Cross-correlations between low-γ nuclei in solids via a common dipolar bath

Protonation tuned dipolar order mediated 1H→13C cross-polarization for dissolution-dynamic nuclear polarization experiments

A strategy of dipolar order mediated nuclear spin polarization transfer has recently been combined with dissolution-dynamic nuclear polarization (dDNP) and improved by employing optimized shaped radiofrequency pulses and suitable molecular modifications. In the context of dDNP experiments, this offers a promising means of transferring polarization from high-gamma ¹H spins to insensitive ¹³C spins with lower peak power and lower energy compared with state-of-the-art cross-polarization schemes. The role of local molecular groups and the glassing matrix protonation level are both postulated to play a key role in the polarization transfer pathway via an intermediary reservoir of dipolar spin order. To gain appreciation of the mechanisms involved in the dipolar order mediated polarization transfer under dDNP conditions, we investigate herein the influence of the pivotal characteristics of the sample makeup: (i) revising the protonation level for the constituents of the DNP glass; and (ii) utilizing deuterated molecular derivatives. Experimental demonstrations are presented for the case of [1-¹³C]sodium acetate. We find that the proton sample molarity has a large impact on both the optimal parameters and the performance of the dipolar order mediated cross-polarization sequence, with the ¹³C signal build-up time drastically shortened in the case of high solvent protonation levels. In the case of a deuterated molecular derivative, we observe that the nearby ²H substituted methyl group is deleterious to the ¹H→¹³C transfer phenomenon (particularly at low levels of sample protonation). Overall, increased solvent protonation makes the dipolar order governed polarization transfer significantly faster and more efficient. This study sheds light on the influential sample formulation traits which govern the dipolar order-controlled transfer of polarization and indicates that the polarization transfer efficiencies of deuterated molecules can be boosted and reach high performances simply by adequate solvent protonation.

Pulse sequence and sample formulation optimization for dipolar order mediated 1H→13C cross-polarization

We have recently demonstrated the use of contactless radiofrequency pulse sequences under dissolution-dynamic nuclear polarization conditions as an attractive way of transferring polarization from sensitive 1H spins to insensitive 13C spins with low peak radiofrequency pulse powers and energies via a reservoir of dipolar order. However, many factors remain to be investigated and optimized to enable the full potential of this polarization transfer process. We demonstrate herein the optimization of several key factors by: (i) implementing more efficient shaped radiofrequency pulses; (ii) adapting 13C spin labelling; and (iii) avoiding methyl group relaxation sinks. Experimental demonstrations are presented for the case of [1-13C]sodium acetate and other relevant molecular candidates. By employing the range of approaches set out above, polarization transfer using the dipolar order mediated cross-polarization radiofrequency pulse sequence is improved by factors approaching ∼1.65 compared with previous results. Dipolar order mediated 1H→13C polarization transfer efficiencies reaching ∼76% were achieved using significantly reduced peak radiofrequency pulse powers relative to the performance of highly sophisticated state-of-the-art cross-polarization methods, indicating 13C nuclear spin polarization levels on the order of ∼32.1% after 10 minutes of 1H DNP. The approach does not require extensive pulse sequence optimization procedures and can easily accommodate high concentrations of 13C-labelled molecules.

Dipolar order mediated 1H → 13C cross-polarization for dissolution-dynamic nuclear polarization

Magnetic resonance imaging and spectroscopy often suffer from a low intrinsic sensitivity, which can in some cases be circumvented by the use of hyperpolarization techniques. Dissolution-dynamic nuclear polarization offers a way of hyperpolarizing 13 C spins in small molecules, enhancing their sensitivity by up to 4 orders of magnitude. This is usually performed by direct 13 C polarization, which is straightforward but often takes more than an hour. Alternatively, indirect 1 H polarization followed by 1 H → 13 C polarization transfer can be implemented, which is more efficient and faster but is technically very challenging and hardly implemented in practice. Here we propose to remove the main roadblocks of the 1 H → 13 C polarization transfer process by using alternative schemes with the following: (i) less rf (radiofrequency) power; (ii) less overall rf energy; (iii) simple rf-pulse shapes; and (iv) no synchronized 1 H and 13 C rf irradiation. An experimental demonstration of such a simple 1 H → 13 C polarization transfer technique is presented for the case of [1-13 C ]sodium acetate, and is compared with the most sophisticated cross-polarization schemes. A polarization transfer efficiency of ∼ 0.43 with respect to cross-polarization was realized, which resulted in a 13 C polarization of ∼ 8.7  % after ∼ 10  min of microwave irradiation and a single polarization transfer step.

Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing

An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on ¹⁵N-¹⁵N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks. This approach is versatile in terms of the parameters that can be specified to achieve the best-fit result. At a minimum the algorithm requires a continuous segment of the main-peak chemical shifts obtained from a uniformly labeled sample and a spin-exchanged experimental spectrum represented as a 2D matrix array. With selective labeling experiments, groups of chemical shifts corresponding to specific locations in the protein backbone can be fixed, thereby decreasing the sampling space. The output from the program consists of a list of top-score main peak assignments, which can be subjected to further scoring criteria until a consensus solution is found. The algorithm has first been tested on a synthetic spectrum with randomly generated chemical shifts and dipolar couplings for the main peaks. The original assignments have been successfully recovered for as many as 100 main peaks when residue-type information was used even in the presence of substantial spectral peak overlap. The algorithm was then applied to assigning two sets of experimental spectra to recover and confirm the previously established assignments in an automated fashion. For the 20-residue transmembrane domain of Pf1 coat protein reconstituted in magnetically aligned bicelles, the original assignment by Park et al. (2010) was recovered by the automated algorithm with additional input from 5 selectively labeled amino acid spectra. The second case considered was the 46 residue Pf1 bacteriophage from Thiriot et al. (2005) and Knox et al. (2010), of which 38 residues were fit. Automated fitting resulted in several possible assignments but not exactly the original assignment. By using a post-fitting filtering procedure based on the number of missed cross peaks and Pf1 helical structure, a consensus spectroscopic assignment is proposed covering 84% of the original assignment. While the automated assignment works best in spectra with well-resolved crosspeaks, it also tolerates substantial spectral crowding to yield reasonable assignments in the cases where ambiguity and degeneracy of possible assignment solutions are inevitable.

Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins

Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the ¹H-¹⁵N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the ¹⁵N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins.

Proton-detected 3D (14)N/(14)N/(1)H isotropic shift correlation experiment mediated through (1)H-(1)H RFDR mixing on a natural abundant sample under ultrafast MAS

In this contribution, we have demonstrated a proton detection-based approach on a natural abundant powdered l-Histidine HCl-H2O sample at ultrafast magic angle spinning (MAS) to accomplish (14)N/(14)N correlation from a 3D (14)N/(14)N/(1)H isotropic shift correlation experiment mediated through (1)H finite-pulse radio frequency-driven recoupling (fp-RFDR). Herein the heteronuclear magnetization transfer between (14)N and (1)H has been achieved by HMQC experiment, whereas (14)N/(14)N correlation is attained through enhanced (1)H-(1)H spin diffusion process due to (1)H-(1)H dipolar recoupling during the RFDR mixing. While the use of ultrafast MAS (90kHz) provides sensitivity enhancement through increased (1)H transverse relaxation time (T2), the use of micro-coil probe which can withstand strong (14)N radio frequency (RF) fields further improves the sensitivity per unit sample volume.

3D ¹⁵N/¹⁵N/¹H chemical shift correlation experiment utilizing an RFDR-based ¹H/¹H mixing period at 100 kHz MAS

Homonuclear correlation NMR experiments are commonly used in the high-resolution structural studies of proteins. While (13)C/(13)C chemical shift correlation experiments utilizing dipolar recoupling techniques are fully utilized under MAS, correlation of the chemical shifts of (15)N nuclei in proteins has been a challenge. Previous studies have shown that the negligible (15)N-(15)N dipolar coupling in peptides or proteins necessitates the use of a very long mixing time (typically several seconds) for effective spin diffusion to occur and considerably slows down a (15)N/(15)N correlation experiment. In this study, we show that the use of mixing proton magnetization, instead of (15)N, via the recoupled (1)H-(1)H dipolar couplings enable faster (15)N/(15)N correlation. In addition, the use of proton-detection under ultrafast MAS overcomes the sensitivity loss due to multiple magnetization transfer (between (1)H and (15)N nuclei) steps. In fact, less than 300 nL (∼1.1 micromole quantity) sample is sufficient to acquire the 3D spectrum within 5 h. Our results also demonstrate that a 3D (15)N/(15)N/(1)H experiment can render higher resolution spectra that will be useful in the structural studies of proteins at ultrafast MAS frequencies. 3D (15)N/(15)N/(1)H and 2D radio frequency-driven dipolar recoupling (RFDR)-based (1)H/(1)H experimental results obtained from a powder sample of N-acetyla-L-(15)N-valyl-L-(15)N-leucine at 70 and 100kHz MAS frequencies are presented.

Mechanism of dilute-spin-exchange in solid-state NMR

In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, (1)H-(1)H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of (15)N-(15)N spin-exchange mediated by (1)H-(1)H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the (1)H to an off-resonance frequency so that it is at the "magic angle" during the spin-exchange interval in the experiment, since the "magic angle" irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in (15)N-(15)N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the "forbidden" spin-exchange condition under "magic angle" irradiation results in (15)N-(15)N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.

Sensitivity and resolution enhancement of oriented solid-state NMR: application to membrane proteins

Oriented solid-state NMR (O-ssNMR) spectroscopy is a major technique for the high-resolution analysis of the structure and topology of transmembrane proteins in native-like environments. Unlike magic angle spinning (MAS) techniques, O-ssNMR spectroscopy requires membrane protein preparations that are uniformly oriented (mechanically or magnetically) so that anisotropic NMR parameters, such as dipolar and chemical shift interactions, can be measured to determine structure and orientation of membrane proteins in lipid bilayers. Traditional sample preparations involving mechanically aligned lipids often result in short relaxation times which broaden the (15)N resonances and encumber the manipulation of nuclear spin coherences. The introduction of lipid bicelles as membrane mimicking systems has changed this scenario, and the more favorable relaxation properties of membrane protein (15)N and (13)C resonances make it possible to develop new, more elaborate pulse sequences for higher spectral resolution and sensitivity. Here, we describe our recent progress in the optimization of O-ssNMR pulse sequences. We explain the theory behind these experiments, demonstrate their application to small and medium size proteins, and describe the technical details for setting up these new experiments on the new generation of NMR spectrometers.

Experiments optimized for magic angle spinning and oriented sample solid-state NMR of proteins

Structure determination by solid-state NMR of proteins is rapidly advancing as a result of recent developments of samples, experimental methods, and calculations. There are a number of different solid-state NMR approaches that utilize stationary samples, aligned samples, or magic angle spinning of unoriented "powder" samples, and depending on the sample and the experimental method they can emphasize the measurement of distances or angles, ideally both, as sources of structural constraints. Multidimensional correlation spectroscopy of low-gamma nuclei such as (15)N and (13)C is an important step for making resonance assignments and measurements of angular restraints in membrane proteins. However, the efficiency of coherence transfer predominantly depends upon the strength of the dipole-dipole interaction, and this can vary from site to site and between sample alignments, for example, during the mixing of (13)C and (15)N magnetization in stationary aligned and in magic angle spinning samples. Here, we demonstrate that the efficiency of polarization transfer can be improved by using adiabatic demagnetization and remagnetization techniques on stationary aligned samples, and proton assisted insensitive nuclei cross-polarization in magic angle sample spinning samples. The adiabatic cross-polarization technique provides an alternative mechanism for spin-diffusion experiments correlating (15)N/(15)N and (15)N/(13)C chemical shifts over large distances. Improved efficiency in cross-polarization with 40-100% sensitivity enhancements is observed in proteins and single crystals, respectively. We describe solid-state NMR experimental techniques that are optimal for membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. The techniques are illustrated with data from single crystals both of peptides and of membrane proteins in phospholipid bilayers.

Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy

The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional (13)C-(13)C chemical shift correlation spectra is presented. With the analyses of (13)C-(13)C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly (13)C labeled protein that are consistent with the high resolution structure of the M2 (22-62) protein (Sharma et al., Science 330(6003):509-512, 2010).

A spectroscopic assignment technique for membrane proteins reconstituted in magnetically aligned bicelles

Oriented-sample NMR (OS-NMR) has emerged as a powerful tool for the structure determination of membrane proteins in their physiological environments. However, the traditional spectroscopic assignment method in OS NMR that uses the "shotgun" approach, though effective, is quite labor- and time-consuming as it is based on the preparation of multiple selectively labeled samples. Here we demonstrate that, by using a combination of the spin exchange under mismatched Hartmann-Hahn conditions and a recent sensitivity-enhancement REP-CP sequence, spectroscopic assignment of solid-state NMR spectra of Pf1 coat protein reconstituted in magnetically aligned bicelles can be significantly improved. This method yields a two-dimensional spin-exchanged version of the SAMPI4 spectrum correlating the (15)N chemical shift and (15)N-(1)H dipolar couplings, as well as spin-correlations between the (i, i ± 1) amide sites. Combining the spin-exchanged SAMPI4 spectrum with the original SAMPI4 experiment makes it possible to establish sequential assignments, and this technique is generally applicable to other uniaxially aligned membrane proteins. Inclusion of an (15)N-(15)N correlation spectrum into the assignment process helps establish correlations between the peaks in crowded or ambiguous spectral regions of the spin-exchanged SAMPI4 experiment. Notably, unlike the traditional method, only a uniformly labeled protein sample is required for spectroscopic assignment with perhaps only a few selectively labeled "seed" spectra. Simulations for the magnetization transfer between the dilute spins under mismatched Hartmann Hahn conditions for various B (1) fields have also been performed. The results adequately describe the optimal conditions for establishing the cross peaks, thus eliminating the need for lengthy experimental optimizations.