The accuracy of distance measurements in solid-state NMR

Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme

Most bacterial, plant and fungal cells possess at their surface a protective layer called the cell wall, conferring strength, plasticity and rigidity to withstand the osmotic pressure. This molecular barrier is crucial for pathogenic microorganisms, as it protects the cell from the local environment and often constitutes the first structural component encountered in the host-pathogen interaction. In pathogenic molds and yeasts, the cell wall constitutes the main target for the development of clinically-relevant antifungal drugs. In the past decade, solid-state NMR has emerged as a powerful analytical technique to investigate the molecular organization of microbial cell walls in the context of intact cells. 13C NMR chemical shift is an exquisite source of information to identify the polysaccharides present in the cell wall, and two-dimensional 13C-13C correlation experiments provide an efficient tool to rapidly access the polysaccharide composition in whole cells. Here we investigate the use of the adiabatic DREAM (for dipolar recoupling enhancement through amplitude modulation) recoupling scheme to improve solid-state NMR analysis of polysaccharides in intact cells. We demonstrate the advantages of two-dimensional 13C-13C experiments using the DREAM recoupling scheme. We report the spectral editing of polysaccharide signals by varying the radio-frequency carrier position. We provide practical considerations for the implementation of DREAM experiments to characterize polysaccharides in whole cells. We demonstrate the approach on intact fungal cells of Neurospora crassa and Aspergillus fumigatus, a model and a pathogenic filamentous fungus, respectively. The approach could be envisioned to efficiently reduce the spectral crowding of more complex cell surfaces, such as cell wall and peptidoglycan in bacteria.

Solid-State NMR: Methods for Biological Solids

In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.

NMR crystallography of molecular organics

Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.

High-Sensitivity Detection of Nanometer 1H-19F Distances for Protein Structure Determination by 1H-Detected Fast MAS NMR

Protein structure determination by solid-state NMR requires the measurement of many interatomic distances through dipole-dipole couplings. To obtain multiple long-range distance restraints rapidly and with high sensitivity, here we demonstrate a new 1H-detected fast magic-angle-spinning NMR technique that yields many long distances in a two-dimensional (2D)-resolved fashion. The distances are measured up to ∼15 Å, with an accuracy of better than 10%, between 1H and 19F, two nuclear spins that have the highest gyromagnetic ratios. Exogenous fluorines are sparsely introduced into the aromatic residues of the protein, which is perdeuterated and back-exchanged to give amide protons. This 1H-19F distance experiment, termed 2D heteronuclear single-quantum coherence rotational-echo double-resonance (HSQC-REDOR), is demonstrated on the singly fluorinated model protein, GB1. We extracted 33 distances between 5-19F-Trp43 and backbone amide protons, using 2D spectral series that were measured in less than 3 days. Combining these 1H-19F distance restraints with 13C-19F distances and chemical shifts, we calculated a GB1 structure with a backbone root-mean-square deviation of 1.73 Å from the high-resolution structure. This 1H-detected 1H-19F distance technique promises to provide a highly efficient tool for constraining the three-dimensional structures of proteins and protein-ligand complexes, with not only precise and fast measurements but also access to truly long-range distances.

Three-Dimensional Nuclear Spin Positioning Using Coherent Radio-Frequency Control

Distance measurements via the dipolar interaction are fundamental to the application of nuclear magnetic resonance (NMR) to molecular structure determination, but they provide information on only the absolute distance r and polar angle θ between spins. In this Letter, we present a protocol to also retrieve the azimuth angle ϕ. Our method relies on measuring the nuclear precession phase after the application of a control pulse with a calibrated external radio-frequency coil. We experimentally demonstrate three-dimensional positioning of individual ^{13}C nuclear spins in a diamond host crystal relative to the central electronic spin of a single nitrogen-vacancy center. The ability to pinpoint three-dimensional nuclear locations is central for realizing a nanoscale NMR technique that can image the structure of single molecules with atomic resolution.

Determination of Long-Range Distances by Fast Magic-Angle-Spinning Radiofrequency-Driven 19F-19F Dipolar Recoupling NMR

Nanometer-range distances are important for restraining the three-dimensional structure and oligomeric assembly of proteins and other biological molecules. Solid-state NMR determination of protein structures typically utilizes ¹³C-¹³C and ¹³C-¹⁵N distance restraints, which can only be measured up to ∼7 Å because of the low gyromagnetic ratios of these nuclear spins. To extend the distance reach of NMR, one can harvest the power of ¹⁹F, whose large gyromagnetic ratio in principle allows distances up to 2 nm to be measured. However, ¹⁹F possesses large chemical shift anisotropies (CSAs) as well as large isotropic chemical shift dispersions, which pose challenges to dipolar coupling measurements. Here, we demonstrate ¹⁹F-¹⁹F distance measurements at high magnetic fields under fast magic-angle spinning (MAS) using radiofrequency-driven dipolar recoupling (RFDR). We show that ¹⁹F-¹⁹F cross-peaks for distances up to 1 nm can be readily observed in two-dimensional ¹⁹F-¹⁹F correlation spectra using less than 5 ms of RFDR mixing. This efficient ¹⁹F-¹⁹F dipolar recoupling is achieved using practically accessible MAS frequencies of 15-55 kHz, moderate ¹⁹F radio frequency field strengths, and no ¹H decoupling. Experiments and simulations show that the fastest polarization transfer for aromatic fluorines with the highest distance accuracy is achieved using either fast MAS (e.g., 60 kHz) with large pulse duty cycles (>50%) or slow MAS with strong ¹⁹F pulses. Fast MAS considerably reduces relaxation losses during the RFDR π-pulse train, making finite-pulse RFDR under fast-MAS the method of choice. Under intermediate MAS frequencies (25-40 kHz) and intermediate pulse duty cycles (15-30%), the ¹⁹F CSA tensor orientation has a quantifiable effect on the polarization transfer rate; thus, the RFDR buildup curves encode both distance and orientation information. At fast MAS, the impact of CSA orientation is minimized, allowing pure distance restraints to be extracted. We further investigate how relayed transfer and dipolar truncation in multifluorine environments affect polarization transfer. This fast-MAS ¹⁹F RFDR approach is complementary to ¹⁹F spin diffusion for distance measurements and will be the method of choice under high-field fast-MAS conditions that are increasingly important for protein structure determination by solid-state NMR.

Strategies for solid-state NMR investigations of supramolecular assemblies with large subunit sizes

Solid-state NMR is a versatile tool to study structure and dynamics of insoluble and non-crystalline biopolymers. Supramolecular protein assemblies are formed by self-association of multiple copies of single small-sized proteins. Because of their high degree of local order, solid-state NMR spectra of such systems exhibit an unusually high level of resolution, rendering them an ideal target for solid-state NMR investigations. Recently, our group has solved the structure of one particular supramolecular assembly, the type-iii-secretion-system needle. The needle subunit comprises around 80 residues. Many interesting supramolecular assemblies with unknown structure have subunits larger in size, which requires development of tailored solid-state NMR strategies to address their structures. In this "Perspective" article, we provide a view on different approaches to enhance sensitivity and resolution in biological solid-state NMR with a focus on the possible application to supramolecular assemblies with large subunit sizes.

Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies

Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively (13)C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved.

Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing (13)C detection only a single set of resonances was observed.

BSH-CP based 3D solid-state NMR experiments for protein resonance assignment

We have recently presented band-selective homonuclear cross-polarization (BSH-CP) as an efficient method for CO-CA transfer in deuterated as well as protonated solid proteins. Here we show how the BSH-CP CO-CA transfer block can be incorporated in a set of three-dimensional (3D) solid-state NMR (ssNMR) pulse schemes tailored for resonance assignment of proteins at high static magnetic fields and moderate magic-angle spinning rates. Due to the achieved excellent transfer efficiency of 33 % for BSH-CP, a complete set of 3D spectra needed for unambiguous resonance assignment could be rapidly recorded within 1 week for the model protein ubiquitin. Thus we expect that BSH-CP could replace the typically used CO-CA transfer schemes in well-established 3D ssNMR approaches for resonance assignment of solid biomolecules.

Efficient band-selective homonuclear CO-CA cross-polarization in protonated proteins

Previously introduced for highly deuterated proteins, band-selective magnetization transfer between CO and CA spins by dipolar-based homonuclear cross polarization is applied here to a protonated protein. Robust and efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate, yielding up to 33% of magnetization transfer efficiency in protonated ubiquitin. The approach is designed for moderate magic-angle spinning rates and high external magnetic fields when the isotropic chemical shift difference of CO and CA considerably exceeds the spinning rate. This method has been implemented in NiCOi-1CAi-1 and CAi(Ni)COi-1CAi-1 two-dimensional interresidual correlation experiments for fast and efficient resonance assignment of ubiquitin by solid-state NMR spectroscopy.

C-REDOR curves of extended spin systems

The convergence of simulated C-REDOR curves of (infinitely) large spin systems is investigated with respect to the number of spins considered in the calculations. Taking a sufficiently large number of spins (>20,000 spins) into account enables the simulation of converged C-REDOR curves over the entire time period and not only the initial regime. The calculations are based on an existing approximation within first order average Hamiltonian theory (AHT), which assumes the absence of homonuclear dipole-dipole interactions. The C-REDOR experiment generates an average Hamiltonian close to the idealized AHT behavior even for multiple spin systems including multiple homonuclear dipole-dipole interactions which is shown from numerically exact calculations of the spin dynamics. Experimentally it is shown that calculations accurately predict the full, experimental C-REDOR curves of the multi-spin systems (31)P-(19)F in apatite, (31)P-(1)H in potassium trimetaphosphimate and (1)H-(31)P in potassium dihydrogen phosphate. We also present (13)C-(1)H and (15)N-(1)H data for the organic compounds glycine, l-alanine and l-histidine hydrochloride monohydrate which require consideration of molecular motion. Furthermore, we investigated the current limits of the method from systematic errors and we suggest a simple way to calculate errors for homogeneous and heterogeneous samples from experimental data.

Structural comparison of mouse and human α-synuclein amyloid fibrils by solid-state NMR

Fibrillar α-synuclein (AS) is the major component of Lewy bodies, the pathological hallmark of Parkinson's disease. Mouse AS (mAS) aggregates much faster than human AS (hAS), although mAS differs from hAS at only seven positions in its primary sequence. Currently, little is known about the site-specific structural differences between mAS and hAS fibrils. Here, we applied state-of-the-art solid-state nuclear magnetic resonance (ssNMR) methods to structurally characterize mAS fibrils. The assignment strategy employed a set of high-resolution 2D and 3D ssNMR spectra recorded on uniformly [(13)C, (15)N], [1-(13)C]glucose, and [2-(13)C]glucose labeled mAS fibrils. An almost complete resonance assignment (96% of backbone amide (15)N and 93% of all (13)C nuclei) was obtained for residues from Gly41 to Val95, which form the core of mAS fibrils. Six β-strands were identified to be within the fibril core of mAS based on a secondary chemical shift and NHHC analysis. Intermolecular (13)C:(15)N labeled restraints obtained from mixed 1:1 (13)C/(15)N-labeled mAS fibrils reveal a parallel, in-register supramolecular β-sheet arrangement. The results were compared in detail to recent structural studies on hAS fibrils and indicate the presence of a structurally conserved motif comprising residues Glu61-Lys80.

Progress in correlation spectroscopy at ultra-fast magic-angle spinning: basic building blocks and complex experiments for the study of protein structure and dynamics

Recent progress in multi-dimensional solid-state NMR correlation spectroscopy at high static magnetic fields and ultra-fast magic-angle spinning is discussed. A focus of the review is on applications to protein resonance assignment and structure determination as well as on the characterization of protein dynamics in the solid state. First, the consequences of ultra-fast spinning on sensitivity and sample heating are considered. Recoupling and decoupling techniques at ultra-fast MAS are then presented, as well as more complex experiments assembled from these basic building blocks. Furthermore, we discuss new avenues in biomolecular solid-state NMR spectroscopy that become feasible in the ultra-fast spinning regime, such as sensitivity enhancement based on paramagnetic doping, and the prospect of direct proton detection.

A master-equation approach to the description of proton-driven spin diffusion from crystal geometry using simulated zero-quantum lineshapes

Measurements of proton-driven carbon-13 spin diffusion (PDSD) by NMR spectroscopy are a central component of structural analyses of biomolecules in the solid-state. However, the quantitative link between experimental PDSD data and structural information is difficult to make. Here we observe that a master-equation approach can be used to model full PDSD dynamics accurately in polycrystalline (13)C-labelled L-histidine·HCl·H(2)O under magic-angle spinning. In the master-equation approach, PDSD rates and effective dipolar couplings are related by a function of the carbon-carbon zero-quantum lineshapes; we find that numerical simulations of the zero-quantum lineshapes are sufficiently accurate so as to allow the calculation of PDSD rates that are in good agreement with the measured rates, directly from crystal geometry and with no adjustable parameters. Finally, using carbon-carbon internuclear distances we illustrate the potential of the master-equation approach for structural studies. Generalisation of these results to proton-driven carbon-13 spin diffusion in more complex molecular systems is readily envisaged.

Dipolar-coupling-mediated total correlation spectroscopy in solid-state 13C NMR: selection of individual 13C-13C dipolar interactions

Herein is described a useful approach in solid-state NMR, for selecting homonuclear (13)C-(13)C spin pairs in a multiple-(13)C homonuclear dipolar coupled spin system. This method builds upon the zero-quantum (ZQ) dipolar recoupling method introduced by Levitt and coworkers (Marin-Montesinos et al., 2006) by extending the originally introduced one-dimensional (1D) experiment into a two-dimensional (2D) method with selective irradiation scheme, while moving the (13)C-(13)C mixing scheme from the transverse to the longitudinal mode, together with a dramatic improvement in the proton decoupling efficiency. Selective spin-pair recoupling experiments incorporating Gaussian and cosine-modulated Gaussian pulses for inverting specific spins were performed, demonstrating the ability to detect informative, simplified/individualized, long-range (13)C-(13)C homonuclear dipolar coupling interactions more accurately by removing less informative, stronger, short-range (13)C-(13)C interactions from 2D correlation spectra. The capability of this new approach was demonstrated experimentally on uniformly (13)C-labeled Glutamine and a tripeptide sample, GAL.

High-resolution solid-state NMR structure of a 17.6 kDa protein

The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.

Indirect detection via spin-1/2 nuclei in solid state NMR spectroscopy: application to the observation of proximities between protons and quadrupolar nuclei

We present a comprehensive comparison of through-space heteronuclear correlation techniques for solid state NMR, combining indirect detection and single-channel recoupling method. These techniques, named D-HMQC and D-HSQC, do not suffer from dipolar truncation and can be employed to correlate quadrupolar nuclei with spin-1/2 nuclei. The heteronuclear dipolar couplings are restored under magic-angle spinning by applying supercycled symmetry-based pulse sequences (SR412) or simultaneous frequency and amplitude modulation (SFAM). The average Hamiltonian theory (AHT) of these recoupling methods is developed. These results are applied to analyze the performances of D-HMQC and D-HSQC sequences. It is shown that, whatever the magnitude of spin interations, D-HMQC experiment offers larger efficiency and higher robustness than D-HSQC. Furthermore, the spectral resolution in both dimensions of proton detected two-dimensional D-HMQC and D-HSQC spectra can be enhanced by applying recently introduced symmetry-based homonuclear dipolar decoupling schemes that cause a z-rotation of the spins. This is demonstrated by 1H-13C and 1H-23Na correlation experiments on l-histidine and NaH2PO4, respectively. The two-dimensional heteronuclear 1H-23Na correlation spectrum yields the assignment of 23Na resonances of NaH2PO4. This assignment is corroborated by first-principles calculations.

Homonuclear dipolar recoupling techniques for structure determination in uniformly 13C-labeled proteins

In solid-state NMR magic angle spinning is often used to remove line broadening associated with anisotropic interactions, such as chemical shift anisotropy and dipolar couplings. Dipolar recoupling refers to sequences of pulses designed to reintroduce dipolar interactions that are otherwise averaged by magic angle spinning. One of the key applications of homonuclear (and heteronuclear) dipolar recoupling is for the purpose of protein structure determination. Recoupling experiments, originally designed for applications in spin-pair labeled samples, have been revised in recent years for applications in samples with extensive or uniform incorporation of isotopic labels. In these samples multiple internuclear distances can in principle be probed simultaneously, but the dipolar truncation effects (i.e. attenuation of the effects of weak couplings by strong ones) circumvent such measurements. In this article we review some of the recent developments in homonuclear recoupling methods that allow overcoming this problem.

Double-quantum NMR spectroscopy of 31P species submitted to very large CSAs

We introduce an original pulse sequence, BR2(2)(1)(taupitau), which is a block super-cycled R2(2)(1) sequence employing as basic element a pi pulse sandwiched by 'window' intervals. This homonuclear dipolar recoupling method allows the efficient excitation of double-quantum coherences between spin-1/2 nuclei submitted to very large chemical shift anisotropy. We demonstrate that this technique can be employed in double-quantum<-->single-quantum (31)P homonuclear correlation experiment at high magnetic field (B(0)>or=14 T) and high MAS frequencies (nu(R)>or=30 kHz). The performances of BR2(2)(1)(taupitau) are compared to those of the double-quantum recoupling methods, such as BABA and bracketed fp-RFDR, which were already employed at fast MAS rates. The BR2(2)(1)(taupitau) sequence displays a higher robustness to CSA and offset than the other existing techniques.

Determining relative proton-proton proximities from the build-up of two-dimensional correlation peaks in 1H double-quantum MAS NMR: insight from multi-spin density-matrix simulations

The build-up of intensity-as a function of the number, n(rcpl), of POST-C7 elements used for the excitation and reconversion of double-quantum (DQ) coherence (DQC)-is analysed for the fifteen distinct DQ correlation peaks that are observed experimentally for the eight separate (1)H resonances in a (1)H (500 MHz) DQ CRAMPS solid-state (12.5 kHz MAS) NMR spectrum of the dipeptide beta-AspAla (S. P. Brown, A. Lesage, B. Elena, and L. Emsley, J. Am. Chem. Soc., 2004, 126, 13230). The simulation in SPINEVOLUTION (M. Veshtort and R. G. Griffin, J. Magn. Reson., 2006, 178, 248) of t(1) ((1)H DQ evolution) FIDs for clusters of eight dipolar-coupled protons gives separate simulated (1)H DQ build-up curves for the CH(2)(a), CH(2)(b), CH(Asp), CH(Ala), NH and OH (1)H single-quantum (SQ) (1)H resonances. An analysis of both the simulated and experimental (1)H DQ build-up leads to the following general observations: (i) considering the build-up of (1)H DQ peaks at a particular SQ frequency, maximum intensity is observed for the DQC corresponding to the shortest H-H distance; (ii) for the maximum intensity (1)H DQ peak at a particular SQ frequency, the recoupling time for the observed maximum intensity depends on the corresponding H-H distance, e.g., maximum intensity for the CH(2)(a)-CH(2)(b) (H-H distance = 1.55 A) and OH-CH(Asp) (H-H distance = 2.49 A) DQ peaks is observed at n(rcpl) = 2 and 3, respectively; (iii) for DQ peaks involving a CH(2) proton at a non-CH(2) SQ frequency, there is much reduced intensity and a maximum intensity at a short recoupling time; (iv) for the other lower intensity (1)H DQ peaks at a particular SQ frequency, maximum intensity is observed for the same (or close to the same) recoupling time, but the relative intensity of the DQ peaks is a reliable indicator of the relative H-H distance-the ratio of the maximum intensities for the peaks at the CH(Ala) SQ frequency due to the two DQCs with the NH and OH protons are found to be approximately in the ratio of the squares of the corresponding dipolar coupling constants. While the simulated (1)H DQ build-up curves reproduce most of the features of the experimental curves, maximum intensity is often observed at a longer recoupling time in simulations. In this respect, simulations for two to eight spins show a trend towards a faster decay for an increasing number of considered spins. Finally, simulations show that increasing either the Larmor frequency (to 1 GHz) or the MAS frequency (to 125 kHz) does not lead to changes in the marked differences between the (1)H DQ build-up curves at the CH(Asp) SQ frequency for DQCs to the CH(2)(a) and OH protons that correspond to similar H-H distances (2.39 A and 2.49 A, respectively).

Dipolar truncation in magic-angle spinning NMR recoupling experiments

Quantitative solid-state NMR distance measurements in strongly coupled spin systems are often complicated due to the simultaneous presence of multiple noncommuting spin interactions. In the case of zeroth-order homonuclear dipolar recoupling experiments, the recoupled dipolar interaction between distant spins is attenuated by the presence of stronger couplings to nearby spins, an effect known as dipolar truncation. In this article, we quantitatively investigate the effect of dipolar truncation on the polarization-transfer efficiency of various homonuclear recoupling experiments with analytical theory, numerical simulations, and experiments. In particular, using selectively (13)C-labeled tripeptides, we compare the extent of dipolar truncation in model three-spin systems encountered in protein samples produced with uniform and alternating labeling. Our observations indicate that while the extent of dipolar truncation decreases in the absence of directly bonded nuclei, two-bond dipolar couplings can generate significant dipolar truncation of small, long-range couplings. Therefore, while alternating labeling alleviates the effects of dipolar truncation, and thus facilitates the application of recoupling experiments to large spin systems, it does not represent a complete solution to this outstanding problem.

Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.

Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy

We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.

Resonance assignments and secondary structure analysis of E. coli thioredoxin by magic angle spinning solid-state NMR spectroscopy

De novo site-specific 13C and 15N backbone and sidechain resonance assignments are presented for uniformly enriched E. coli thioredoxin, established using two-dimensional homo- and heteronuclear solid-state magic angle spinning NMR correlation spectroscopy. Backbone dihedral angles and secondary structure were derived from the statistical analysis of the secondary chemical shifts, and are in good agreement with solution values for the intact full-length thioredoxin, with the exception of a small number of residues located at the termini of the individual secondary structure elements. A large number of cross-peaks observed in the DARR spectra with long mixing times correspond to the pairs of carbon atoms separated by 4-6 angstroms, suggesting that DARR could be efficiently employed for observation of medium- and long-range correlations. The 108 amino acid residue E. coli thioredoxin is the largest uniformly enriched protein assigned to this degree of completeness by solid-state NMR spectroscopy to date. It is anticipated that with a combination of two-dimensional correlation experiments and high magnetic fields, resonance assignments and secondary structure can be generally derived for other noncrystalline proteins.

Proton-detected solid-state NMR spectroscopy of fully protonated proteins at 40 kHz magic-angle spinning

Remarkable progress in solid-state NMR has enabled complete structure determination of uniformly labeled proteins in the size range of 5-10 kDa. Expanding these applications to larger or mass-limited systems requires further improvements in spectral sensitivity, for which inverse detection of 13C and 15N signals with 1H is one promising approach. Proton detection has previously been demonstrated to offer sensitivity benefits in the limit of sparse protonation or with approximately 30 kHz magic-angle spinning (MAS). Here we focus on experimental schemes for proteins with approximately 100% protonation. Full protonation simplifies sample preparation and permits more complete chemical shift information to be obtained from a single sample. We demonstrate experimental schemes using the fully protonated, uniformly 13C,15N-labeled protein GB1 at 40 kHz MAS rate with 1.6-mm rotors. At 500 MHz proton frequency, 1-ppm proton line widths were observed (500 +/- 150 Hz), and the sensitivity was enhanced by 3 and 4 times, respectively, versus direct 13C and 15N detection. The enhanced sensitivity enabled a family of 3D experiments for spectral assignment to be performed in a time-efficient manner with less than a micromole of protein. CANH, CONH, and NCAH 3D spectra provided sufficient resolution and sensitivity to make full backbone and partial side-chain proton assignments. At 750 MHz proton frequency and 40 kHz MAS rate, proton line widths improve further in an absolute sense (360 +/- 115 Hz). Sensitivity and resolution increase in a better than linear manner with increasing magnetic field, resulting in 14 times greater sensitivity for 1H detection relative to that of 15N detection.

Solid state NMR analysis of the dipolar couplings within and between distant CF3-groups in a membrane-bound peptide

Dipolar couplings contain information on internuclear distances as well as orientational constraints. To characterize the structure of the antimicrobial peptide gramicidin S when bound to model membranes, two rigid 4-CF3-phenylglycine labels were attached to the cyclic backbone such that they reflect the behavior of the entire peptide. By solid state 19F NMR we measured the homonuclear dipolar couplings of the two trifluoromethyl-groups in oriented membrane samples. Using the CPMG experiment, both the strong couplings within each CF3-group as well as the weak coupling between the two CF3-groups could be detected. An intra-CF3-group dipolar coupling of 86 Hz and a weak inter-group coupling of 20 Hz were obtained by lineshape simulation of the complex dipolar spectrum. It is thus possible to explore the large distance range provided by 19F-labels and to resolve weak dipolar couplings even in the presence of strong intra-CF3 couplings. We applied this approach to distinguish and assign two epimers of the labeled gramicidin S peptide on the basis of their distinct 19F dipolar coupling patterns.

Effective dipolar couplings determined by dipolar dephasing of double-quantum coherences

It is shown how homonuclear distances and homonuclear dipolar lattice sums between spin-1/2 nuclei can be measured by a pulsed solid-state NMR experiment under magic-angle spinning conditions. The presented technique is based on double-quantum coherence filtering. Instead of measuring a build-up of double-quantum coherence the pulse sequence is designed to dephase double-quantum coherence. This is achieved by exciting double-quantum coherence either with the help of the through-space dipolar coupling or the through-bond dipolar coupling while the dephasing relies on the through-space dipolar coupling as selected by a gamma-encoded pulse sequence from the C/R symmetry class. Since dephasing curves can be normalized on zero dephasing, it is possible to analyze the initial dephasing regime and hence determine dipolar lattice sums (effective dipolar couplings) in multiple-spin systems. A formula for the effective dipolar coupling is derived theoretically and validated by numerical calculations and experiments on crystalline model compounds for (13)C and (31)P spin systems. The double-quantum dephasing experiment can be combined with constant-time data sampling to compensate for relaxation effects, consequently only two experimental data points are necessary for a single distance measurement. The phase cycling overhead for the constant-time experiment is minimal because a short cogwheel phase cycle exists. A 2D implementation is demonstrated on [(13)C(3)]alanine.

1H/31P distance determination by solid state NMR in multiple-spin systems

The results of two techniques of dipolar recoupling, REDOR and CPMAS, are compared in the case of a coupled multiple-spin system. A fundamentally different behavior is observed for these two techniques. In REDOR, the terms associated with each interaction S-I(k) commute with each other and no truncation takes place so that each addition of spin I(k) causes a splitting with its dipolar frequency. In CPMAS, the flip-flop terms of the dipolar Hamiltonian do not commute with the dominant term from the strongly coupled spin pair so that the weak coupling terms from the neighboring spin I(k) are effectively truncated by the dominant pair interaction. Spin dynamics calculations are in agreement with the experimental data in a cubane shaped cluster.

Band-selective carbonyl to aliphatic side chain 13C-13C distance measurements in U-13C,15N-labeled solid peptides by magic angle spinning NMR

We describe three-dimensional magic angle spinning NMR experiments that enable simultaneous band-selective measurement of the multiple distance constraints between carbonyl and side chain carbons in uniformly 13C,15N-labeled peptides. The approaches are designed to circumvent the dipolar truncation and to allow experimental separation of the multiple quantum (MQ) relaxation and dipolar effects. The pulse sequences employ the double quantum (DQ) rotational resonance in the tilted frame (R2TR) to perform selective polarization transfers that reintroduce the 13C'-13Cgamma,delta dipolar interactions. The scheme avoids recoupling of the strongly coupled C'-Calpha and C'-Cbeta spin pairs, therefore minimizing dipolar truncation effects. The experiment is performed in a constant time fashion as a function of the radio frequency irradiation intensity and measures the line shape of the DQ transition. The width and the intensity of this line shape are analyzed in terms of the DQ relaxation and dipolar coupling. The attenuation of the multispin effects in the presence of relaxation enables a two-spin approximation to be employed for the analysis of the experimental data. The systematic error introduced by this approximation is estimated by comparing the results with a three-spin simulation. The contributions of B1-inhomogeneity, CSA orientation effects, and the effects of inhomogeneous line broadening are also estimated. The experiments are demonstrated in model U-13C,15N-labeled peptides, N-acetyl-L-Val-L-Leu and N-formyl-L-Met-L-Leu-L-Phe, where 10 and 6 distances, ranging between 3 and 6 A, were measured, respectively.

Identification of NH...N hydrogen bonds by magic angle spinning solid state NMR in a double-stranded RNA associated with myotonic dystrophy

RNA plays a central role in biological processes and exhibits a variety of secondary and tertiary structural features that are often stabilized via hydrogen bonds. The distance between the donor and acceptor nitrogen nuclei involved in NH...N hydrogen bonds in nucleic acid base pairs is typically in the range of 2.6-2.9 A. Here, we show for the first time that such spatial proximity between 15N nitrogen nuclei can be conveniently monitored via magic angle spinning solid state NMR on a uniformly 15N-labelled RNA. The presence of NH.N hydrogen bonds is reflected as cross-peaks between the donor and acceptor nitrogen nuclei in 2D 15N dipolar chemical shift correlation spectra. The RNA selected for this experimental study was a CUG repeat expansion implicated in the neuromuscular disease myotonic dystrophy. The results presented provide direct evidence that the CUG repeat expansion adopts a double-stranded conformation.

Multiple-spin analysis of chemical-shift-selective (13C, 13C) transfer in uniformly labeled biomolecules

Chemical-shift-selective (13C, 13C) polarization transfer is analyzed in uniformly labeled biomolecules. It is shown that the spin system dynamics remain sensitive to the distance of interest and can be well reproduced within a quantum-mechanical multiple-spin analysis. These results lead to a general approach on how to describe chemical-shift-selective transfer in uniformly labeled systems. As demonstrated in the case of ubiquitin, this methodology can be used to detect long-range distance constraints in uniformly labeled proteins.

Determination of solid-state NMR structures of proteins by means of three-dimensional 15N-13C-13C dipolar correlation spectroscopy and chemical shift analysis

In this paper, a three-dimensional (3D) NMR-based approach for the determination of the fold of moderately sized proteins by solid-state magic-angle spinning (MAS) NMR is presented and applied to the alpha-spectrin SH3 domain. This methodology includes the measurement of multiple (13)C-(13)C distance restraints on biosynthetically site-directed (13)C-enriched samples, obtained by growing bacteria on [2-(13)C]glycerol and [1,3-(13)C]glycerol. 3D (15)N-(13)C-(13)C dipolar correlation experiments were applied to resolve overlap of signals, in particular in the region where backbone carbon-carbon correlations of the C(alpha)-C(alpha), CO-CO, C(alpha)-CO, and CO-C(alpha) type appear. Additional restraints for confining the structure were obtained from phi and psi backbone torsion angles of 29 residues derived from C(alpha), C(beta), CO, NH, and H(alpha) chemical shifts. Using both distance and angular restraints, a refined structure was calculated with a backbone root-mean-square deviation of 0.7 A with respect to the average structure.

Spin-state selection in solid-state NMR

Spin-state selection in solid-state NMR is demonstrated, using similar pulse sequences as used in liquid-state NMR. The different transitions of all three carbon resonances in fully 13C-labeled L-alanine are separated in different spectra. By selecting spin-states, the contribution of the J-coupling to the linewidth is removed, leading to a considerable enhancement in resolution. The spin-state-selective technique is demonstrated for magic-angle spinning frequencies from 6 to 35kHz. Other experimental conditions affecting the sensitivity of the experiments are discussed. Sensitivity losses due to the introduction of the spin-state-selective filter are shown to be acceptable. Finally, spin-state selection was used to experimentally confirm the differential broadening expected for the two transitions of the CH3 resonance.

Measurement of multiple psi torsion angles in uniformly 13C,15N-labeled alpha-spectrin SH3 domain using 3D 15N-13C-13C-15N MAS dipolar-chemical shift correlation spectroscopy

We demonstrate the simultaneous measurement of several backbone torsion angles psi in the uniformly (13)C,(15)N-labeled alpha-Spectrin SH3 domain using two different 3D 15N-13C-13C-15N dipolar-chemical shift magic-angle spinning (MAS) NMR experiments. The first NCCN experiment utilizes double quantum (DQ) spectroscopy combined with the INADEQUATE type 13C-13C chemical shift correlation. The decay of the DQ coherences formed between 13C'(i) and 13C(alphai) spin pairs is determined by the "correlated" dipolar field due to 15N(i)-13C(alphai) and 13C'(i)-15N(i+1) dipolar couplings and is particularly sensitive to variations of the torsion angle in the regime |psi| > 140 degrees. However, the ability of this experiment to constrain multiple psi-torsion angles is limited by the resolution of the 13C(alpha)-(13)CO correlation spectrum. This problem is partially addressed in the second approach described here, which is an NCOCA NCCN experiment. In this case the resolution is enhanced by the superior spectral dispersion of the 15N resonances present in the 15N(i+1)-13C(alphai) part of the NCOCA chemical shift correlation spectrum. For the case of the 62-residue alpha-spectrin SH3 domain, we determined 13 psi angle constraints with the INADEQUATE NCCN experiment and 22 psi constraints were measured in the NCOCA NCCN experiment.