Measurement of 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection

Mechanisms of coherent re-arrangement for long-lived spin order

Long-lived spin order-based approaches for magnetic resonance rely on the transition between two magnetic environments of different symmetries, one governed by the magnetic field of the spectrometer and the other where this strong magnetic field is inconsequential. Research on the excitation of magnetic-symmetry transitions in nuclear spins is a scientific field that debuted in Southampton in the year 2000. We advanced in this field carrying the baggage of pre-established directions in NMR spectroscopy. We propose to reveal herein the part of discoveries that may have been obscured by our choice to only look at them through the experience of such pre-established directions at the time. The methodological developments that are emphasised herein are the mechanisms of translation between the symmetric and non-symmetric environments with respect to the main magnetic field B 0 . More specifically, we look again thoroughly at zero-quantum rotations in the starting blocks of long-lived state populations, magnetisation transfers between hyperpolarised heteronuclei, and protons. These pulse sequences seed subsequent magnetic mechanisms that contribute to further applications. For instance, we show how some of the introduced coherence rotations were combined with classical pulse blocks to obtain two-dimensional correlations between protons and heteronuclei. We hope the pulse sequence building blocks discussed herein will open further perspectives for magnetic resonance experiments with long-lived spin order.

15N transverse relaxation measurements for the characterization of µs-ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange

¹⁵N R₂ relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide-water exchange can severely skew Hahn-echo based ¹⁵N R₂ relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the ¹⁵N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. This results in an artificial increase of the measured apparent ¹⁵N R₂ rate constants-which should not be mistaken with protein inherent chemical exchange contributions, R_ex, to ¹⁵N R₂. For measurements of ¹⁵N R₂ rate constants of IDPs and folded proteins at physiological temperatures and pH, we recommend therefore the use of a very low D₂O molar fraction in the sample buffer, as low as 1%, or the use of an external D₂O reference along with a modified ¹⁵N R₂ Hahn-echo based experiment. This combination allows for the measurement of R_ex contributions to ¹⁵N R₂ originating from conformational exchange in a time window from µs to ms.

Nitrogen-detected TROSY yields comparable sensitivity to proton-detected TROSY for non-deuterated, large proteins under physiological salt conditions

Direct detection of the TROSY component of proton-attached (15)N nuclei ((15)N-detected TROSY) yields high quality spectra with high field magnets, by taking advantage of the slow (15)N transverse relaxation. The slow transverse relaxation and narrow line width of the (15)N-detected TROSY resonances are expected to compensate for the inherently low (15)N sensitivity. However, the sensitivity of (15)N-detected TROSY in a previous report was one-order of magnitude lower than in the conventional (1)H-detected version. This could be due to the fact that the previous experiments were performed at low salt (0-50 mM), which is advantageous for (1)H-detected experiments. Here, we show that the sensitivity gap between (15)N and (1)H becomes marginal for a non-deuterated, large protein (τ c = 35 ns) at a physiological salt concentration (200 mM). This effect is due to the high salt tolerance of the (15)N-detected TROSY. Together with the previously reported benefits of the (15)N-detected TROSY, our results provide further support for the significance of this experiment for structural studies of macromolecules when using high field magnets near and above 1 GHz.

Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR

Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.

NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines

Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).

H/D exchange of a 15N labelled Tau fragment as measured by a simple Relax-EXSY experiment

We present an equilibrium H/D exchange experiment to measure the exchange rates of labile amide protons in intrinsically unfolded proteins. By measuring the contribution of the H/D exchange to the apparent T₁ relaxation rates in solvents of different D₂O content, we can easily derive the rates of exchange for rapidly exchanging amide protons. The method does not require double isotope labelling, is sensitive, and requires limited fitting of the data. We demonstrate it on a functional fragment of Tau, and provide evidence for the hydrogen bond formation of the phosphate moiety of Ser214 with its own amide proton in the same fragment phosphorylated by the PKA kinase.

Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins

(15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We anticipate that the new experiment will be a valuable addition to the NMR toolbox for studies of IDPs.

Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding

A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself.

A study on the influence of fast amide exchange on the accuracy of (15)N relaxation rate constants

(15)N relaxation rates of amide moieties provide insight both into global as well as local backbone dynamics of peptides and proteins. As the differences in the relaxation rates in general are small, their accurate determination is of prime importance. One potential source of error is fast amide exchange. It is well known that in its presence the effects of saturation transfer and H/D exchange may result in erroneous apparent relaxation rates R (1) and R (2). Here, the extent of these errors is rigorously examined. Theoretical considerations reveal that even when saturation effects are absent, H/D exchange will easily result in significant deviations from the true values. In particular overestimations of up to 10 % in R (1) and up to 5 % in R (2) are observed. An alternative scheme for fitting the relaxation data to the corresponding exponentials is presented that in the best cases not only delivers more accurate relaxation rates but also allows extracting estimates for the exchange rates. The theoretical computations were tested and verified for the case of ubiquitin.

Speeding up direct (15)N detection: hCaN 2D NMR experiment

Experiments detecting low gyromagnetic nuclei have recently been proposed to utilize the relatively slow relaxation properties of these nuclei in comparison to (1)H. Here we present a new type of (15)N direct-detection experiment. Like the previously proposed CaN experiment (Takeuchi et al. in J Biomol NMR 47:271-282, 2010), the hCaN experiment described here sequentially connects amide (15)N resonances, but utilizes the initial high polarization and the faster recovery of the (1)H nucleus to shorten the recycling delay. This allows recording 2D (15)N-detected NMR experiments on proteins within a few hours, while still obtaining superior resolution for (13)C and (15)N, establishing sequential assignments through prolines, and at conditions where amide protons exchange rapidly. The experiments are demonstrated on various biomolecules, including the small globular protein GB1, the 22 kDa HEAT2 domain of eIF4G, and an unstructured polypeptide fragment of NFAT1, which contains many SerPro sequence repeats.

Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G

We performed density functional calculations of backbone (15)N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3. The applicability of several computational models developed previously (Cai et al. in J Biomol NMR 45:245-253, 2009) to compute (15)N shielding tensors of alpha-helical residues is assessed. We show that the proposed quantum chemical computational model is capable of predicting isotropic (15)N chemical shifts for an entire protein that are in good correlation with experimental data. However, the individual components of the predicted (15)N shielding tensor agree with experiment less well: the computed values show much larger spread than the experimental data, and there is a profound difference in the behavior of the tensor components for alpha-helix/turns and beta-sheet residues. We discuss possible reasons for this.

Solution-state nuclear magnetic resonance spectroscopy and protein folding

A protein undergoes a variety of structural changes during its folding and misfolding and a knowledge of its behaviour is key to understanding the molecular details of these events. Solution-state NMR spectroscopy is unique in that it can provide both structural and dynamical information at both high-resolution and at a residue-specific level, and is particularly useful in the study of dynamic systems. In this chapter, we describe NMR strategies and how they are applied in the study of protein folding and misfolding.

Variation in quadrupole couplings of alpha deuterons in ubiquitin suggests the presence of C(alpha)-H(alpha)...O=C hydrogen bonds

Nuclear quadrupolar couplings are sensitive probes of hydrogen bonding. Experimental quadrupolar coupling constants of alpha deuterons (D(alpha) QCC) are reported for the residues of human ubiquitin that do not experience large-amplitude internal dynamics on the pico- to nanosecond time scale. Two different methods for D(alpha) QCC estimation are employed: (i) direct estimation of D(alpha) QCC values from R(1) and R(2) (2)H D(alpha) rates using the dynamics parameters (S(C(alpha)-H(alpha))(2)) derived from 1 micros molecular dynamics simulations as well as from (13)C(alpha) relaxation measurements and (ii) indirect measurements via scalar relaxation of the second kind that affects (13)C(alpha) relaxation rates in (13)C(alpha)-D(alpha) spin systems. A relatively large variability of D(alpha) QCC values is produced by both methods. The average value of 170.6 +/- 3 kHz is derived from the combined data set, with D(alpha) QCC values ranging from 159.2 to 177.2 kHz. The set of lowest quadrupolar couplings in all data sets corresponds to the residues that are likely to form weak C(alpha)-H(alpha)...O=C hydrogen bonds as predicted from the analysis of short H(alpha)...O distances in three-dimensional structures of ubiquitin. These D(alpha) nuclei show up to 10 kHz reduction in their QCC values, which is in agreement with earlier solid-state NMR measurements in alpha deuterons of glycine. A statistically significant correlation is observed between the QCC values of alpha-deuterons and the inverse cube of C(alpha)-H(alpha)...O=C distances in ubiquitin.

Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments

Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low gamma nuclei, such as (13)C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel (15)N direct-detection experiments. The CAN experiment sequentially connects amide (15)N resonances using (13)C(alpha) chemical shift matching, and the CON experiment connects the preceding (13)C' nuclei. When starting from the same carbon polarization, the intensities of nitrogen signals detected in the CAN or CON experiments would be expected four times lower than those of carbon resonances observed in the corresponding (13)C-detecting experiment, NCA-DIPAP or NCO-IPAP (Bermel et al. 2006b; Takeuchi et al. 2008). However, the disadvantage due to the lower gamma is counteracted by the slower (15)N transverse relaxation during detection, the possibility for more efficient decoupling in both dimensions, and relaxation optimized properties of the pulse sequences. As a result, the median S/N in the (15)N observe CAN experiment is 16% higher than in the (13)C observe NCA-DIPAP experiment. In addition, significantly higher sensitivity was observed for those residues that are hard to detect in the NCA-DIPAP experiment, such as Gly, Ser and residues with high-field C(alpha) resonances. Both CAN and CON experiments are able to detect Pro resonances that would not be observed in conventional proton-detected experiments. In addition, those experiments are free from problems of incomplete deuterium-to-proton back exchange in amide positions of perdeuterated proteins expressed in D(2)O. Thus, these features and the superior resolution of (15)N-detected experiments provide an attractive alternative for main chain assignments. The experiments are demonstrated with the small model protein GB1 at conditions simulating a 150 kDa protein, and the 52 kDa glutathione S-transferase dimer, GST.

Estimating quadrupole couplings of amide deuterons in proteins from direct measurements of 2H spin relaxation rates

The measurements of longitudinal and transverse 2H spin relaxation rates of backbone amide deuterons (D(N)) in the [U-13C,15N]-labeled protein ubiquitin show that the utility of amide deuterons as probes of backbone order in proteins is compromised by substantial variability of D(N) quadrupolar coupling constants (QCC) from one amide site to another. However, using the dynamics parameters of 15N-2H bond vectors evaluated from 15N relaxation data, site-specific QCC values can be estimated directly from D(N)R1 and R2 rates providing useful information on hydrogen bonding in proteins. In agreement with previous indirect scalar relaxation-based measurements, the D(N) QCC values estimated directly from R1 and R2 2H relaxation rates correlate with the inverse cube of the X-ray structure-derived hydrogen bond distances in ubiquitin: QCC=(232+/-2.3)+(118+/-17) summation operator(i)(cosalpha)r(i)(-3) where r is the inter-nuclear hydrogen bond distance in ångströms, and alpha is the N-D....O(i) angle.

Density functional calculations of 15N chemical shifts in solvated dipeptides

We performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on 15N chemical shielding in proteins. We used N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) as model systems. In addition, calculations were performed for selected fragments from protein GB3. The conducting polarizable continuum model was employed to include the effect of solvent in the density functional calculations. Our calculations for NMA show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic 15N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard beta-sheet and alpha-helical conformations ranges from 0.8 to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the 15N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins.

Co-acquisition of hyperpolarised 13C and 15N NMR spectra

Recent developments in dynamic nuclear polarisation now allow significant enhancements to be generated in the cryo solid state and transferred to the liquid state for detection at high resolution. We demonstrate that the Ardenkjaer-Larsen method can be extended by taking advantage of the properties of the trityl radicals used. It is possible to hyperpolarise 13C and 15N simultaneously in the solid state, and to maintain these hyperpolarisations through rapid dissolution into the liquid state. We demonstrate the almost simultaneous measurement of hyperpolarised 13C and hyperpolarised 15N NMR spectra. The prospects for further improvement of the method using contemporary technology are also discussed.

TROSY of side-chain amides in large proteins

By using the mixed solvent of 50% H2O/50% D2O and employing deuterium decoupling, TROSY experiments exclusively detect NMR signals from semideuterated isotopomers of carboxamide groups with high sensitivities for proteins with molecular weights up to 80 kDa. This isotopomer-selective strategy extends TROSY experiments from exclusively detecting backbone to both backbone and side-chain amides, particularly in large proteins. Because of differences in both TROSY effect and dynamics between 15N-H(E){D(Z)} and 15N-H(Z){D(E)} isotopomers of the same carboxamide, the 15N transverse magnetization of the latter relaxes significantly faster than that of the former, which provides a direct and reliable stereospecific distinction between the two configurations. The TROSY effects on the 15N-H(E){D(Z)} isotopomers of side-chain amides are as significant as on backbone amides.

Measuring fast hydrogen exchange rates by NMR spectroscopy

We introduce a method to measure hydrogen exchange rates based on the observation of the coherence of a neighboring spin S such as (15)N that has a scalar coupling J(IS) to the exchanging proton I. The decay of S(x) coherence under a Carr-Purcell-Meiboom-Gill (CPMG) multiple echo train is recorded in the presence and absence of proton decoupling. This method allows one to extract proton exchange rates up to 10(5)s(-1). We could extend the pH range for the study of the indole proton in tryptophan, allowing the determination of the exchange constants of the cationic, zwitterionic, and anionic forms of tryptophan.