Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz

Structural characterization of E22G Aβ1-42 fibrils via1H detected MAS NMR

Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aβ1-42, E22G-Aβ1-42. We found E22G-AβM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aβ1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aβ1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aβ, E22G-Aβ1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aβ1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aβ1-42 fibrils. These results suggest that E22G-Aβ1-42 fibrils have a structure similar to that of wild type Aβ1-42.

Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy

Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein-DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.

High and fast: NMR protein-proton side-chain assignments at 160 kHz and 1.2 GHz

The NMR spectra of side-chain protons in proteins provide important information, not only about their structure and dynamics, but also about the mechanisms that regulate interactions between macromolecules. However, in the solid-state, these resonances are particularly difficult to resolve, even in relatively small proteins. We show that magic-angle-spinning (MAS) frequencies of 160 kHz, combined with a high magnetic field of 1200 MHz proton Larmor frequency, significantly improve their spectral resolution. We investigate in detail the gain for MAS frequencies between 110 and 160 kHz MAS for a model sample as well as for the hepatitis B viral capsid assembled from 120 core-protein (Cp) dimers. For both systems, we found a significantly improved spectral resolution of the side-chain region in the 1H-13C 2D spectra. The combination of 160 kHz MAS frequency with a magnetic field of 1200 MHz, allowed us to assign 61% of the aliphatic protons of Cp. The side-chain proton assignment opens up new possibilities for structural studies and further characterization of protein-protein or protein-nucleic acid interactions.

3D-Printable centrifugal devices for biomolecular solid state NMR rotors

The advent of magic angle spinning (MAS) rates exceeding 100 kHz has facilitated the acquisition of 1H-detected solid-state NMR spectra of biomolecules with high resolution. However, challenges can arise when preparing rotors for these experiments, due to the physical properties of biomolecular solid samples and the small dimensions of the rotors. In this study, we have designed 3D-printable centrifugal devices that facilitate efficient and consistent packing of crystalline protein slurries or viscous phospholipids into 0.7 mm rotors. We demonstrate the efficacy of these packing devices using 1H-detected solid state NMR at 105 kHz. In addition to devices for 0.7 mm rotors, we have also developed devices for other frequently employed rotor sizes and styles. We have made all our designs openly accessible, and we encourage their usage and ongoing development as a shared effort within the solid state NMR community.

Diamond rotors

The resolution of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra remains bounded by the spinning frequency, which is limited by the material strength of MAS rotors. Since diamond is capable of withstanding 1.5-2.5x greater MAS frequencies, compared to state-of-the art zirconia, we fabricated rotors from single crystal diamond. When combined with bearings optimized for spinning with helium gas, diamond rotors could achieve the highest MAS frequencies to date. Furthermore, the excellent microwave transmission properties and thermal conductivity of diamond could improve sensitivity enhancements in dynamic nuclear polarization (DNP) experiments. The fabrication protocol we report involves novel laser micromachining and produced rotors that presently spin at ωr/2π = 111.000 ± 0.004 kHz, with stable spinning up to 124 kHz, using N2 gas as the driving fluid. We present the first proton-detected 13C/15N MAS spectra recorded using diamond rotors, a critical step towards studying currently inaccessible ex-vivo protein samples with MAS NMR. Previously, the high aspect ratio of MAS rotors (∼10:1) precluded fabrication of MAS rotors from diamond.

A roadmap to high-resolution standard microcoil MAS NMR spectroscopy for metabolomics

Current microcoil probe technology has emerged as a significant advancement in NMR applications to biofluids research. It has continued to excel as a hyphenated tool with other prominent microdevices, opening many new possibilities in multiple omics fields. However, this does not hold for biological samples such as intact tissue or organisms, due to the considerable challenges of incorporating the microcoil in a magic-angle spinning (MAS) probe without relinquishing the high-resolution spectral data. Not until 2012 did a microcoil MAS probe show promise in profiling the metabolome in a submilligram tissue biopsy with spectral resolution on par with conventional high-resolution MAS (HR-MAS) NMR. This result subsequently triggered a great interest in the possibility of NMR analysis with microgram tissues and striving toward the probe development of "high-resolution" capable microcoil MAS NMR spectroscopy. This review gives an overview of the issues and challenges in the probe development and summarizes the advancements toward metabolomics.

Simultaneous recoupling of chemical shift tensors of two nuclei by R-symmetry sequences

Chemical shift tensors (CSTs) are sensitive probes of structure and dynamics. R-symmetry pulse sequences (RNCSA) can efficiently recouple CSTs of varying magnitudes in magic angle spinning (MAS) NMR experiments, for a broad range of conditions and MAS frequencies. Herein, we introduce dual-channel R-symmetry pulse sequences for simultaneously recording CSTs of two different nuclei in a single experiment (DORNE-CSA). We demonstrate the performance of DORNE-CSA sequences for simultaneous measurement of 13C and 15N CSTs, on a U-13C,15N-labeled microcrystalline l-histidine. We show that the DORNE-CSA method is robust, provides accurate CST parameters, and takes only half of the measurement time compared to a pair of RNCSA experiments otherwise required for recording the CSTs of individual nuclei. DORNE-CSA approach is broadly applicable to a wide range of biological and inorganic systems.

Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications

Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.

19F fast MAS (60-111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations

¹⁹F magic angle spinning (MAS) NMR spectroscopy is a powerful tool for characterization of fluorinated solids. The recent development of ¹⁹F MAS NMR probes, operating at spinning frequencies of 60-111 kHz, enabled analysis of systems spanning from organic molecules to pharmaceutical formulations to biological assemblies, with unprecedented resolution. Herein, we systematically evaluate the benefits of high MAS frequencies (60-111 kHz) for 1D and 2D ¹⁹F-detected experiments in two pharmaceuticals, the antimalarial drug mefloquine and a formulation of the cholesterol-lowering drug atorvastatin calcium. We demonstrate that ¹H decoupling is essential and that scalar-based, heteronuclear single quantum coherence (HSQC) and heteronuclear multiple quantum coherence (HMQC) correlation experiments become feasible and efficient at the MAS frequency of 100 kHz. This study opens doors for the applications of high frequency ¹⁹F MAS NMR to a wide range of problems in chemistry and biology.

Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation

Microtubules (MTs) and their associated proteins play essential roles in maintaining cell structure, organelle transport, cell motility, and cell division. Two motors, kinesin and cytoplasmic dynein link the MT network to transported cargos using ATP for force generation. Here, we report an all-atom NMR structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The structure reveals the position and orientation of the functionally important neck linker and how ADP induces structural and dynamic changes that ensue in the neck linker. These results demonstrate that the neck linker is in the undocked conformation and oriented in the direction opposite to the KIF5B movement. Chemical shift perturbations and intensity changes indicate that a significant portion of ADP-KIF5B is in the neck linker docked state. This study also highlights the unique capability of MAS NMR to provide atomic-level information on dynamic regions of biological assemblies.

Field and magic angle spinning frequency dependence of proton resonances in rotating solids

Proton detection in solid state NMR is continuously developing and allows one to gain new insights in structural biology. Overall, this progress is a result of the synergy between hardware development, new NMR methodology and new isotope labeling strategies, to name a few factors. Even though current developments are rapid, it is worthwhile to summarize what can currently be achieved employing proton detection in biological solids. We illustrate this by analysing the signal-to-noise ratio (SNR) for spectra obtained for a microcrystalline α-spectrin SH3 domain protein sample by (i) employing different degrees of chemical dilution to replace protons by incorporating deuterons in different sites, by (ii) variation of the magic angle spinning (MAS) frequencies between 20 and 110 kHz, and by (iii) variation of the static magnetic field B₀. The experimental SNR values are validated with numerical simulations employing up to 9 proton spins. Although in reality a protein would contain far more than 9 protons, in a deuterated environment this is a sufficient number to achieve satisfactory simulations consistent with the experimental data. The key results of this analysis are (i) with current hardware, deuteration is still necessary to record spectra of optimum quality; (ii) 13CH3 isotopomers for methyl groups yield the best SNR when MAS frequencies above 100 kHz are available; and (iii) sensitivity increases with a factor beyond B0 3/2 with the static magnetic field due to a transition of proton-proton dipolar interactions from a strong to a weak coupling limit.

1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning

Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.

PHRONESIS: a one-shot approach for sequential assignment of protein resonances by ultrafast MAS solid-state NMR spectroscopy

Solid‐state NMR (ssNMR) spectroscopy has emerged as the method of choice to analyze the structural dynamics of fibrillar, membrane‐bound, and crystalline proteins that are recalcitrant to other structural techniques. Recently, ¹H detection under fast magic angle spinning and multiple acquisition ssNMR techniques have propelled the structural analysis of complex biomacromolecules. However, data acquisition and resonance‐specific assignments remain a bottleneck for this technique. Here, we present a comprehensive multi‐acquisition experiment (PHRONESIS) that simultaneously generates up to ten 3D ¹H‐detected ssNMR spectra. PHRONESIS utilizes broadband transfer and selective pulses to drive multiple independent polarization pathways. High selectivity excitation and de‐excitation of specific resonances were achieved by high‐fidelity selective pulses that were designed using a combination of an evolutionary algorithm and artificial intelligence. We demonstrated the power of this approach with microcrystalline U‐¹³C,¹⁵N GB1 protein, reaching 100 % of the resonance assignments using one data set of ten 3D experiments. The strategy outlined in this work opens up new avenues for implementing novel ¹H‐detected multi‐acquisition ssNMR experiments to speed up and expand the application to larger biomolecular systems.

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.

A 13C three-dimensional DQ-SQ-SQ correlation experiment for high-resolution analysis of complex carbohydrates using solid-state NMR

Complex carbohydrates are the key components of the protective cell walls of microbial pathogens and the bioenergy reservoir in plants and algae. Structural characterization of these polymorphic molecules requires assistance from multidimensional ¹³C correlation approaches. To facilitate the analysis of carbohydrate structure using solid-state NMR, we present a three-dimensional (3D) ¹³C-¹³C-¹³C experiment that includes a double-quantum (DQ) dimension and is thus free of the cube's body diagonal. The enhanced resolution supports the unambiguous resonance assignment of many polysaccharides in plant and fungal cell walls using uniformly ¹³C-labeled cells of spruce and Aspergillus fumigatus. Long-range structural restraints were effectively obtained to revisit our understanding of the spatial organization of plant cellulose microfibrils. The method is widely applicable to the investigations of cellular carbohydrates and carbon-based biomaterials.

Investigating Crystalline Protein Suspension Formulations of Pembrolizumab from MAS NMR Spectroscopy

Developing biological formulations to maintain the chemical and structural integrity of therapeutic antibodies remains a significant challenge. Monoclonal antibody (mAb) crystalline suspension formulation is a promising alternative for high concentration subcutaneous drug delivery. It demonstrates many merits compared to the solution formulation to reach a high concentration at the reduced viscosity and enhanced stability. One main challenge in drug development is the lack of high-resolution characterization of the crystallinity and stability of mAb microcrystals in the native formulations. Conventional analytical techniques often cannot evaluate structural details of mAb microcrystals in the native suspension due to the presence of visible particles, relatively small crystal size, high protein concentration, and multicomponent nature of a liquid formulation. This study demonstrates the first high-resolution characterization of mAb microcrystalline suspension using magic angle spinning (MAS) NMR spectroscopy. Crystalline suspension formulation of pembrolizumab (Keytruda, Merck & Co., Inc., Kenilworth, NJ 07033, U.S.) is utilized as a model system. Remarkably narrow ¹³C spectral linewidth of approximately 29 Hz suggests a high order of crystallinity and conformational homogeneity of pembrolizumab crystals. The impact of thermal stress and dehydration on the structure, dynamics, and stability of these mAb crystals in the formulation environment is evaluated. Moreover, isotopic labeling and heteronuclear ¹³C and ¹⁵N spectroscopies have been utilized to identify the binding of caffeine in the pembrolizumab crystal lattice, providing molecular insights into the cocrystallization of the protein and ligand. Our study provides valuable structural details for facilitating the design of crystalline suspension formulation of Keytruda and demonstrates the high potential of MAS NMR as an advanced tool for biophysical characterization of biological therapeutics.

Separating an overlapped 1H peak and identifying its 1H-1H correlations with the use of single-channel 1H solid-state NMR at fast MAS

Fast magic-angle spinning (≥60 ​kHz) technique has enabled the acquisition of high-resolution ¹H NMR spectra of solid materials. However, the spectral interpretation is still difficult because the ¹H peaks are overlapped due to the narrow chemical shift range and broad linewidths. An additional ¹³C or ¹⁴N or ¹H dimension possibly addresses the issues of overlapped proton resonances, but it leads to the elongated experimental time. Herein, we introduce a single-channel ¹H experiment to separate the overlapped ¹H peak and identify its spatially proximal ¹H-¹H correlations. This sequence combines selective excitation, selective ¹H-¹H polarization transfer by selective recoupling of protons (SERP), and broadband ¹H recoupling by back-to-back (BABA) recoupling sequences. The concept for ¹H separation is based on (i) the selective excitation of a well-resolved ¹H peak and (ii) the selective dipolar polarization transfer from this isolated ¹H peak to one of the ¹H peaks in the overlapped/poor resolution region by SERP and (iii) the detection of ¹H-¹H correlations from these two ¹H peaks to other neighboring ¹Hs by BABA. We demonstrated the applicability of this approach to identify overlapped peaks on two molecules, β-L-aspartyl-l-alanine and Pioglitazone.HCl. The sequence allows the clear observation of ¹H-¹H correlations from an overlapped ¹H peak without an additional heteronuclear dimension and ensures efficient polarization transfers that leads to twelve fold reduction in experimental time compared to ¹⁴N edited experiments. The limitation and the conditions of applicability for this approach are discussed in detail.

Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems

With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.

Proton-phosphorous connectivities revealed by high-resolution proton-detected solid-state NMR

Proton-detected solid-state NMR enables atomic-level insight in solid-state reactions, for instance in heterogeneous catalysis, which is fundamental for deciphering chemical reaction mechanisms. We herein introduce a phosphorus-31 radiofrequency channel in...

Optimisation of 1H PMLG homonuclear decoupling at 60 kHz MAS to enable 15N-1H through-bond heteronuclear correlation solid-state NMR spectroscopy

The Lee–Goldburg condition for homonuclear decoupling in ¹H magic-angle spinning (MAS) solid-state NMR sets the angle θ, corresponding to arctan of the ratio of the rf nutation frequency, ν₁, to the rf offset, to be the magic angle, θ_m, equal to tan⁻¹(√2) = 54.7°. At 60 kHz MAS, we report enhanced decoupling compared to MAS alone in a ¹H spectrum of ¹⁵N-glycine with at θ = 30° for a ν₁ of ∼100 kHz at a ¹H Larmor frequency, ν₀, of 500 MHz and 1 GHz, corresponding to a high chemical shift scaling factor (λ_CS) of 0.82. At 1 GHz, we also demonstrate enhanced decoupling compared to 60 kHz MAS alone for a lower ν₁ of 51 kHz, i.e., a case where the nutation frequency is less than the MAS frequency, with θ = 18°, λ_CS = 0.92. The ratio of the rotor period to the decoupling cycle time, Ψ = τ_r/τ_c, is in the range 0.53 to 0.61. Windowed decoupling using the optimised parameters for a ν₁ of ∼100 kHz also gives good performance in a ¹H spin-echo experiment, enabling implementation in a ¹H-detected ¹⁵N–¹H cross polarisation (CP)-refocused INEPT heteronuclear correlation NMR experiment. Specifically, initial ¹⁵N transverse magnetisation as generated by ¹H–¹⁵N CP is transferred back to ¹H using a refocused INEPT pulse sequence employing windowed ¹H decoupling. Such an approach ensures the observation of through-bond N–H connectivities. For ¹⁵N-glycine, while the CP-refocused INEPT experiment has a lower sensitivity (∼50%) as compared to a double CP experiment (with a 200 μs ¹⁵N to ¹H CP contact time), there is selectivity for the directly bonded NH₃⁺ moiety, while intensity is observed for the CH₂¹H resonances in the double CP experiment. Two-dimensional ¹⁵N–¹H correlation MAS NMR spectra are presented for the dipeptide β-AspAla and the pharmaceutical cimetidine at 60 kHz MAS, both at natural isotopic abundance. For the dipeptide β-AspAla, different build-up dependence on the first spin-echo duration is observed for the NH and NH₃⁺ moieties demonstrating that the experiment could be used to distinguish resonances for different NH_x groups.

¹⁵N–¹H heteronuclear NMR correlation at natural abundance in the solid state via J couplings is enabled by optimisation of phase-modulated Lee–Goldburg (PMLG) ¹H homonuclear decoupling during the spin echoes, far from the ideal magic-angle condition.

Production and Preparation of Isotopically Labeled Human Membrane Proteins in Pichia pastoris for Fast-MAS-NMR Analyses

Membrane proteins (MPs) comprise about one-third of the human proteome, playing critical roles in many physiological processes and associated disorders. Consistently, they represent one of the largest classes of targets for the pharmaceutical industry. Their study at the molecular level is however particularly challenging, resulting in a severe lack of structural and dynamic information that is hindering their detailed functional characterization and the identification of novel potent drug candidates.Magic Angle Spinning (MAS) NMR is a reliable and efficient method for the determination of protein structures and dynamics and for the identification of ligand binding sites and equilibria. MAS-NMR is particularly well suited for MPs since they can be directly analysed in a native-like lipid bilayer environment but used to require aggravating large amounts of isotope enriched material. The frequent toxicity of human MP overexpression in bacterial cultures poses an additional hurdle, resulting in the need for alternative (and often more costly) expression systems. The recent development of very fast (up to 150 kHz) MAS probes has revolutionized the field of biomolecular solid-state NMR enabling higher spectral resolution with significant reduction of the required sample, rendering eukaryotic expression systems cost-effective.Here is presented a set of accessible procedures validated for the production and preparation of eukaryotic MPs for Fast-MAS ¹H-detected NMR analysis. The methodology is illustrated with the human copper uptake protein hCTR1 recombinantly produced and ¹³C-¹⁵N uniformly labeled with the versatile and affordable Pichia pastoris system. Subsequent purification procedures allow the recovery of mg amounts that are then reconstituted into liposome formulations compatible with solid-state NMR handling and analysis.

Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants

Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.

Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS

Solid-state NMR spectroscopy is a powerful technique to study insoluble and non-crystalline proteins and protein complexes at atomic resolution. The development of proton (¹H) detection at fast magic-angle spinning (MAS) has considerably increased the analytical capabilities of the technique, enabling the acquisition of ¹H-detected fingerprint experiments in few hours. Here an approach based on double-quantum (DQ) ¹³C spectroscopy, detected on ¹H, is proposed for fast MAS regime (> 60 kHz) to perform the sequential assignment of insoluble proteins of small size, without any specific deuteration requirement. By combining two three-dimensional ¹H detected experiments correlating a ¹³C DQ dimension respectively to its intra-residue and sequential ¹⁵ N-¹H pairs, a sequential walk through DQ (Ca + CO) resonance is obtained. The approach takes advantage of fast MAS to achieve an efficient sensitivity and the addition of a DQ dimension provides spectral features useful for the resonance assignment process.

Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology

The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.

Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Proton-detected fast-magic-angle spinning NMR of paramagnetic inorganic solids

Fast (60 kHz) magic angle spinning solid-state NMR allows very sensitive proton detection in highly paramagnetic organometallic powders. We showcase this technique with the complete assignment of ¹H and ¹³C resonances in a high-spin Fe(ii) polymerisation catalyst with less than 2 mg of sample at natural abundance.

Identification of RNA base pairs and complete assignment of nucleobase resonances by 1H-detected solid-state NMR spectroscopy at 100 kHz MAS

Knowledge of RNA structure, either in isolation or in complex, is fundamental to understand the mechanism of cellular processes. Solid‐state NMR (ssNMR) is applicable to high molecular‐weight complexes and does not require crystallization; thus, it is well‐suited to study RNA as part of large multicomponent assemblies. Recently, we solved the first structures of both RNA and an RNA‐protein complex by ssNMR using conventional ¹³C‐ and ¹⁵N‐detection. This approach is limited by the severe overlap of the RNA peaks together with the low sensitivity of multidimensional experiments. Here, we overcome the limitations in sensitivity and resolution by using ¹H‐detection at fast MAS rates. We develop experiments that allow the identification of complete nucleobase spin‐systems together with their site‐specific base pair pattern using sub‐milligram quantities of one uniformly labelled RNA sample. These experiments provide rapid access to RNA secondary structure by ssNMR in protein‐RNA complexes of any size.

Biomolecular solid-state NMR spectroscopy at 1200 MHz: the gain in resolution

Progress in NMR in general and in biomolecular applications in particular is driven by increasing magnetic-field strengths leading to improved resolution and sensitivity of the NMR spectra. Recently, persistent superconducting magnets at a magnetic field strength (magnetic induction) of 28.2 T corresponding to 1200 MHz proton resonance frequency became commercially available. We present here a collection of high-field NMR spectra of a variety of proteins, including molecular machines, membrane proteins, viral capsids, fibrils and large molecular assemblies. We show this large panel in order to provide an overview over a range of representative systems under study, rather than a single best performing model system. We discuss both carbon-13 and proton-detected experiments, and show that in ¹³C spectra substantially higher numbers of peaks can be resolved compared to 850 MHz while for ¹H spectra the most impressive increase in resolution is observed for aliphatic side-chain resonances.

Selective 1H-1H recoupling via symmetry sequences in fully protonated samples at fast magic angle spinning

Proton-detected solid-state NMR at fast Magic Angle Spinning (MAS) is becoming the norm to characterize molecules. Routinely ¹H-¹H and ¹H-X dipolar couplings are used to characterize the structure and dynamics of molecules. Selective proton recoupling techniques are emerging as a method for structural characterization via estimation of qualitative and quantitative distances. In the present study, we demonstrate through numerical simulations and experiments that the well-characterized CN^v_n sequences can also be tailored for selective recoupling of proton spins by employing C elements of the type (β)_Φ(4β)_Φ+π(3β)_Φ. Herein, several CN^v_n sequences were examined through numerical simulations and experiments. C6¹₄ recoupling sequence with a modified POST-element ((β)_Φ(4β)_Φ+π(3β)_Φ) shows selective polarization transfer efficiencies on the order of 40-50% between various proton spin pairs in fully protonated samples at rf amplitudes ranging from 0.3 to 0.8 times the MAS frequency. These selective recoupling sequences have been labeled as frequency-selective-CN^v_n sequences. The extent of selectivity, polarization transfer efficiency and the feasibility of experimentally measuring proton-proton distances in fully protonated samples are explored here. The development of efficient and robust selective ¹H-¹H recoupling experiments is required to structurally characterize molecules without artificial isotope enrichment or the need for diffracting crystals.

Residual dipolar line width in magic-angle spinning proton solid-state NMR

Magic-angle spinning is routinely used to average anisotropic interactions in solid-state nuclear magnetic resonance (NMR). Due to the fact that the homonuclear dipolar Hamiltonian of a strongly coupled spin system does not commute with itself at different time points during the rotation, second-order and higher-order terms lead to a residual dipolar line broadening in the observed resonances. Additional truncation of the residual broadening due to isotropic chemical-shift differences can be observed. We analyze the residual line broadening in coupled proton spin systems based on theoretical calculations of effective Hamiltonians up to third order using Floquet theory and compare these results to numerically obtained effective Hamiltonians in small spin systems. We show that at spinning frequencies beyond 75 kHz, second-order terms dominate the residual line width, leading to a 1 / ω r dependence of the second moment which we use to characterize the line width. However, chemical-shift truncation leads to a partial ω r - 2 dependence of the line width which looks as if third-order effective Hamiltonian terms are contributing significantly. At slower spinning frequencies, cross terms between the chemical shift and the dipolar coupling can contribute in third-order effective Hamiltonians. We show that second-order contributions not only broaden the line, but also lead to a shift of the center of gravity of the line. Experimental data reveal such spinning-frequency-dependent line shifts in proton spectra in model substances that can be explained by line shifts induced by the second-order dipolar Hamiltonian.

Protein structural dynamics by Magic-Angle Spinning NMR

Magic-Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR) is a fast-developing technique, capable of complementing solution NMR, X-ray crystallography, and electron microscopy for the biophysical characterization of microcrystalline, poorly crystalline or disordered protein samples, such as enzymes, biomolecular assemblies, membrane-embedded systems or fibrils. Beyond structures, MAS NMR is an ideal tool for the investigation of dynamics, since it is unique in its ability to distinguish static and dynamic disorder, and to characterize not only amplitudes but also timescales of motion. Building on seminal work on model proteins, the technique is now ripe for widespread application in structural biology. This review briefly summarizes the recent evolutions in biomolecular MAS NMR and accounts for the growing number of systems where this spectroscopy has provided a description of conformational dynamics over the very last few years.

Dimer Organization of Membrane-Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive 1 H-Detected Solid-State NMR

The Hepatitis C virus nonstructural protein 5A (NS5A) is a membrane-associated protein involved in multiple steps of the viral life cycle. Direct-acting antivirals (DAAs) targeting NS5A are a cornerstone of antiviral therapy, but the mode-of-action of these drugs is poorly understood. This is due to the lack of information on the membrane-bound NS5A structure. Herein, we present the structural model of an NS5A AH-linker-D1 protein reconstituted as proteoliposomes. We use highly sensitive proton-detected solid-state NMR methods suitable to study samples generated through synthetic biology approaches. Spectra analyses disclose that both the AH membrane anchor and the linker are highly flexible. Paramagnetic relaxation enhancements (PRE) reveal that the dimer organization in lipids requires a new type of NS5A self-interaction not reflected in previous crystal structures. In conclusion, we provide the first characterization of NS5A AH-linker-D1 in a lipidic environment shedding light onto the mode-of-action of clinically used NS5A inhibitors.

Signal Deconvolution and Generative Topographic Mapping Regression for Solid-State NMR of Multi-Component Materials

Solid-state nuclear magnetic resonance (ssNMR) spectroscopy provides information on native structures and the dynamics for predicting and designing the physical properties of multi-component solid materials. However, such an analysis is difficult because of the broad and overlapping spectra of these materials. Therefore, signal deconvolution and prediction are great challenges for their ssNMR analysis. We examined signal deconvolution methods using a short-time Fourier transform (STFT) and a non-negative tensor/matrix factorization (NTF, NMF), and methods for predicting NMR signals and physical properties using generative topographic mapping regression (GTMR). We demonstrated the applications for macromolecular samples involved in cellulose degradation, plastics, and microalgae such as Euglena gracilis. During cellulose degradation, ¹³C cross-polarization (CP)-magic angle spinning spectra were separated into signals of cellulose, proteins, and lipids by STFT and NTF. GTMR accurately predicted cellulose degradation for catabolic products such as acetate and CO₂. Using these methods, the ¹H anisotropic spectrum of poly-ε-caprolactone was separated into the signals of crystalline and amorphous solids. Forward prediction and inverse prediction of GTMR were used to compute STFT-processed NMR signals from the physical properties of polylactic acid. These signal deconvolution and prediction methods for ssNMR spectra of macromolecules can resolve the problem of overlapping spectra and support macromolecular characterization and material design.

Solid-state NMR approaches to investigate large enzymes in complex with substrates and inhibitors

Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies.

Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR

Protein–nucleic acid interactions are essential in a variety of biological events ranging from the replication of genomic DNA to the synthesis of proteins. Noncovalent interactions guide such molecular recognition events, and protons are often at the center of them, particularly due to their capability of forming hydrogen bonds to the nucleic acid phosphate groups. Fast magic-angle spinning experiments (100 kHz) reduce the proton NMR line width in solid-state NMR of fully protonated protein–DNA complexes to such an extent that resolved proton signals from side-chains coordinating the DNA can be detected. We describe a set of NMR experiments focusing on the detection of protein side-chains from lysine, arginine, and aromatic amino acids and discuss the conclusions that can be obtained on their role in DNA coordination. We studied the 39 kDa enzyme of the archaeal pRN1 primase complexed with DNA and characterize protein–DNA contacts in the presence and absence of bound ATP molecules.

Structural biology of human GPCR drugs and endogenous ligands - insights from NMR spectroscopy

G protein-coupled receptors (GPCRs) represent the largest class of "druggable" proteins in the human genome. For more than a decade, crystal structures and, more recently, cryoEM structures of GPCR complexes have provided unprecedented insight into GPCR drug binding and cell signaling. Nevertheless, structure determination of receptors in complexes with weakly binding molecules or complex polypeptides remains especially challenging, including for hormones, many of which have so far eluded researchers. Nuclear magnetic resonance (NMR) spectroscopy has emerged as a promising approach to determine structures of ligands bound to their receptors and to provide insights into the dynamics of GPCR-bound drugs. The capability to investigate compounds with weak binding affinities has also been leveraged in NMR applications to identify novel lead compounds in drug screening campaigns. We review recent structural biology studies of GPCR ligands by NMR, highlighting new methodologies enabling studies of GPCRs with native sequences and in native-like membrane environments that provide insights into important drugs and endogenous ligands.

Multi-receiver solid-state NMR using polarization optimized experiments (POE) at ultrafast magic angle spinning

Ultrafast magic angle spinning (MAS) technology and ¹H detection have dramatically enhanced the sensitivity of solid-state NMR (ssNMR) spectroscopy of biopolymers. We previously showed that, when combined with polarization optimized experiments (POE), these advancements enable the simultaneous acquisition of multi-dimensional ¹H- or ¹³C-detected experiments using a single receiver. Here, we propose a new sub-class within the POE family, namely HC-DUMAS, HC-MEIOSIS, and HC-MAeSTOSO, that utilize dual receiver technology for the simultaneous detection of ¹H and ¹³C nuclei. We also expand this approach to record ¹H-, ¹³C-, and ¹⁵N-detected homonuclear 2D spectra simultaneously using three independent receivers. The combination of POE and multi-receiver technology will further shorten the total experimental time of ssNMR experiments for biological solids.

CCMRD: a solid-state NMR database for complex carbohydrates

Carbohydrates are essential to various life activities in living organisms and serve as the central component in many biomaterials. As an emerging technique with steadily improving resolution, solid-state Nuclear Magnetic Resonance (NMR) spectroscopy has the unique capability in revealing the polymorphic structure and heterogeneous dynamics of insoluble complex carbohydrates. Here, we report the first solid-state NMR database for complex carbohydrates, Complex Carbohydrates Magnetic Resonance Database (CCMRD). This database currently holds the chemical shift information of more than four hundred solid-state NMR compounds and expects rapid expansion. CCMRD provides open portals for data deposition and supports search options based on NMR chemical shifts, carbohydrate names, and compound classes. With the timely implementation, this platform will facilitate spectral analysis and structure determination of carbohydrates and promote software development to benefit the research community. The database is freely accessible at www.ccmrd.org.

Simultaneous recording of intra- and inter-residue linking experiments for backbone assignments in proteins at MAS frequencies higher than 60 kHz

Obtaining site-specific assignments for the NMR spectra of proteins in the solid state is a significant bottleneck in deciphering their biophysics. This is primarily due to the time-intensive nature of the experiments. Additionally, the low resolution in the [Formula: see text]-dimension requires multiple complementary experiments to be recorded to lift degeneracies in assignments. We present here an approach, gleaned from the techniques used in multiple-acquisition experiments, which allows the recording of forward and backward residue-linking experiments in a single experimental block. Spectra from six additional pathways are also recovered from the same experimental block, without increasing the probe duty cycle. These experiments give intra- and inter residue connectivities for the backbone [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] resonances and should alone be sufficient to assign these nuclei in proteins at MAS frequencies > 60 kHz. The validity of this approach is tested with experiments on a standard tripeptide N-formyl methionyl-leucine-phenylalanine (f-MLF) at a MAS frequency of 62.5 kHz, which is also used as a test-case for determining the sensitivity of each of the experiments. We expect this approach to have an immediate impact on the way assignments are obtained at MAS frequencies [Formula: see text].

MAS NMR detection of hydrogen bonds for protein secondary structure characterization

Hydrogen bonds are essential for protein structure and function, making experimental access to long-range interactions between amide protons and heteroatoms invaluable. Here we show that measuring distance restraints involving backbone hydrogen atoms and carbonyl- or α-carbons enables the identification of secondary structure elements based on hydrogen bonds, provides long-range contacts and validates spectral assignments. To this end, we apply specifically tailored, proton-detected 3D (H)NCOH and (H)NCAH experiments under fast magic angle spinning (MAS) conditions to microcrystalline samples of SH3 and GB1. We observe through-space, semi-quantitative correlations between protein backbone carbon atoms and multiple amide protons, enabling us to determine hydrogen bonding patterns and thus to identify β-sheet topologies and α-helices in proteins. Our approach shows the value of fast MAS and suggests new routes in probing both secondary structure and the role of functionally-relevant protons in all targets of solid-state MAS NMR.

Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy

Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.

Suppressing 1H Spin Diffusion in Fast MAS Proton Detected Heteronuclear Correlation Solid-State NMR Experiments

Fast magic angle spinning (MAS) and indirect detection by high gyromagnetic ratio (γ) nuclei such as proton or fluorine are increasingly utilized to obtain 2D heteronuclear correlation (HETCOR) solid-state NMR spectra of spin-1/2 nuclei by using cross polarization (CP) for coherence transfer. However, one major drawback of CP HETCOR pulse sequences is that ¹H spin diffusion during the back X→¹H CP transfer step may result in relayed correlations. This problem is particularly pronounced for the indirect detection of very low-γ nuclei such as ⁸⁹Y, ¹⁰³Rh, ¹⁰⁹Ag and ¹⁸³W where long contact times on the order of 10-30 ms are necessary for optimal CP transfer. Here we propose two methods that eliminate relayed correlations and allow more reliable distance information to be obtained from 2D HETCOR NMR spectra. The first method uses Lee-Goldburg (LG) CP during the X→¹H back-transfer step to suppress ¹H spin diffusion. We determine LG conditions compatible with fast MAS frequencies (ν_rot) of 40-95 kHz and show that ¹H spin diffusion can be efficiently suppressed at low effective radiofrequency (RF) fields (ν_1,eff ≪ 0.5ν_rot) and also at high effective RF fields (ν_1,eff ≫ 2ν_rot). We describe modified Hartmann-Hahn LG-CP match conditions compatible with fast MAS and suitable for indirect detection of moderate-γ nuclei such as ¹³C, and low-γ nuclei such as ⁸⁹Y. The second method uses D-RINEPT (dipolar refocused insensitive nuclei enhanced by polarization transfer) during the X→¹H back-transfer step of the HETCOR pulse sequence. The effectiveness of these methods for acquiring HETCOR spectra with reduced relayed signal intensities is demonstrated with ¹H{¹³C} HETCOR NMR experiments on l-histidine⋅HCl⋅H₂O and ¹H{⁸⁹Y} HETCOR NMR experiments on an organometallic yttrium complex.

Ultrafast 1H MAS NMR Crystallography for Natural Abundance Pharmaceutical Compounds

Magic angle spinning (MAS) NMR is a powerful method for the study of pharmaceutical compounds, and probes with spinning frequencies above 100 kHz enable an atomic-resolution analysis of sub-micromole quantities of fully protonated solids. Here, we present an ultrafast NMR crystallography approach for structural characterization of organic solids at MAS frequencies of 100-111 kHz. We assess the efficiency of ¹H-detected experiments in the solid state and demonstrate the utility of 2D and 3D homo- and heteronuclear correlation spectra for resonance assignments. These experiments are demonstrated for an amino acid, U-¹³C,¹⁵N-histidine, and also for the significantly larger, natural product Posaconazole, an antifungal compound investigated at natural abundance. Our results illustrate the power for characterizing organic molecules, enabled by exploiting the increased ¹H resolution and sensitivity at MAS frequencies above 100 kHz.

Molecular packing of pharmaceuticals analyzed with paramagnetic relaxation enhancement and ultrafast magic angle pinning NMR

Probing molecular details of fluorinated pharmaceutical compounds at a faster acquisition utilizing paramagnetic relaxation enhancement and better resolution from ultrafast magic angle spinning (ν_rot = 110 kHz) and high magnetic field (B₀ = 18.8 T).