Sensitivity enhancement using paramagnetic relaxation in MAS solid-state NMR of perdeuterated proteins

Previously, Ishii et al., could show that chelated paramagnetic ions can be employed to significantly decrease the recycle delay of a MAS solid-state NMR experiment [N.P. Wickramasinghe, M. Kotecha, A. Samoson, J. Past, Y. Ishii, Sensitivity enhancement in C-13 solid-state NMR of protein microcrystals by use of paramagnetic metal ions for optimizing H-1 T-1 relaxation, J. Magn. Reson. 184 (2007) 350-356]. Application of the method is limited to very robust samples, for which sample stability is not compromised by RF induced heating. In addition, probe integrity might be perturbed in standard MAS PRE experiments due to the use of very short duty cycles. We show that these deleterious effects can be avoided if perdeuterated proteins are employed that have been re-crystallized from D(2)O:H(2)O=9:1 containing buffer solutions. The experiments are demonstrated using the SH3 domain of chicken alpha-spectrin as a model system. The labeling scheme allows to record proton detected (1)H, (15)N correlation spectra with very high resolution in the absence of heteronuclear dipolar decoupling. Cu-edta as a doping reagent yields a reduction of the recycle delay by up to a factor of 15. In particular, we find that the (1)H T(1) for the bulk H(N) magnetization is reduced from 4.4s to 0.3s if the Cu-edta concentration is increased from 0mM to 250 mM. Possible perturbations like chemical shift changes or line broadening due to the paramagnetic chelate complex are minimal. No degradation of our samples was observed in the course of the experiments.     

Structural analysis of solid-state NMR measurements of peptides and proteins

A method for analyzing NMR measurements of peptides and proteins in terms of back-bone structure is presented. Various dipole, chemical-shift, and quadrupole interactions can be utilized to yield angles describing the orientations of individual peptide planes with respect to the magnetic field. The computer program LINK can then be used to join two peptide planes together and determine backbone torsion angles. Calculated and experimental examples are given.     

Rotor-synchronized dipolar-filter sequence at fast MAS in solid-state NMR

Dipolar filters are of considerable importance for eliminating the ¹H NMR signal of the rigid components of heterogeneous compounds while selecting the signal of their mobile parts. On the basis of such filters, structural and dynamical information of these compounds can often be acquired through further manipulations (e.g. spin diffusion) on the spin systems. To overcome the destructive interferences between the magic angle spinning (MAS) speed and the cycle-time of the widely-used Rotor-Asynchronized Dipolar Filter (RADF) sequence, we introduce a new method called Rotor-Synchronized Dipolar Filter (RSDF). This communication shows that this sequence does not present any interference with the spinning speed and is more compatible than RADF with high MAS frequencies (ν_R > 12 kHz). This new pulse sequence will potentially contribute to future researches on heterogeneous materials, such as multiphase polymer and membrane systems.     

Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins

Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the ¹⁵N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken α-spectrin, which was re-crystallized in H₂O/D₂O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu^II to enable rapid data acquisition.     

Enhanced resolution in proton solid-state NMR with very-fast MAS experiments

We present a new smooth amplitude-modulated (SAM) method that allows to observe highly resolved ¹H spectra in solid-state NMR. The method, which works mainly at fast or ultra-fast MAS speed (ν_R > 25 kHz) is complementary to previous methods, such as DUMBO, FSLG/PMLG or symmetry-based sequences. The method is very robust and efficient and does not present line-shape distortions or fake peaks. The main limitation of the method is that it requires a modern console with fast electronics that must be able to define the cosine line-shape in a smooth way, without any transient. However, this limitation mainly occurs at ultra-fast MAS where the rotation period is very short.     

NH-NH vector correlation in peptides by solid-state NMR

We present a novel solid-state magic angle-spinning NMR method for measuring the NH(i)-NH(i+1) projection angle θ(i,i+1) in peptides. The experiment is applicable to uniformly (15)N-labeled peptides and is demonstrated on the chemotactic tripeptide N-formyl-l-Met-l-Leu-l-Phe. The projection angle θ(i,i+1) is directly related to the peptide backbone torsion angles φ(i) and psi(i). The method utilizes the T-MREV recoupling scheme to restore (15)N-(1)H interactions, and proton-mediated spin diffusion to establish (15)N-(15)N correlations. T-MREV has recently been shown to increase the dynamic range of the (15)N-(1)H recoupling by gamma-encoding, and permits an accurate determination of the recoupled NH dipolar interaction. The results are interpreted in a quasi-analytical fashion that permits efficient extraction of the structural parameters.     

Advances in solid-state NMR of membrane proteins

Solid-state nuclear magnetic resonance (SSNMR) is an NMR spectroscopy applied to condensed-phase systems, including membrane proteins. Membrane protein fold and function are dependent upon interactions with surrounding bilayer components. Structural and functional analyses are thus challenging, and new approaches are needed to better characterise these systems. SSNMR is uniquely suited to the examination of membrane proteins in native environments, and has the capabilities to elucidate complex protein mechanisms and structures. Notable research implementing SSNMR is aimed at developing new strategies and technology to efficiently target membrane proteins within synthetic and biological membranes. Significant advances have been made: observation of protein function in native environments, emergence of in situ methods to examine integral proteins within natural membranes, sensitivity enhancement techniques and cutting-edge structure determination methods. We present how these advances are applied to answer outstanding questions in structural biology. Experiments have shown consistent results for protein investigations in biological membranes and synthetic lipid compositions, indicating that SSNMR is an innovative and direct approach for the study of these systems.     

Fast acquisition of multi-dimensional spectra in solid-state NMR enabled by ultra-fast MAS

The advantages offered by ultra-fast (>60 kHz) magic angle spinning (MAS) rotation for the study of biological samples, notably containing paramagnetic centers are explored.It is shown that optimal conditions for performing solid-state ¹³C NMR under 60 kHz MAS are obtained with low-power CW ¹H decoupling, as well as after a low-power ¹H,¹³C cross-polarization step at a double-quantum matching condition. Acquisition with low-power decoupling highlights the existence of rotational decoupling sidebands. The sideband intensities and the existence of first and second rotary conditions are explained in the framework of the Floquet–van Vleck theory.As a result, optimal ¹³C spectra of the oxidized, paramagnetic form of human copper zinc superoxide dismutase (SOD) can be obtained employing rf-fields which do not exceed 40 kHz during the whole experiment. This enables the removal of unwanted heating which can lead to deterioration of the sample. Furthermore, combined with the short ¹H T₁s, this allows the repetition rate of the experiments to be shortened from 3 s to 500 ms, thus compensating for the sensitivity loss due to the smaller sample volume in a 1.3 mm rotor. The result is that 2D ¹³C–¹³C correlation could be acquired in about 24 h on less than 1 mg of SOD sample.     

Accurate measurement of one-bond H-X heteronuclear dipolar couplings in MAS solid-state NMR

The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol--based on REDOR--to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP, R18(2)(5), and R18(1)(7)) is provided.     

Spectral editing in solid-state MAS NMR of quadrupolar nuclei using selective satellite inversion

A sensitivity enhancement method based on selective adiabatic inversion of a satellite transition has been employed in a (pi/2)CT-(pi)ST1-(pi/2)CT spectral editing sequence to both enhance and resolve multisite NMR spectra of quadrupolar nuclei. In addition to a total enhancement of 2.5 times for spin 3/2 nuclei, enhancements up to 2.0 times is reported for the edited sites in a mixture of rubidium salts.     

Efficient analysis of 51V solid-state MAS NMR spectra using genetic algorithms

A program for iterative fitting procedures to determine the NMR parameters from ⁵¹V solid-state MAS NMR spectra was developed. It contains options to use genetic algorithms and downhill-simplex optimizing procedures to extract the optimal parameter sets, which describe our spectra. As computational kernel the SIMPSON program is employed. Other kernels like SPINEVOLUTION are easily incorporable. The algorithms are checked for their suitability for the present optimization problem and optimal simulation conditions are determined, with the focus on minimal processing time. The procedure leads to a very good agreement between experimental and simulated spectra in a passable period of time. First results for spectra of model compounds for the active site of vanadium haloperoxidases are presented.     

Characterization of dynamic processes using deuterium in uniformly 2H,13C,15N enriched peptides by MAS solid-state NMR

We present in this paper 2H,13C MAS correlation experiments that are performed on a uniformly 2H,13C,15N labeled sample of Nac-Val, and on the uniformly 2H,15N labeled dipeptide Nac-Val-Leu-OH. The experiments involve the measurement of 2H T1 relaxation times at two different magnetic fields, as well as the measurement of the 2H tensor parameters by evolution of the 2H chemical shift. The data are interpreted quantitatively to differentiate between different side chain motional models.     

High-field 19.6T 27Al solid-state MAS NMR of in vitro aluminated brain tissue

The combination of (27)Al high-field solid-state NMR (19.6T) with rapid spinning speeds (17.8 kHz) is used to acquire (27)Al NMR spectra of total RNA human brain temporal lobe tissues exposed to 0.10 mM Al(3+) (as AlCl(3)) and of human retinal pigment epithelial cells (ARPE-19), grown in 0.10 mM AlCl(3). The spectra of these model systems show multiple Al(3+) binding sites, good signal/noise ratios and apparent chemical shift dispersions. A single broad peak (-3 to 11 ppm) is seen for the aluminated ARPE-19 cells, consistent with reported solution-state NMR chemical shifts of Al-transferrin. The aluminated brain tissue has a considerably different (27)Al MAS NMR spectrum. In addition to the transferrin-type resonance, additional peaks are seen. Tentative assignments include: -9 to -3 ppm, octahedral AlO(6) (phosphate and water); 9 ppm, condensed AlO(6) units (Al-O-Al bridges); 24 ppm, tetrahedral AlO(3)N and/or octahedral Al-carbonate; and 35 ppm, more N-substituted aluminum and /or tetrahedral AlO(4). Thus, brain tissue is susceptible to a broad range of coordination by aluminum. Furthermore, the moderate (27)Al C(Q) values (all less than 10 MHz) suggest future NMR studies may be performed at 9.4T and a spin rate of 20 kHz.     

Soft-triple resonance solid-state NMR experiments for assignments of U-13C, 15N labeled peptides and proteins

The process of obtaining sequential resonance assignments for heterogeneous polypeptides and large proteins by solid-state NMR (ssNMR) is impeded by extensive spectral degeneracy in these systems. Even in these challenging cases, the cross peaks are not distributed uniformly over the entire spectral width. Instead, there exist both well-resolved single resonances and distinct groups of resonances well separated from the most crowded region of the spectrum. Here, we present a series of new triple resonance experiments that exploit the non-uniform clustering of resonances in heteronuclear correlation spectra to obtain additional resolution in the more crowded regions of a spectrum. Homonuclear and heteronuclear dipolar recoupling sequences are arranged to achieve directional transfer of coherence between neighboring residues in the peptide sequence. A frequency-selective (soft) pulse is applied to select initial polarization from a limited (and potentially) well-resolved region of the spectrum. The pre-existing resolution of one or more spins is thus utilized to obtain additional resolution in the more crowded regions of the spectrum. A new protocol to utilize these experiments for sequential resonance assignments in peptides and proteins is also demonstrated.     

Observation of hydroxyl groups by 17O solid-state multiple quantum MAS NMR in sol-gel-produced silica

17O NMR parameters (CQ, eta, delta(iso) and T1) are reported for both Si-O-Si and Si-OH fragments within a silica gel. The Si-OH units have a wide spread of parameters but are typically characterised by a very short T1 (approximately 0.1 ms) and CQ < 200 kHz. These observations have extremely important implications for the quantification of such units in these gels and related glassy materials by 17O NMR. In light of these observations, the 17O NMR experiments have been optimised and a distinct resonance from the OH group is observed in 1D static and magic angle spinning (MAS) NMR measurements as well in the multiple quantum (MQ) experiment.     

Resolution enhancement in MAS solid-state NMR by application of 13C homonuclear scalar decoupling during acquisition

Spectral resolution imposes a major problem on the evaluation of MAS solid-state NMR experiments as larger biomolecular systems are concerned. We show in this communication that decoupling of the (13)C-(13)C homonuclear scalar couplings during stroboscopic detection can be successfully applied to increase the spectral resolution up to a factor of 2-2.5 and sensitivity up to a factor of 1.2. We expect that this approach will be useful for the study of large biomolecular systems like membrane proteins and amyloidogenic peptides and proteins where spectral overlap is critical. The experiments are demonstrated on a uniformly (13)C,(15)N-labelled sample of Nac-Val-Leu-OH and applied to a uniformly (13)C,(15)N-enriched sample of a hexameric amyloidogenic peptide.     

Quantitative characterization of coal structure by high-resolution CP/MAS 13C solid-state NMR spectroscopy

A method for quantitatively characterizing the carbon skeletal structure of coal by variable contact time experiment using high-resolution CP/MAS ¹³C solid-state NMR spectroscopy is proposed in this paper. The initial polarization transfer intensity from protons directly bonded with carbons, instead of dipolar-dephasing techniques which had to run on a lower frequency NMR spectrometer (100.02 MHz for proton), was used to divide the bridgehead and protonated aromatic carbons, making all the NMR data in this paper obtained on a high frequency NMR spectrometer (500.12 MHz for proton). On this basis, the fractions of different carbons in coal were further divided by the initial polarization transfer intensity from spin diffusion of protons unbonded with carbons. The structure of Naomaohu coal, a subbituminous coal from China, was measured. The change of polarization transfer with contact time was analyzed quantitatively. The fractions of aromatic, aliphatic, carboxyl and carbonyl carbons, and corrective aromaticity are 0.61, 0.39, 0.1 and 0.51, respectively. The fractions of protonated and bridgehead aromatic carbons are 0.22 and 0.09, respectively. These results agreed with literatures, and bond concentration calculated by the carbon skeletal structure distribution of coal was reasonable.     

Assigning solid-state NMR spectra of aligned proteins using isotropic chemical shifts

A method for assigning solid-state NMR spectra of membrane proteins aligned in phospholipid bicelles that makes use of isotropic chemical shift frequencies and assignments is demonstrated. The resonance assignments are based on comparisons of 15N chemical shift differences in spectra obtained from samples with their bilayer normals aligned perpendicular and parallel to the direction of the applied magnetic field.     

Pure-exchange solid-state NMR

Three exchange nuclear magnetic resonance (NMR) techniques are presented that yield (13)C NMR spectra exclusively of slowly reorienting segments, suppressing the often dominant signals of immobile components. The first technique eliminates the diagonal ridge that usually dominates two-dimensional (2D) exchange NMR spectra and that makes it hard to detect the broad and low off-diagonal exchange patterns. A modulation of the 2D exchange spectrum by the sine-square of a factor which is proportional to the difference between evolution and detection frequencies is generated by fixed additional evolution and detection periods of duration tau, yielding a 2D pure-exchange (PUREX) spectrum. Smooth off-diagonal intensity is obtained by systematically incrementing tau and summing up the resulting spectra. The related second technique yields a static one-dimensional (1D) spectrum selectively of the exchanging site(s), which can thus be identified. Efficient detection of previously almost unobservable slow motions in a semicrystalline polymer is demonstrated. The third approach, a 1D pure-exchange experiment under magic-angle spinning, is an extension of the exchange-induced sideband (EIS) method. A TOSS (total suppression of sidebands) spectrum obtained after the same number of pulses and delays, with a simple swap of z periods, is subtracted from the EIS spectrum, leaving only the exchange-induced sidebands and a strong, easily detected centerband of the mobile site(s).