Determination of Through-Bond Carbon−Carbon Connectivities in Solid-State NMR Using the INADEQUATE Experiment

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.

Molecular architecture of chitin and chitosan-dominated cell walls in zygomycetous fungal pathogens by solid-state NMR

Zygomycetous fungal infections pose an emerging medical threat among individuals with compromised immunity and metabolic abnormalities. Our pathophysiological understanding of these infections, particularly the role of fungal cell walls in growth and immune response, remains limited. Here we conducted multidimensional solid-state NMR analysis to examine cell walls in five Mucorales species, including key mucormycosis causative agents like Rhizopus and Mucor species. We show that the rigid core of the cell wall primarily comprises highly polymorphic chitin and chitosan, with minimal quantities of β-glucans linked to a specific chitin subtype. Chitosan emerges as a pivotal molecule preserving hydration and dynamics. Some proteins are entrapped within this semi-crystalline chitin/chitosan layer, stabilized by the sidechains of hydrophobic amino acid residues, and situated distantly from β-glucans. The mobile domain contains galactan- and mannan-based polysaccharides, along with polymeric α-fucoses. Treatment with the chitin synthase inhibitor nikkomycin removes the β-glucan-chitin/chitosan complex, leaving the other chitin and chitosan allomorphs untouched while simultaneously thickening and rigidifying the cell wall. These findings shed light on the organization of Mucorales cell walls and emphasize the necessity for a deeper understanding of the diverse families of chitin synthases and deacetylases as potential targets for novel antifungal therapies.

Dynamics in the Intact fd Bacteriophage Revealed by Pseudo 3D REDOR-Based Magic Angle Spinning NMR

The development of robust NMR methodologies to probe dynamics on the atomic scale is vital to elucidate the close relations between structure, motion, and function in biological systems. Here, we present an automated protocol to measure, using magic-angle spinning NMR, the effective 13C-15N dipolar coupling constants between multiple spin pairs simultaneously with high accuracy. We use the experimental dipolar coupling constants to quantify the order parameters of multiple C-N bonds in the thousands of identical copies of the coat protein in intact fd-Y21M filamentous bacteriophage virus and describe its overall dynamics on the submillisecond time scale. The method is based on combining three pseudo three-dimensional NMR experiments, where a rotational echo double resonance (REDOR) dephasing block, designed to measure internuclear distances, is combined with three complementary 13C-13C mixing schemes: dipolar-assisted rotational resonance, through-bond transfer-based double quantum/single quantum correlation, and radio frequency driven recoupling. These mixing schemes result in highly resolved carbon spectra with correlations that are created by different transfer mechanisms. We show that the helical part of the coat protein undergoes a uniform small (∼30°) amplitude motion, while the N-terminus is highly flexible. In addition, our results suggest that the reduced mobility of lysine sidechains at the C-terminus are a signature of binding to the single stranded DNA.

Quantitative and Structural Characterization of Native Lignin in Hardwood and Softwood Bark via Solid-State NMR Spectroscopy

A major factor limiting bark's industrial use is its greater recalcitrance compared to wood. While lignin is widely recognized as a significant contributor, precise characterization of lignin in bark remains sparse, presenting a crucial gap that impedes understanding of its impact. In this study, we employed advanced solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze bark samples from various species, including willow, poplar, and pine. We established and verified that lignin methoxy peak at 56 ppm serves as a reliable quantitative metric to assess lignin content, with which we calculated the lignin contents in bark are significantly reduced by more than 70% compared to those in wood. Furthermore, in situ characterization revealed significant reduction of β-ether linkage in bark lignin across species, revealing a more condensed and resistant structural configuration. Our results have substantially advanced our comprehension of the composition and structure of native lignin in tree bark.

Molecular unraveling of polysaccharide digestion in wood-feeding termites: A solid-state NMR perspective

Termites are among the most efficient organisms utilizing polysaccharides from wood and play a significant role in global carbon recycling, especially within tropical and subtropical ecosystems. Yet, the molecular details in polysaccharide degradation by termites remain largely unexplored. In this work, we have elucidated the shared and distinct molecular details in polysaccharides digestion by the higher termite Nasutitermes on poplar and the lower termite Cryptotermes on pine using high resolution solid-state nuclear magnetic resonance spectroscopy. For the first time, structural polymers are partitioned into the minor mobile and dominant rigid phases for individual examination. The mobile polysaccharides receive less structural impacts and exhibit greater digestibility compared to the rigid counterparts. While both termites effectively degrade cellulose, Nasutitermes significantly outperforms Cryptotermes in hemicellulose breakdown. In the rigid phase, cellulose is comprehensively degraded into a fragmented and more dynamically consistent structure; As Nasutitermes breaks down hemicellulose in a similar manner to cellulose, Cryptotermes selectively digests hemicellulose at its interfaces with cellulose. Additionally, crystalline cellulose undergoes selective degradation, and the digestion of amorphous cellulose might involve sugar chain detachment within microfibrils. Overall, our findings offer significant advancements and fresh perspectives on the polysaccharide digestion strategies of different termite lineages.

Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy

The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.

NMR crystallography of amino acids

The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.

Polarization Amplification in Dynamic Nuclear Polarization Magic-Angle Spinning Solid-State Nuclear Magnetic Resonance by Solubilizing Traditional Ionic Salts

Dynamic nuclear polarization can improve the sensitivity of magic-angle spinning solid-state NMR experiments by 1-2 orders of magnitude. In aqueous media, experiments are usually performed using the so-called DNP juice, a glycerol-d8/D2O/H2O mixture (60/30/10, v/v/v) that can form a homogeneous glass at cryogenic temperatures. This acts as a cryoprotectant and prevents phase separation of the paramagnetic polarizing agents (PAs) that are added to the mixture to provide the source of electron spin polarization required for DNP. Here, we show that relatively high 1H DNP enhancements (∼60) can also be obtained in water without glycerol (or other glass forming agents) simply by dissolving high concentrations of electrolytes (such as NaCl or LiCl), which perturb the otherwise unavoidable ice crystallization observed upon cooling, thereby reducing PA phase separation and restoring DNP efficiency.

Barriers to resolution in 1H NMR of rotating solids

The role of 1H solid-state NMR in structure elucidation of solids is becoming more preponderant, particularly as faster magic-angle spinning rates (MAS) become available which improve 1H detected assignment strategies. However, current 1H spectral resolution is still relatively poor, with linewidths of typically a few hundred Hz, even at the fastest rates available today. Here we detail and assess the factors limiting proton linewidths and line shapes in MAS experiments with five different samples, exemplifying the different sources of broadening that affect the residual linewidth. We disentangle the different contributions through one- and two-dimensional experiments: by using dilution to identify the contribution of ABMS; by using extensive deuteration to identify the dipolar contributions; and by using variable MAS rates to determine the ratio between homogeneous and inhomogeneous components. We find that the overall widths and the nature of the different contributions to the linewidths can vary very considerably. While we find that faster spinning always yields narrower lines and longer coherence lifetimes, we also find that for some resonances the dipolar contribution is no longer dominant at 100 kHz MAS. When the inhomogeneous sources of broadening, such as ABMS and chemical shift disorder, are dominant, two-dimensional 1H-1H correlation experiments yield better resolution for assignment. Particularly the extraction of the antidiagonal of a 2D peak will remove any correlated inhomogeneous broadening, giving substantially narrower 1H linewidths.

Elongated galactan side chains mediate cellulose-pectin interactions in engineered Arabidopsis secondary cell walls

The plant secondary cell wall is a thickened matrix of polysaccharides and lignin deposited at the cessation of growth in some cells. It forms the majority of carbon in lignocellulosic biomass, and it is an abundant and renewable source for forage, fiber, materials, fuels, and bioproducts. The complex structure and arrangement of the cell wall polymers mean that the carbon is difficult to access in an economical and sustainable way. One solution is to alter the cell wall polymer structure so that it is more suited to downstream processing. However, it remains difficult to predict what the effects of this engineering will be on the assembly, architecture, and properties of the cell wall. Here, we make use of Arabidopsis plants expressing a suite of genes to increase pectic galactan chain length in the secondary cell wall. Using multi-dimensional solid-state nuclear magnetic resonance, we show that increasing galactan chain length enhances pectin-cellulose spatial contacts and increases cellulose crystallinity. We also found that the increased galactan content leads to fewer spatial contacts of cellulose with xyloglucan and the backbone of pectin. Hence, we propose that the elongated galactan side chains compete with xyloglucan and the pectic backbone for cellulose interactions. Due to the galactan topology, this may result in comparatively weak interactions and disrupt the cell wall architecture. Therefore, introduction of this strategy into trees or other bioenergy crops would benefit from cell-specific expression strategies to avoid negative effects on plant growth.

Pure Isotropic Proton NMR Spectra in Solids using Deep Learning

The resolution of proton solid-state NMR spectra is usually limited by broadening arising from dipolar interactions between spins. Magic-angle spinning alleviates this broadening by inducing coherent averaging. However, even the highest spinning rates experimentally accessible today are not able to completely remove dipolar interactions. Here, we introduce a deep learning approach to determine pure isotropic proton spectra from a two-dimensional set of magic-angle spinning spectra acquired at different spinning rates. Applying the model to 8 organic solids yields high-resolution 1 H solid-state NMR spectra with isotropic linewidths in the 50-400 Hz range.

Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS

The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.

Eudicot primary cell wall glucomannan is related in synthesis, structure, and function to xyloglucan

Hemicellulose polysaccharides influence assembly and properties of the plant primary cell wall (PCW), perhaps by interacting with cellulose to affect the deposition and bundling of cellulose fibrils. However, the functional differences between plant cell wall hemicelluloses such as glucomannan, xylan, and xyloglucan (XyG) remain unclear. As the most abundant hemicellulose, XyG is considered important in eudicot PCWs, but plants devoid of XyG show relatively mild phenotypes. We report here that a patterned β-galactoglucomannan (β-GGM) is widespread in eudicot PCWs and shows remarkable similarities to XyG. The sugar linkages forming the backbone and side chains of β-GGM are analogous to those that make up XyG, and moreover, these linkages are formed by glycosyltransferases from the same CAZy families. Solid-state nuclear magnetic resonance indicated that β-GGM shows low mobility in the cell wall, consistent with interaction with cellulose. Although Arabidopsis β-GGM synthesis mutants show no obvious growth defects, genetic crosses between β-GGM and XyG mutants produce exacerbated phenotypes compared with XyG mutants. These findings demonstrate a related role of these two similar but distinct classes of hemicelluloses in PCWs. This work opens avenues to study the roles of β-GGM and XyG in PCWs.

Protein secondary structure in spider silk nanofibrils

Nanofibrils play a pivotal role in spider silk and are responsible for many of the impressive properties of this unique natural material. However, little is known about the internal structure of these protein fibrils. We carry out polarized Raman and polarized Fourier-transform infrared spectroscopies on native spider silk nanofibrils and determine the concentrations of six distinct protein secondary structures, including β-sheets, and two types of helical structures, for which we also determine orientation distributions. Our advancements in peak assignments are in full agreement with the published silk vibrational spectroscopy literature. We further corroborate our findings with X-ray diffraction and magic-angle spinning nuclear magnetic resonance experiments. Based on the latter and on polypeptide Raman spectra, we assess the role of key amino acids in different secondary structures. For the recluse spider we develop a highly detailed structural model, featuring seven levels of structural hierarchy. The approaches we develop are directly applicable to other proteinaceous materials.

Secondary fibril structure is a key component of the mechanical properties of protein materials like silk, yet, limited information is known about the internal structure of these protein fibrils. Here, the authors report on the use of polarised Raman and FTIR spectroscopy to study silk materials and identify six distinct secondary structures.

Pulse induced resonance with angular dependent total enhancement of multi-dimensional solid-state NMR correlation spectra

We demonstrate a new resonance condition that obeys the relation Δδ=nν_R/2, where Δδ is the chemical shift difference between two homonuclear-coupled spins, ν_R is the magic-angle spinning speed and n is an integer. This modulation on the rotational resonance recoupling condition is obtained by the application of rotor-synchronous ¹H pulses when at least one proton is dipolar-coupled to one of the homonuclear spins. We suggest a new experimental scheme entitled 'pulse induced resonance with angular dependent total enhancement' (PIRATE) that can enhance proton-driven spin diffusion by the application of a single ¹H pulse every rotor period. Experimental evidence is demonstrated on the two carbon spins of glycine and on the Y21M mutant of fd bacteriophage virus. Numerical simulations reveal the existence of the resonances and report on the important interactions governing these phenomena.

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.

Carbohydrate-aromatic interface and molecular architecture of lignocellulose

Plant cell walls constitute the majority of lignocellulosic biomass and serve as a renewable resource of biomaterials and biofuel. Extensive interactions between polysaccharides and the aromatic polymer lignin make lignocellulose recalcitrant to enzymatic hydrolysis, but this polymer network remains poorly understood. Here we interrogate the nanoscale assembly of lignocellulosic components in plant stems using solid-state nuclear magnetic resonance and dynamic nuclear polarization approaches. We show that the extent of glycan-aromatic association increases sequentially across grasses, hardwoods, and softwoods. Lignin principally packs with the xylan in a non-flat conformation via non-covalent interactions and partially binds the junction of flat-ribbon xylan and cellulose surface as a secondary site. All molecules are homogeneously mixed in softwoods; this unique feature enables water retention even around the hydrophobic aromatics. These findings unveil the principles of polymer interactions underlying the heterogeneous architecture of lignocellulose, which may guide the rational design of more digestible plants and more efficient biomass-conversion pathways.

The plant biomass is a composite formed by a variety of polysaccharides and an aromatic polymer named lignin. Here, the authors use solid-state NMR spectroscopy to unveil the carbohydrate-aromatic interface that leads to the variable architecture of lignocellulose biomaterials.

Solid-State Nuclear Magnetic Resonance as a Tool to Probe the Impact of Mechanical Preprocessing on the Structure and Arrangement of Plant Cell Wall Polymers

Efficient separation of the plant cell wall polymers during lignocellulose processing has been historically challenging due to insolubility of the polymers and their propensity for recalcitrant reassembly. Methods, such as "lignin first" extraction techniques, have advanced efficient biomass use, but the molecular mechanisms for recalcitrance remain enigmatic. Here, we discuss how solid-state Nuclear Magnetic Resonance (NMR) approaches report on the 3D organization of cellulose, xylan, and lignin in the plant cell wall. Recent results illustrate that the organization of these polymers varies across biomass sources and sample preparation methods, with even minimal physical processing causing significant effects. These structural differences contribute to variable extraction efficiencies for bioproducts after downstream processing. We propose that solid-state NMR methods can be applied to follow biomass processing, providing an understanding of the polymer rearrangements that can lead to poor yields for the desired bioproducts. The utility of the technique is illustrated for mechanical processing using lab-scale vibratory ball milling of Sorghum bicolor.

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.

Bayesian probabilistic assignment of chemical shifts in organic solids

A prerequisite for NMR studies of organic materials is assigning each experimental chemical shift to a set of geometrically equivalent nuclei. Obtaining the assignment experimentally can be challenging and typically requires time-consuming multidimensional correlation experiments. An alternative solution for determining the assignment involves statistical analysis of experimental chemical shift databases, but no such database exists for molecular solids. Here, by combining the Cambridge Structural Database with a machine learning model of chemical shifts, we construct a statistical basis for probabilistic chemical shift assignment of organic crystals by calculating shifts for more than 200,000 compounds, enabling the probabilistic assignment of organic crystals directly from their two-dimensional chemical structure. The approach is demonstrated with the ¹³C and ¹H assignment of 11 molecular solids with experimental shifts and benchmarked on 100 crystals using predicted shifts. The correct assignment was found among the two most probable assignments in more than 80% of cases.

Identification and Quantification of Glycans in Whole Cells: Architecture of Microalgal Polysaccharides Described by Solid-State Nuclear Magnetic Resonance

Microalgae are photosynthetic organisms widely distributed in nature and serve as a sustainable source of bioproducts. Their carbohydrate components are also promising candidates for bioenergy production and bioremediation, but the structural characterization of these heterogeneous polymers in cells remains a formidable problem. Here we present a widely applicable protocol for identifying and quantifying the glycan content using magic-angle-spinning (MAS) solid-state NMR (ssNMR) spectroscopy, with validation from glycosyl linkage and composition analysis deduced from mass-spectrometry (MS). Two-dimensional 13C-13C correlation ssNMR spectra of a uniformly 13C-labeled green microalga Parachlorella beijerinckii reveal that starch is the most abundant polysaccharide in a naturally cellulose-deficient strain, and this polymer adopts a well-organized and highly rigid structure in the cell. Some xyloses are present in both the mobile and rigid domains of the cell wall, with their chemical shifts partially aligned with the flat-ribbon 2-fold xylan identified in plants. Surprisingly, most other carbohydrates are largely mobile, regardless of their distribution in glycolipids or cell walls. These structural insights correlate with the high digestibility of this cellulose-deficient strain, and the in-cell ssNMR methods will facilitate the investigations of other economically important algae species.

Importance of Water in Maintaining Softwood Secondary Cell Wall Nanostructure

Water is one of the principal constituents by mass of living plant cell walls. However, its role and interactions with secondary cell wall polysaccharides and the impact of dehydration and subsequent rehydration on the molecular architecture are still to be elucidated. This work combines multidimensional solid-state ¹³C magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) with molecular dynamics modeling to decipher the role of water in the molecular architecture of softwood secondary cell walls. The proximities between all main polymers, their molecular conformations, and interaction energies are compared in never-dried, oven-dried, and rehydrated states. Water is shown to play a critical role at the hemicellulose–cellulose interface. After significant molecular shrinkage caused by dehydration, the original molecular conformation is not fully recovered after rehydration. The changes include xylan becoming more closely and irreversibly associated with cellulose and some mannan becoming more mobile and changing conformation. These irreversible nanostructural changes provide a basis for explaining and improving the properties of wood-based materials.

A molecular vision of fungal cell wall organization by functional genomics and solid-state NMR

Vast efforts have been devoted to the development of antifungal drugs targeting the cell wall, but the supramolecular architecture of this carbohydrate-rich composite remains insufficiently understood. Here we compare the cell wall structure of a fungal pathogen Aspergillus fumigatus and four mutants depleted of major structural polysaccharides. High-resolution solid-state NMR spectroscopy of intact cells reveals a rigid core formed by chitin, β-1,3-glucan, and α-1,3-glucan, with galactosaminogalactan and galactomannan present in the mobile phase. Gene deletion reshuffles the composition and spatial organization of polysaccharides, with significant changes in their dynamics and water accessibility. The distribution of α-1,3-glucan in chemically isolated and dynamically distinct domains supports its functional diversity. Identification of valines in the alkali-insoluble carbohydrate core suggests a putative function in stabilizing macromolecular complexes. We propose a revised model of cell wall architecture which will improve our understanding of the structural response of fungal pathogens to stresses.

The fungal cell wall is a complex structure composed mainly of glucans, chitin and glycoproteins. Here, the authors use solid-state NMR spectroscopy to assess the cell wall architecture of Aspergillus fumigatus, comparing wild-type cells and mutants lacking major structural polysaccharides, with insights into the distinct functions of these components.

Probing 29Si-17O connectivities and proximities by solid-state NMR

The measurement of dipolar and J- couplings between ²⁹Si and ¹⁷O isotopes is challenging owing to (i) the low abundance of both isotopes and (ii) their close Larmor frequencies, which only differ by 19%. These issues are circumvented here by the use of isotopic enrichment and dedicated triple-resonance magic-angle spinning NMR probe. The surface of ²⁹Si-enriched silica was labelled with ¹⁷O isotope and heated at 80 and 200 °C. ²⁹Si-¹⁷O connectivities and proximities were probed using two-dimensional (2D) through-bond and through-space heteronuclear multiple-quantum coherences (J- and D-HMQC) experiments between ¹⁷O and ²⁹Si nuclei. The simulation of the build-up of the J- and D-HMQC signals allowed the first experimental measurement of J- and dipolar coupling constants between ¹⁷O and ²⁹Si nuclei. These HMQC experiments allow distinguishing two distinct siloxane (SiOSi) oxygen sites: (i) those covalently bonded to Q³ and Q⁴ groups, having a hydroxyl group as a second neighbour and (ii) those covalently bonded to two Q⁴ groups. The measured J- and dipolar coupling constants of siloxane ¹⁷O nucleus with Q^{4 29}Si nuclei differ from those with Q^{3 29}Si nuclei. These results indicate that the ²⁹Si-¹⁷O one-bond J-coupling and Si-O bond length depend on the second neighbours of the Si atoms.

A pectin methyltransferase modulates polysaccharide dynamics and interactions in Arabidopsis primary cell walls: Evidence from solid-state NMR

Plant cell walls contain cellulose embedded in matrix polysaccharides. Understanding carbohydrate structures and interactions is critical to the production of biofuel and biomaterials using these natural resources. Here we present a solid-state NMR study of cellulose and pectin in ¹³C-labeled cell walls of Arabidopsis wild-type and mutant plants. Using 1D ¹³C and 2D ¹³C-¹³C correlation experiments, we detected a highly branched arabinan structure in qua2 and tsd2 samples, two allelic mutants for a pectin methyltransferase. Both mutants show close physical association between cellulose and the backbones of pectic homogalacturonan and rhamnogalacturonan-I. Relaxation and dipolar order parameters revealed enhanced microsecond dynamics due to polymer disorder in the mutants, but restricted motional amplitudes due to tighter pectin-cellulose associations. These molecular data shed light on polymer structure and packing in these two pectin mutants, helping to elucidate how pectin could influence cell wall architecture at the nanoscale, cell wall mechanics, and plant growth.

Revealing the Surface Structure of CdSe Nanocrystals by Dynamic Nuclear Polarization-Enhanced 77Se and 113Cd Solid-State NMR Spectroscopy

Dynamic nuclear polarization (DNP) solid-state NMR (SSNMR) spectroscopy was used to obtain detailed surface structures of zinc blende CdSe nanocrystals (NCs) with plate or spheroidal morphologies which are capped by carboxylic acid ligands. 1D ¹¹³Cd and ⁷⁷Se cross-polarization magic angle spinning (CPMAS) NMR spectra revealed distinct signals from Cd and Se atoms on the surface of the NCs, and those residing in bulk-like environments, below the surface. ¹¹³Cd cross-polarization magic-angle-turning (CP-MAT) experiments identified CdSe₃O, CdSe₂O₂, and CdSeO₃ Cd coordination environments on the surface of the NCs, where the oxygen atoms are presumably from coordinated carboxylate ligands. The sensitivity gain from DNP enabled natural isotopic abundance 2D homonuclear ¹¹³Cd-¹¹³Cd and ⁷⁷Se-⁷⁷Se and heteronuclear ¹¹³Cd-⁷⁷Se scalar correlation solid-state NMR experiments which revealed the connectivity of the Cd and Se atoms. Importantly, ⁷⁷Se{¹¹³Cd} scalar heteronuclear multiple quantum coherence (J-HMQC) experiments were used to selectively measure one-bond ⁷⁷Se-¹¹³Cd scalar coupling constants (¹J(⁷⁷Se, ¹¹³Cd)). With knowledge of ¹J(⁷⁷Se, ¹¹³Cd), heteronuclear ⁷⁷Se{¹¹³Cd} spin echo (J-resolved) NMR experiments were used to determine the number of Cd atoms bonded to Se atoms and vice versa. The J-resolved experiments directly confirmed that major Cd and Se surface species have CdSe₂O₂ and SeCd₄ stoichiometries, respectively. Considering the crystal structure of zinc blende CdSe and the similarity of the solid-state NMR data for the platelets and spheroids, we conclude that the surface of the spheroidal CdSe NCs is primarily composed of {100} facets. The methods outlined here will generally be applicable to obtain detailed surface structures of various main group semiconductor nanoparticles.

Using Solid-State 13C NMR Spectroscopy to Study the Molecular Organization of Primary Plant Cell Walls

A knowledge of the mobilities of the polysaccharides or parts of polysaccharides in a cell-wall preparation provides information about possible molecular interactions among the polysaccharides in the cell wall and the relative locations of polysaccharides within the cell wall. A number of solid-state ¹³C NMR techniques have been developed that can be used to investigate different types of polysaccharide mobilities: rigid, semirigid, mobile, and highly mobile. In this chapter techniques are described for obtaining spectra from primary cell-wall preparations using CP/MAS, proton-rotating frame, proton spin-spin, spin-echo relaxation spectra and single-pulse excitation. We also describe how proton spin relaxation editing can be used to obtain subspectra for cell-wall polysaccharides of different mobilities, and how 2D and 3D solid-state NMR experiments have recently been applied to plant cell walls.

Solid-state NMR of unlabeled plant cell walls: high-resolution structural analysis without isotopic enrichment

BACKGROUND

Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope (13C) enrichment provides feasible sensitivity for measuring 2D/3D correlation spectra, but this time-consuming procedure and its associated expenses have restricted the application of ssNMR in lignocellulose analysis.

RESULTS

Here, we present a method that relies on the sensitivity-enhancing technique Dynamic Nuclear Polarization (DNP) to eliminate the need for 13C-labeling. With a 26-fold sensitivity enhancement, a series of 2D 13C-13C correlation spectra were successfully collected using the unlabeled stems of wild-type Oryza sativa (rice). The atomic resolution allows us to observe a large number of intramolecular cross peaks for fully revealing the polymorphic structure of cellulose and xylan. NMR relaxation and dipolar order parameters further suggest a sophisticated change of molecular motions in a ctl1 ctl2 double mutant: both cellulose and xylan have become more dynamic on the nanosecond and microsecond timescale, but the motional amplitudes are uniformly small for both polysaccharides.

CONCLUSIONS

By skipping isotopic labeling, the DNP strategy demonstrated here is universally extendable to all lignocellulose materials. This time-efficient method has landed the technical foundation for understanding polysaccharide structure and cell wall assembly in a large variety of plant tissues and species.

Unconventional Constituents and Shared Molecular Architecture of the Melanized Cell Wall of C. neoformans and Spore Wall of S. cerevisiae

The fungal cell wall serves as the interface between the cell and the environment. Fungal cell walls are composed largely of polysaccharides, primarily glucans and chitin, though in many fungi stress-resistant cell types elaborate additional cell wall structures. Here, we use solid-state nuclear magnetic resonance spectroscopy to compare the architecture of cell wall fractions isolated from Saccharomyces cerevisiae spores and Cryptococcus neoformans melanized cells. The specialized cell walls of these two divergent fungi are highly similar in composition. Both use chitosan, the deacetylated derivative of chitin, as a scaffold on which a polyaromatic polymer, dityrosine and melanin, respectively, is assembled. Additionally, we demonstrate that a previously identified but uncharacterized component of the S. cerevisiae spore wall is composed of triglycerides, which are also present in the C. neoformans melanized cell wall. Moreover, we identify a tyrosine-derived constituent in the C. neoformans wall that, although it is not dityrosine, is a non-pigment constituent of the cell wall. The similar composition of the walls of these two phylogenetically distant species suggests that triglycerides, polyaromatics, and chitosan are basic building blocks used to assemble highly stress-resistant cell walls and the use of these constituents may be broadly conserved in other fungal species.

A grass-specific cellulose-xylan interaction dominates in sorghum secondary cell walls

Sorghum (Sorghum bicolor L. Moench) is a promising source of lignocellulosic biomass for the production of renewable fuels and chemicals, as well as for forage. Understanding secondary cell wall architecture is key to understanding recalcitrance i.e. identifying features which prevent the efficient conversion of complex biomass to simple carbon units. Here, we use multi-dimensional magic angle spinning solid-state NMR to characterize the sorghum secondary cell wall. We show that xylan is mainly in a three-fold screw conformation due to dense arabinosyl substitutions, with close proximity to cellulose. We also show that sorghum secondary cell walls present a high ratio of amorphous to crystalline cellulose as compared to dicots. We propose a model of sorghum cell wall architecture which is dominated by interactions between three-fold screw xylan and amorphous cellulose. This work will aid the design of low-recalcitrance biomass crops, a requirement for a sustainable bioeconomy.

Sorghum is a source of lignocellulosic biomass for the production of renewable fuels. Here the authors characterise the sorghum secondary cell wall using multi-dimensional magic angle spinning solid-state NMR and present a model dominated by interactions between three-fold screw xylan and amorphous cellulose.

Tailoring NMR experiments for structural characterization of amorphous biological solids: A practical guide

Many interesting solid-state targets for biological research do not form crystalline structures; these materials include intrinsically disordered proteins, plant biopolymer composites, cell-wall polysaccharides, and soil organic matter. The absence of aligned repeating structural elements and atomic-level rigidity presents hurdles to achieving structural elucidation and obtaining functional insights. We describe strategies for adapting several solid-state NMR methods to determine the molecular structures and compositions of these amorphous biosolids. The main spectroscopic problems in studying amorphous structures by NMR are over/under-sampling of the spin signals and spectral complexity. These problems arise in part because amorphous biosolids typically contain a mix of rigid and mobile domains, making it difficult to select a single experiment or set of acquisition conditions that fairly represents all nuclear spins in a carbon-based organic sample. These issues can be addressed by running hybrid experiments, such as using direct excitation alongside cross polarization-based methods, to develop a more holistic picture of the macromolecular system. In situations of spectral crowding or overlap, the structural elucidation strategy can be further assisted by coupling 13C spins to nuclei such as 15N, filtering out portions of the spectrum, highlighting individual moieties of interest, and adding a second or third spectral dimension to an NMR experiment in order to spread out the resonances and link them pairwise through space or through bonds. We discuss practical aspects and illustrations from the recent literature for 1D experiments that use cross or direct polarization and both homo- and heteronuclear 2D and 3D solid-state NMR experiments.

Solid-state NMR spectroscopy identifies three classes of lipids in Cryptococcus neoformans melanized cell walls and whole fungal cells

A primary virulence-associated trait of the opportunistic fungal pathogen Cryptococcus neoformans is the production of melanin pigments that are deposited into the cell wall and interfere with the host immune response. Previously, our solid-state NMR studies of isolated melanized cell walls (melanin "ghosts") revealed that the pigments are strongly associated with lipids, but their identities, origins, and potential roles were undetermined. Herein, we exploited spectral editing techniques to identify and quantify the lipid molecules associated with pigments in melanin ghosts. The lipid profiles were remarkably similar in whole C. neoformans cells, grown under either melanizing or nonmelanizing conditions; triglycerides (TGs), sterol esters (SEs), and polyisoprenoids (PPs) were the major constituents. Although no quantitative differences were found between melanized and nonmelanized cells, melanin ghosts were relatively enriched in SEs and PPs. In contrast to lipid structures reported during early stages of fungal growth in nutrient-rich media, variants found herein could be linked to nutrient stress, cell aging, and subsequent production of substances that promote chronic fungal infections. The fact that TGs and SEs are the typical cargo of lipid droplets suggests that these organelles could be connected to C. neoformans melanin synthesis. Moreover, the discovery of PPs is intriguing because dolichol is a well-established constituent of human neuromelanin. The presence of these lipid species even in nonmelanized cells suggests that they could be produced constitutively under stress conditions in anticipation of melanin synthesis. These findings demonstrate that C. neoformans lipids are more varied compositionally and functionally than previously recognized.

Measuring multiple 17O–13C J-couplings in naphthalaldehydic acid: a combined solid state NMR and density functional theory approach

A combined multinuclear solid-state NMR and a density functional theory computational approach, with SIMPSON simulations, is evaluated to determine the four heteronuclear ¹J(¹³C,¹⁷O) couplings in naphthalaldehydic acid.

Molecular architecture of softwood revealed by solid-state NMR

Economically important softwood from conifers is mainly composed of the polysaccharides cellulose, galactoglucomannan and xylan, and the phenolic polymer, lignin. The interactions between these polymers lead to wood mechanical strength and must be overcome in biorefining. Here, we use 13C multidimensional solid-state NMR to analyse the polymer interactions in never-dried cell walls of the softwood, spruce. In contrast to some earlier softwood cell wall models, most of the xylan binds to cellulose in the two-fold screw conformation. Moreover, galactoglucomannan alters its conformation by intimately binding to the surface of cellulose microfibrils in a semi-crystalline fashion. Some galactoglucomannan and xylan bind to the same cellulose microfibrils, and lignin is associated with both of these cellulose-bound polysaccharides. We propose a model of softwood molecular architecture which explains the origin of the different cellulose environments observed in the NMR experiments. Our model will assist strategies for improving wood usage in a sustainable bioeconomy.

Structural characterization of bacteriophage viruses by NMR

Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.

Probing the Surface Structure of Semiconductor Nanoparticles by DNP SENS with Dielectric Support Materials

Surface characterization is crucial for understanding how the atomic-level structure affects the chemical and photophysical properties of semiconducting nanoparticles (NPs). Solid-state nuclear magnetic resonance spectroscopy (NMR) is potentially a powerful technique for the characterization of the surface of NPs, but it is hindered by poor sensitivity. Dynamic nuclear polarization surface enhanced NMR spectroscopy (DNP SENS) has previously been demonstrated to enhance the sensitivity of surface-selective solid-state NMR experiments by 1-2 orders of magnitude. Established sample preparations for DNP SENS experiments on NPs require the dilution of the NPs on mesoporous silica. Using hexagonal boron nitride (h-BN) to disperse the NPs doubles DNP enhancements and absolute sensitivity in comparison to standard protocols with mesoporous silica. Alternatively, precipitating the NPs as powders, mixing them with h-BN, and then impregnating the powdered mixture with radical solution leads to further 4-fold sensitivity enhancements by increasing the concentration of NPs in the final sample. This modified procedure provides a factor of 9 improvement in NMR sensitivity in comparison to previously established DNP SENS procedures, enabling challenging homonuclear and heteronuclear 2D NMR experiments on CdS, Si, and Cd₃P₂ NPs. These experiments allow NMR signals from the surface, subsurface, and core sites to be observed and assigned. For example, we demonstrate the acquisition of DNP-enhanced 2D ¹¹³Cd-¹¹³Cd correlation NMR experiments on CdS NPs and natural isotropic abundance 2D ¹³C-²⁹Si HETCOR of functionalized Si NPs. These experiments provide a critical understanding of NP surface structures.

High-Field Magic Angle Spinning Dynamic Nuclear Polarization Using Radicals Created by γ-Irradiation

High-field magic angle spinning dynamic nuclear polarization (MAS DNP) is often used to enhance the sensitivity of solid-state nuclear magnetic resonance experiments by transferring spin polarization from electron spins to nuclear spins. Here, we demonstrate that γ-irradiation induces the formation of stable radicals in inorganic solids, such as fused quartz and borosilicate glasses, as well as organic solids, such as glucose, cellulose, and a urea/polyethylene polymer. The radicals were then used to polarize ²⁹Si or ¹H spins in the core of some of these materials. Significant MAS DNP enhancements (ε) of more than 400 and 30 were obtained for fused quartz and glucose, respectively. For other samples, negligible values of ε were obtained, likely due to low concentrations of radicals or the presence of abundant quadrupolar spins. These results demonstrate that ionizing radiation is a promising alternative method for generating stable radicals that are suitable for high-field MAS DNP experiments.

Natural Isotopic Abundance 13C and 15N Multidimensional Solid-State NMR Enabled by Dynamic Nuclear Polarization

Dynamic nuclear polarization (DNP) has made feasible solid-state NMR experiments that were previously thought impractical due to sensitivity limitations. One such class of experiments is the structural characterization of organic and biological samples at natural isotopic abundance (NA). Herein, we describe the many advantages of DNP-enabled ssNMR at NA, including the extraction of long-range distance constraints using dipolar recoupling pulse sequences without the deleterious effects of dipolar truncation. In addition to the theoretical underpinnings in the analysis of these types of experiments, numerous applications of DNP-enabled ssNMR at NA are discussed.

Atomic Resolution of Cotton Cellulose Structure Enabled by Dynamic Nuclear Polarization Solid-State NMR

The insufficient resolution of conventional methods has long limited the structural elucidation of cellulose and its derivatives, especially for those with relatively low crystallinities or in native cell walls. Recent 2D/3D solid-state NMR studies of ¹³C uniformly labeled plant biomaterials have initiated a re-investigation of our existing knowledge in cellulose structure and its interactions with matrix polymers but for unlabeled materials, this spectroscopic method becomes impractical due to limitations in sensitivity. Here, we investigate the molecular structure of unlabeled cotton cellulose by combining natural abundance ¹³C-¹³C 2D correlation solid-state NMR spectroscopy, as enabled by the sensitivity-enhancing technique of dynamic nuclear polarization (DNP), with statistical analysis of the observed and literature-reported chemical shifts. The atomic resolution allows us to monitor the loss of Iα and Iβ allomorphs and the generation of a novel structure during ball-milling, which reveals the importance of large crystallite size for maintaining the Iα and Iβ model structures. Partial order has been identified in the "disordered" domains, as evidenced by a discrete distribution of well-resolved peaks. This study not only provides heretofore unavailable high-resolution insights into cotton cellulose but also presents a widely applicable strategy for analyzing the structure of cellulose-rich materials without isotope-labeling. This work was part of a multi-technique study of ball-milled cotton described in the previous article in the same issue.

Detection of nucleic acids and other low abundance components in native bone and osteosarcoma extracellular matrix by isotope enrichment and DNP-enhanced NMR

Sensitivity enhancement by isotope enrichment and DNP NMR enables detection of minor but biologically relevant species in native intact bone, including nucleic acids, choline from phospholipid headgroups, and histidinyl and hydroxylysyl groups. Labelled matrix from the aggressive osteosarcoma K7M2 cell line confirms the assignments of nucleic acid signals arising from purine, pyrimidine, ribose, and deoxyribose species. Detection of these species is an important and necessary step in elucidating the atomic level structural basis of their functions in intact tissue.

Towards elucidating their biological roles in intact tissue, DNP NMR reveals nucleic acids, and other important low abundance biomolecules in a complex biomaterial, bone, and in cancer extracellular matrix.

Unambiguous Ex Situ and in Cell 2D 13C Solid-State NMR Characterization of Starch and Its Constituents

Starch is the most abundant energy storage molecule in plants and is an essential part of the human diet. This glucose polymer is composed of amorphous and crystalline domains in different forms (A and B types) with specific physicochemical properties that determine its bioavailability for an organism, as well as its value in the food industry. Using two-dimensional (2D) high resolution solid-state nuclear magnetic resonance (SS-NMR) on 13C-labelled starches that were obtained from Chlamydomonas reinhardtii microalgae, we established a complete and unambiguous assignment for starch and its constituents (amylopectin and amylose) in the two crystalline forms and in the amorphous state. We also assigned so far unreported non-reducing end groups and assessed starch chain length, crystallinity and amylose content. Starch was then characterized in situ, i.e., by 13C solid-state NMR of intact microalgal cells. Our in-cell methodology also enabled the identification of the effect of nitrogen starvation on starch metabolism. This work shows how solid-state NMR can enable the identification of starch structure, chemical modifications and biosynthesis in situ in intact microorganisms, eliminating time consuming and potentially altering purification steps.

Ultrafast Maximum-Quantum NMR Spectroscopy for the Analysis of Aromatic Mixtures

Maximum-quantum (MaxQ) NMR experiments have been introduced to overcome issues related to peak overlap and high spectral density in the NMR spectra of aromatic mixtures. In MaxQ NMR, spin systems are separated on the basis of the highest-quantum coherence that they can form. MaxQ experiments are however time consuming and methods have been introduced to accelerate them. In this article, we demonstrate the ultrafast, single-scan acquisition of MaxQ NMR spectra using spatial encoding of the multiple-quantum dimension. So far, the spatial encoding methodology has been applied only for the encoding of up to double-quantum coherences, and here we show that it can be extended to higher coherence orders, to yield a massive reduction of the acquisition time of multi-quantum spectra of aromatic mixtures, and also to monitor chemical reactions.

Molecular architecture of fungal cell walls revealed by solid-state NMR

The high mortality of invasive fungal infections, and the limited number and inefficacy of antifungals necessitate the development of new agents with novel mechanisms and targets. The fungal cell wall is a promising target as it contains polysaccharides absent in humans, however, its molecular structure remains elusive. Here we report the architecture of the cell walls in the pathogenic fungus Aspergillus fumigatus. Solid-state NMR spectroscopy, assisted by dynamic nuclear polarization and glycosyl linkage analysis, reveals that chitin and α-1,3-glucan build a hydrophobic scaffold that is surrounded by a hydrated matrix of diversely linked β-glucans and capped by a dynamic layer of glycoproteins and α-1,3-glucan. The two-domain distribution of α-1,3-glucans signifies the dual functions of this molecule: contributing to cell wall rigidity and fungal virulence. This study provides a high-resolution model of fungal cell walls and serves as the basis for assessing drug response to promote the development of wall-targeted antifungals.

Elucidating an Amorphous Form Stabilization Mechanism for Tenapanor Hydrochloride: Crystal Structure Analysis Using X-ray Diffraction, NMR Crystallography, and Molecular Modeling

By the combined use of powder and single-crystal X-ray diffraction, solid-state NMR, and molecular modeling, the crystal structures of two systems containing the unusually large tenapanor drug molecule have been determined: the free form, ANHY, and a dihydrochloride salt form, 2HCl. Dynamic nuclear polarization (DNP) assisted solid-state NMR (SSNMR) crystallography investigations were found essential for the final assignment and were used to validate the crystal structure of ANHY. From a structural informatics analysis of ANHY and 2HCl, conformational ring differences in one part of the molecule were observed which influence the relative orientation of a methyl group on a ring nitrogen and thereby impact the crystallizability of the dihydrochloride salt. From quantum chemistry calculations, the dynamics between different ring conformations in tenapanor is predicted to be fast. Addition of HCl to tenapanor results in general in a mixture of protonated ring conformers and hence a statistical mix of diastereoisomers which builds up the amorphous form, a-2HCl. This was qualitatively verified by ¹³C CP/MAS NMR investigations of the amorphous form. Thus, to form any significant amount of the crystalline material 2HCl, which originates from the minor (i.e., energetically less stable) ring conformations, one needs to involve nitrogen deprotonation to allow exchange between the minor and major conformations of ANHY in solution. Thus, by controlling the solution pH value to well below the p K_a of ANHY, the equilibrium between ANHY and 2HCl can be controlled and by this mechanism the crystallization of 2HCl can be avoided and the amorphous form of the dichloride salt can therefore be stabilized.

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured ¹³C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (¹H, ¹³C, ¹⁵N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct ¹³C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental ¹³C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of ¹³C shift tensors and the observation of residual dipolar coupling between ¹³C and ¹⁴N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD₁₆ = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD₁₆ = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

Filamentous Bacteriophage Viruses: Preparation, Magic-Angle Spinning Solid-State NMR Experiments, and Structure Determination

Filamentous bacteriophages are elongated semi-flexible viruses that infect bacteria. They consist of a circular single-stranded DNA (ssDNA) wrapped by a capsid consisting of thousands of copies of a major coat protein subunit. Given the increasing number of discovered phages and the existence of only a handful of structures, the development of methods for phage structure determination is valuable for biophysics and structural virology. In recent years, we developed and applied techniques to elucidate the 3D atomic-resolution structures of intact bacteriophages using experimental magic-angle spinning (MAS) solid-state NMR data. The flexibility in sample preparation - precipitated homogeneous solids - and the fact that ssNMR presents no limitation on the size, weight or morphology of the system under study makes it an ideal approach to study phage systems in detail.In this contribution, we describe approaches to prepare isotopically carbon-13 and nitrogen-15 enriched intact phage samples in high yield and purity, and we present experimental MAS NMR methods to study the capsid secondary and tertiary structure, and the DNA-capsid interface. Protocols for the capsid structure determination using the Rosetta modeling software are provided. Specific examples are given from studies of the M13 and fd filamentous bacteriophage viruses.