantum coherences show the highest resolution and contrast, respectively.     

CHHC and H–H magnetization exchange: Analysis by experimental solid-state NMR and 11-spin density-matrix simulations

A protocol is presented for correcting the effect of non-specific cross-polarization in CHHC solid-state MAS NMR experiments, thus allowing the recovery of the ¹H–¹H magnetization exchange functions from the mixing-time dependent buildup of experimental CHHC peak intensity. The presented protocol also incorporates a scaling procedure to take into account the effect of multiplicity of a CH₂ or CH₃ moiety. Experimental CHHC buildup curves are presented for l-tyrosine·HCl samples where either all or only one in 10 molecules are U–¹³C labeled. Good agreement between experiment and 11-spin SPINEVOLUTION simulation (including only isotropic ¹H chemical shifts) is demonstrated for the initial buildup (t_mix < 100 μs) of CHHC peak intensity corresponding to an intramolecular close (2.5 Å) H–H proximity. Differences in the initial CHHC buildup are observed between the one in 10 dilute and 100% samples for cases where there is a close intermolecular H–H proximity in addition to a close intramolecular H–H proximity. For the dilute sample, CHHC cross-peak intensities tended to significantly lower values for long mixing times (500 μs) as compared to the 100% sample. This difference is explained as being due to the dependence of the limiting total magnetization on the ratio N_obs/N_tot between the number of protons that are directly attached to a ¹³C nucleus and hence contribute significantly to the observed ¹³C CHHC NMR signal, and the total number of ¹H spins into the system. ¹H–¹H magnetization exchange curves extracted from CHHC spectra for the 100% l-tyrosine·HCl sample exhibit a clear sensitivity to the root sum squared dipolar coupling, with fast buildup being observed for the shortest intramolecular distances (2.5 Å) and slower, yet observable buildup for the longer intermolecular distances (up to 5 Å).     

Recoupled Polarization Transfer Heteronuclear H–C Multiple-Quantum Correlation in Solids under Ultra-fast MAS

A new approach for high-resolution solid-state heteronuclear multiple-quantum MAS NMR spectroscopy of dipolar-coupled spin- nuclei is introduced. The method is a heteronuclear chemical shift correlation technique of abundant spins, like ¹H with rare spins, like ¹³C in natural abundance. High resolution is provided by ultra-fast MAS and high magnetic fields, high sensitivity being ensured by a direct polarization transfer from the abundant protons to ¹³C. In a rotor-synchronized variant, the method can be used to probe heteronuclear through-space proximities, while the heteronuclear dipolar coupling constant can quantitatively be determined by measuring multiple-quantum spinning-sideband patterns. By means of recoupling, even weak heteronuclear dipolar interactions are accessible. The capabilities of the technique are demonstrated by measurements on crystalline -tyrosine hydrochloride salt.     

Two Simple NMR Experiments for Measuring Dipolar Couplings in Asparagine and Glutamine Side Chains

Residual dipolar couplings are now widely used for structure determination of biological macromolecules. Until recently, the main focus has been on measurement of dipolar couplings in the protein main chain. However, with the aim of more complete protein structure, it is also essential to have information on the orientation of protein side chains. In addition, residual dipolar couplings can potentially be employed to study molecular dynamics. In this Communication, two simple NH(2) and spin-state edited experiments are presented for rapid and convenient determination of five residual dipolar couplings from (15)N, (1)H correlation spectrum in asparagine and glutamine side chains. The pulse sequences are demonstrated on two proteins, 30.4-kDa Cel6A in diluted liquid crystal phase and 18-kDa human cardiac troponin C in water.     

Semi-Constant-Time HMSQC (SCT-HMSQC-HA) for the Measurement of JHH Couplings in N-Labeled Proteins

A simple method for accurately measuring ³J_H^NH^α coupling constants in ¹⁵N-labeled proteins is described. This semi-constant-time HMSQC-HA experiment combines the rapidity and convenience of the recently introduced CT-HMQC-HA scheme (Postingl and Otting, J. Biomol. NMR 12, 319–324 (1998)) with the high resolution and robustness of the HSQC experiment. The proposed method is demonstrated for the 76-residue human ubiquitin and Saccharopolyspora erythraea calerythrin (176 residues). Our results imply that the SCT-HMSQC-HA experiment is suitable also for proteins with less favorable NMR properties due to its good resolution and sensitivity.     

Recoupled Polarization-Transfer Methods for Solid-State H–C Heteronuclear Correlation in the Limit of Fast MAS

An in-depth account of the effects of homonuclear couplings and multiple heteronuclear couplings is given for a recently published technique for ¹H–¹³C dipolar correlation in solids under very fast MAS, where the heteronuclear dipolar coupling is recoupled by means of REDOR π-pulse trains. The method bears similarities to well-known solution-state NMR techniques, which form the framework of a heteronuclear multiple-quantum experiment. The so-called recoupled polarization-transfer (REPT) technique is versatile in that rotor-synchronized ¹H–¹³C shift correlation spectra can be recorded. In addition, weak heteronuclear dipolar coupling constants can be extracted by means of spinning sideband analysis in the indirect dimension of the experiment. These sidebands are generated by rotor encoding of the reconversion Hamiltonian. We present generalized variants of the initially described heteronuclear multiple-quantum correlation (HMQC) experiment, which are better suited for certain applications. Using these techniques, measurements on model compounds with ¹³C in natural abundance, as well as simulations, confirm the very weak effect of ¹H–¹H homonuclear couplings on the spectra recorded with spinning frequencies of 25–30 kHz. The effect of remote heteronuclear couplings on the spinning-sideband patterns of CH_n groups is discussed, and ¹³C spectral editing of rigid organic solids is shown to be practicable with these techniques.     

Electron Spin–Nuclear Spin Cross-Correlation Effects on Multiplet Splittings in Paramagnetic Proteins

The effects of cross-correlation between Curie spin–nuclear dipole and nuclear dipole–nuclear dipole interactions on the linewidths and resonance frequencies of the individual lines of anAXmultiplet in paramagnetic systems have been calculated. The implication of the relaxation-induced frequency shift of the lines (dynamic frequency shift) for the accurate measurement of residual dipolar couplings in field-oriented systems has been discussed. Our simulations indicate that these effects may play a role in the precise measurement of residual dipolar couplings in systems which belong to the small and intermediate tumbling regime, i.e., correlation times less than 5 ns.     

Residual 31P, 35,37Cl dipolar coupling in 31P MAS spectra of chlorocyclophosphazenes

In ³¹P MAS NMR spectra of chlorocyclophosphazenes, characteristic splittings have been observed for PCl or PCl₂ groups. At different applied magnetic fields, the fine structure and total width of the patterns change in a characteristic way, demonstrating that the splittings are due to indirect spin–spin and residual dipolar interactions with the chlorine nuclei directly bonded to phosphorus. For trans-nongeminal N₃P₃Cl₃(NMe₂)₃ and N₃P₃Cl₆ as examples, the spectra have been analyzed to obtain information on chlorine nuclear quadrupole coupling constants and ^35,37Cl, ³¹P indirect spin–spin coupling constants. Neglect of these interactions may result in misinterpretations of the multiplicity in ³¹P MAS spectra of chlorophosphazenes.     

Sensitivity-enhanced IPAP experiments for measuring one-bond C–C and C–H residual dipolar couplings in proteins

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C'-13Calpha and 1Halpha-13Calpha dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2Delta. For cases of limited resolution in the 2D 15N-1HN HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.     

Optimization of Three-Dimensional TROSY-Type HCCH NMR Correlation of Aromatic H–C Groups in Proteins

Improved methods for three-dimensional TROSY-Type HCCH correlation involving protons of negligible CSA are presented. The TROSY approach differs from the conventional approach of heteronuclear decoupling in evolution and detection periods by not mixing fast and slowly relaxing coherences and usually suppressing the former. Pervushin et al. (J. Am. Chem. Soc. 120, 6394–6400 (1998)) have proposed a 3D TROSY-type HCCH experiment where the TROSY approach is applied only in one of the ¹³C dimensions. A new pulse sequence applying the TROSY approach in both indirect dimensions is advantageous when the TROSY effect of the carbons is large or when a relatively high resolution is required. For lower resolutions or moderate TROSY effects we show that it is possible to combine the best of both worlds, namely to suppress heteronuclear couplings without mixing fast and slowly relaxing coherences while at the same time superimpose the two components and thus have both contribute to the detected signal. That is possible using the novel technique of Spin-State-Selective Time-Proportional Phase Incrementation (S³ TPPI). The new 3D S³ TPPI TROSY HCCH method is demonstrated on a ¹³C,¹⁵N-labeled protein sample, RAP 18–112 (N-terminal domain of α₂-macroglobulin receptor associated protein), at 750 MHz and average sensitivity enhancements of 10% are obtained for the cross peaks in comparison to methods based on conventional decoupling on one of the carbons or on TROSY on both carbons.     

Quantitative Measurement of Transverse and Longitudinal Cross-Correlation betweenC–H Dipolar Interaction andC Chemical Shift Anisotropy: Application to aC-Labeled DNA Duplex

Measurement of both longitudinal and transverse relaxation interference (cross-correlation) between¹³C chemical shift anisotropy and¹³C–¹H dipolar interactions is described. The ratio of the transverse to longitudinal cross-correlation rates readily yields the ratio of spectral densitiesJ(0)/J(ω_C), independent of any structural attributes such as internuclear distance or chemical shift tensor. The spectral density at zero frequencyJ(0) is also independent of chemical exchange effects. With limited internal motions, the ratio also enables an accurate evaluation of the correlation time for overall molecular tumbling. Applicability of this approach to investigating dynamics has been demonstrated by measurements made at three temperatures using a DNA decamer duplex with purines randomly enriched to 15% in¹³C.