Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins

Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks

Computer prediction of NMR chemical shifts plays an increasingly important role in molecular structure assignment and elucidation for organic molecule studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) have established a framework to predict NMR chemical shifts but often at a significant computational expense with a limited prediction accuracy. Recent advancements in deep learning methods, especially graph neural networks (GNNs), have shown promise in improving the accuracy of predicting experimental chemical shifts, either by using 2D molecular topological features or 3D conformational representation. This study presents a new 3D GNN model to predict 1H and 13C chemical shifts, CSTShift, that combines atomic features with DFT-calculated shielding tensor descriptors, capturing both isotropic and anisotropic shielding effects. Utilizing the NMRShiftDB2 data set and conducting DFT optimization and GIAO calculations at the B3LYP/6-31G(d) level, we prepared the NMRShiftDB2-DFT data set of high-quality 3D structures and shielding tensors with corresponding experimentally measured 1H and 13C chemical shifts. The developed CSTShift models achieve the state-of-the-art prediction performance on both the NMRShiftDB2-DFT test data set and external CHESHIRE data set. Further case studies on identifying correct structures from two groups of constitutional isomers show its capability for structure assignment and elucidation. The source code and data are accessible at https://yzhang.hpc.nyu.edu/IMA.

Polydopamine Adhesion: Catechol, Amine, Dihydroxyindole, and Aggregation Dynamics

While polydopamine (PDA) possesses the surface-independent adhesion property of mussel-binding proteins, significant differences exist between them. Particularly, PDA's short and rigid backbone differs from the long and flexible protein sequence of mussel-binding proteins. Given that adhesion relies on achieving a conformal contact with large surface coverage, PDA has drawbacks as an adhesive. In our study, we investigated the roles of each building block of PDA to build a better understanding of their binding mechanisms. Initially, we anticipated that catecholamine oligomers form specific binding with substrates. However, our study showed that the universal adhesion of PDA is initiated by the solubility limit of growing oligomers by forming agglomerates, complemented by multiple binding modes of catechol. Notably, in the absence of amines, poly(catechol) either remained in solution or formed minor suspensions without any surface coating, underscoring the essential role of amines in the adhesion process by facilitating insoluble aggregate formation. To substantiate our findings, we induced poly(catechol) aggregation using quaternized poly(4-vinylpyridine) (qPVP), leading to subsequent surface adhesion upon agglomerate formation.

Analyzing atomic scale structural details and nuclear spin dynamics of four macrolide antibiotics: erythromycin, clarithromycin, azithromycin, and roxithromycin

The current investigation centers on elucidating the intricate molecular architecture and dynamic behavior of four macrolide antibiotics, specifically erythromycin, clarithromycin, azithromycin, and roxithromycin, through the application of sophisticated solid-state nuclear magnetic resonance (SSNMR) methodologies. We have measured the principal components of chemical shift anisotropy (CSA) parameters, and the site-specific spin-lattice relaxation time at carbon nuclei sites. To extract the principal components of CSA parameters, we have employed 13C 2DPASS CP-MAS SSNMR experiments at two different values of magic angle spinning (MAS) frequencies, namely 2 kHz and 600 Hz. Additionally, the spatial correlation between 13C and 1H nuclei has been investigated using 1H-13C frequency switched Lee-Goldburg heteronuclear correlation (FSLGHETCOR) experiment at a MAS frequency of 24 kHz. Our findings demonstrate that the incorporation of diverse functional groups, such as the ketone group and oxime group with the lactone ring, exerts notable influences on the structure and dynamics of the macrolide antibiotic. In particular, we have observed a significant decrease in the spin-lattice relaxation time of carbon nuclei residing on the lactone ring, desosamine, and cladinose in roxithromycin, compared to erythromycin. Overall, our findings provide detailed insight into the relationship between the structure and dynamics of macrolide antibiotics, which is eventually correlated with their biological activity. This knowledge can be utilized to develop new and more effective drugs by providing a rational basis for drug discovery and design.

Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion. Here, we present a new method that combines molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The calculations include the spectra arising from non α-helical molecules and molecules with non-uniform intrinsic mobility. In a first step, dipolar or quadrupolar interaction tensors drive molecular rotations and reorientations to obtain the proper mean values as observed in corresponding NMR experiments. In a second step, the coordinate snapshots of the MDOC simulations are geometry optimized with the isotropic 15 N chemical shifts as constraints using Bond Polarization Theory (BPT) to provide reliable 15 N CS tensor data. The averaged dipolar 1 H-15 N couplings and the δzz tensor components can then be combined to simulate PISEMA patterns. We apply this method to the ß-helical peptide gramicidin A (gA) and demonstrate that this method enables the assignment of most PISEMA resonances. In addition, MDOC simulations provide local order parameters for the calculated sites. These local order parameters reveal large differences in backbone mobility between L- and D-amino acids of gA.

Probing Molecular Packing of Lipid Nanoparticles from 31P Solution and Solid-State NMR

Lipid nanoparticles (LNPs) are intricate multicomponent systems widely recognized for their efficient delivery of oligonucleotide cargo to host cells. Gaining insights into the molecular properties of LNPs is crucial for their effective design and characterization. However, analysis of their internal structure at the molecular level presents a significant challenge. This study introduces 31P nuclear magnetic resonance (NMR) methods to acquire structural and dynamic information about the phospholipid envelope of LNPs. Specifically, we demonstrate that the 31P chemical shift anisotropy (CSA) parameters serve as a sensitive indicator of the molecular assembly of distearoylphosphatidylcholine (DSPC) lipids within the particles. An analytical protocol for measuring 31P CSA is developed, which can be implemented using either solution NMR or solid-state NMR, offering wide accessibility and adaptability. The capability of this method is demonstrated using both model DSPC liposomes and real-world pharmaceutical LNP formulations. Furthermore, our method can be employed to investigate the impact of formulation processes and composition on the assembly of specifically LNP particles or, more generally, phospholipid-based delivery systems. This makes it an indispensable tool for evaluating critical pharmaceutical properties such as structural homogeneity, batch-to-batch reproducibility, and the stability of the particles.

NaGaPO4F - a KTiOPO4-structured solid sodium-ion conductor

Advanced ionic conductors are crucial for a large variety of contemporary technologies spanning solid state ion batteries, fuel cells, gas sensors, water desalination, etc. In this work, we report on a new member of KTiOPO4-structured materials, NaGaPO4F, with sodium-ion conductivity. NaGaPO4F has been obtained for the first time via a facile two-step synthesis consisting of a hydrothermal preparation of an ammonia-based precursor, NH4GaPO4F, followed by an ion exchange reaction with NaNO3. Its crystal structure was precisely refined using a combination of synchrotron X-ray powder diffraction and electron diffraction tomography. The material is thermally stable upon 450 °C showing no significant structural transformations or degradation but only a ∼1% cell volume expansion. Na-ion mobility in NaGaPO4F was investigated by a joint experimental and computational approach comprising solid-state nuclear magnetic resonance (NMR) and density functional theory (DFT). DFT and bond-valence site energy (BVSE) calculations reveal 3D diffusion of sodium in the [GaPO4F] framework with migration barriers amounting to 0.22 and 0.44 eV, respectively, while NMR yields 0.3-0.5 eV that, being coupled with a calculated bandgap of ∼4.25 eV, makes NaGaPO4F a promising fast Na-ion conductor.

Machine learning assisted interpretation of 2D solid-state nuclear magnetic resonance spectra

A machine learning methodology using deep neural network (DNN) for interpreting multidimensional solid-state nuclear magnetic resonance (SSNMR) of various synthetic and natural polymers is presented. The separated local field (SLF) SSNMR which correlates local well-defined heteronuclear dipolar with the tensor orientation of the chemical shift anisotropy (CSA) of spin in the solid state can provide valuable structure and molecular dynamics information of synthetic and biopolymers. Compared with the traditional linear least-square fitting, the proposed DNN-based methodology can efficiently and accurately determine the tensor orientation of CSA of both 13C and 15N in all four samples. The method achieves prediction precisions of the Euler angles with < ±5° and is characterized by low training costs and high efficiency (<1 s). The feasibility and robustness of the DNN-based analysis methodology are confirmed by comparison to reported-literature values. This strategy is expected to aid in the interpretation of complex multidimensional NMR spectra of complicated polymer system.

Torsion Angle Analysis of a Thermally Activated Delayed Fluorescence Emitter in an Amorphous State Using Dynamic Nuclear Polarization Enhanced Solid-State NMR

The torsion angle between donor and acceptor segments of a thermally activated delayed fluorescence (TADF) molecule is one of the most critical factors in determining the performance of TADF-based organic light-emitting diodes (OLEDs) because the torsion angle affects not only the energy gap between the singlet and triplet but also the oscillator strength and spin-orbit coupling. However, the torsion angle is difficult to analyze, because organic molecules are in an amorphous state in OLEDs. Here, we determined the torsion angle of a highly efficient TADF emitter, DACT-II, in an amorphous state by dynamic nuclear polarization enhanced solid-state NMR measurements. From the experimentally obtained chemical shift principal values of ¹⁵N on carbazole, we determined the average torsion angle to be 52°. Such quantification of the torsion angles in TADF molecules in amorphous solids will provide deep insight into the TADF mechanism in amorphous OLEDs.

Cl@Si20X20 cages: evaluation of encapsulation nature, structural rigidity, and 29Si-NMR patterns using relativistic DFT calculations

The experimental characterization of Cl@Si₂₀ endohedral clusters, featuring different ligands such as [Cl@Si₂₀H₂₀]^- (1) [Cl@Si₂₀H₁₂Cl₈]^- (2), and [Cl@Si₂₀Cl₂₀]^- (3), provides insight into the variable encapsulation environment for chloride anions. The favorable formation of such species enables the evaluation of the encapsulation nature and the role of the inner anion in the rigidity of the overall cluster. Our results show a sizable interaction which increases as -66.7, -100.8, and -130.3 kcal mol^-1 from 1 to 3, respectively, featuring electrostatic character. The orbital interaction involves 3p-Cl → Si₂₀X₂₀ and 3s-Cl → Si₂₀X₂₀ charge transfer channels and a slight contribution from London dispersion-type interactions. These results show that the inner bonding environment can be modified by the choice of exobonded ligands. Moreover, ²⁹Si-NMR parameters are depicted in terms of the chemical shift anisotropy (CSA), leading to a strong variation of the three principal tensor components (δ₁₁, δ₂₂, δ₃₃), unraveling the origin of the experimental ²⁹Si-NMR chemical shift (δ_iso) differences along the given series. Thus, the Si₂₀ cage is a useful template to further evaluate different environments for encapsulating atomic species.

Atomic-Scale Resolution Insights into Structural and Dynamic Differences between Ofloxacin and Levofloxacin

This study employs advanced solid-state NMR techniques to investigate the atomic-level structure and dynamics of two enantiomers: ofloxacin and levofloxacin. The investigation focuses on critical attributes, such as the principal components of the chemical shift anisotropy (CSA) tensor, the spatial proximity of ¹H and ¹³C nuclei, and site-specific ¹³C spin-lattice relaxation time, to reveal the local electronic environment surrounding specific nuclei. Levofloxacin, the levo-isomer of ofloxacin, exhibits higher antibiotic efficacy than its counterpart, and the dissimilarities in the CSA parameters indicate significant differences in the local electronic configuration and nuclear spin dynamics between the two enantiomers. Additionally, the study employs the ¹H-¹³C frequency-switched Lee-Goldburg heteronuclear correlation (FSLGHETCOR) experiment to identify the presence of heteronuclear correlations between specific nuclei (C15 and H7 nuclei and C13 and H12 nuclei) in ofloxacin but not in levofloxacin. These observations offer insights into the link between bioavailability and nuclear spin dynamics, underscoring the significance of NMR crystallography approaches in advanced drug design.

Photocycle of a cyanobacteriochrome: a charge defect on ring impairs conjugation in chromophore

A large number of novel phytochromes named cyanobacteriochromes (CBCRs) have been recently identified. CBCRs appear to be attractive for further in-depth studies as paradigms for phytochromes because of their related photochemistry, but simpler domain architecture. Elucidating the mechanisms of spectral tuning for the bilin chromophore down to the molecular/atomic level is a prerequisite to design fine-tuned photoswitches for optogenetics. Several explanations for the blue shift during photoproduct formation associated with the red/green CBCRs represented by Slr1393g3 have been developed. There are, however, only sparse mechanistic data concerning the factors controlling stepwise absorbance changes along the reaction pathways from the dark state to the photoproduct and vice versa in this subfamily. Conventional cryotrapping of photocycle intermediates of phytochromes has proven experimentally intractable for solid-state NMR spectroscopy within the probe. Here, we have developed a simple method to circumvent this hindrance by incorporating proteins into trehalose glasses which allows four photocycle intermediates of Slr1393g3 to be isolated for NMR use. In addition to identifying the chemical shifts and chemical shift anisotropy principal values of selective chromophore carbons in various photocycle states, we generated QM/MM models of the dark state and photoproduct as well as of the primary intermediate of the backward-reaction. We find the motion of all three methine bridges in both reaction directions but in different orders. These molecular events channel light excitation to drive distinguishable transformation processes. Our work also suggests that polaronic self-trapping of a conjugation defect by displacement of the counterion during the photocycle would play a role in tuning the spectral properties of both the dark state and photoproduct.

Determination of the mutual orientation between proton CSA tensors mediated through band-selective 1H-1H recoupling under fast MAS

The mutual orientation of nuclear spin interaction tensors provides critical information on the conformation and arrangement of molecules in chemicals, materials, and biological systems at an atomic level. Proton is a ubiquitous and important element in a variety of substances, and its NMR is highly sensitive due to their virtually 100% natural abundance and large gyromagnetic ratio. Nevertheless, the measurement of mutual orientation between the ¹H CSA tensors has remained largely untouched in the past due to strong ¹H-¹H homonuclear interactions in a dense network of protons. In this study, we have developed a proton-detected 3D ¹H CSA/¹H CSA/¹H CS correlation method that utilizes three techniques to manage homonuclear interactions, namely fast magic-angle spinning, windowless C-symmetry-based CSA recoupling (windowless-ROCSA), and a band-selective ¹H-¹H polarization transfer. The asymmetric ¹H CSA/¹H CSA correlated powder patterns produced by the C-symmetry-based methods are highly sensitive to the sign and asymmetry parameter of the ¹H CSA, and the Euler angle β as compared to the symmetric pattern obtained by the existing γ-encoded R-symmetry-based CSA/CSA correlation methods and allows a larger spectral area for data fitting. These features are beneficial for determining the mutual orientation between the nuclear spin interaction tensors with improved accuracy.

Local and global aromaticity under rotation: analysis of two- and three-dimensional representative carbon nanostructures

Nanoscaled 2D and 3D carbon structures with closed curved π-surfaces are of relevance in the development of desirable building units for materials science. Such species are able to sustain local and global aromatic circuits involving isolated regions or the overall structural backbone, respectively. Here we account for local and global aromaticity under rotation of representative two- and three-dimensional species involving para-connected and fused edge-sharing phenyl rings ([8]CPP, [10]CPP, CNB), and C₆₀ fullerene at different charge states. Our results denote that nanoscaled 2D global aromatics mimic the behaviour of the most prototypical aromatic 6π-circuit, given by benzene, where the shielding cone properties vary along the rotation motion. In contrast, 3D spherical aromatics remain almost invariant under rotation, given the distinctive characteristics of such species, differing from 2D global aromatics. Dissection of orbital contributions reveals that π-orbitals are determinants for shifting from non-aromatic to spherical aromatic species. Under rotation, the variation of the anisotropic effect inherent to such nanoscaled structures is accounted for, which is relevant to rationalize variation in NMR signal shifts upon the formation of host-guest aggregates.

Dynamic membrane interaction and amyloid fibril formation of glucagon, melittin and human calcitonin

Glucagon is a 29-amino acid peptide hormone secreted by pancreatic α-cells and interacts with specific receptors located in various organs. Glucagon tends to form gel-like fibril aggregates that are cytotoxic. It is important to reveal the glucagon-membrane interaction to understand activity and cytotoxicity of glucagon and glucagon oligomers. In this review, first glucagon-membrane interactions are described as morphological changes in dimyristoylphosphatidylcholine (DMPC) bilayers containing glucagon in acidic and neutral conditions as compared to the case of melittin. Second, fibril formation by glucagon in acidic solution is discussed in light of morphological and structural changes. Third, kinetic analysis of glucagon fibril formation was performed using a two-step autocatalytic reaction mechanism, as investigated in the case of human calcitonin. The first step is a nuclear formation, and the second step is an autocatalytic fibril elongation. Forth, fibril formation of glucagon inside glucagon-DMPC bilayers in neutral solution under near physiological condition is described.

Effects of the Hubbard potential on the NMR shielding and optoelectronic properties of BiMnVO5 compound

This study explores the nuclear magnetic shielding, chemical shifts, and the optoelectronic properties of the BiMnVO₅ compound using the full-potential linearized augmented plane wave method within the generalized gradient approximation by employing the Hubbard model (GGA + U). The ²⁰⁹Bi and ⁵¹V chemical shifts and bandgap values of the BiMnVO₅ compound in a triclinic crystal structure are found to be directly related to Hubbard potential. The relationship between the isotropic nuclear magnetic shielding σ_iso and chemical shift δ_iso is obtained with a slope of 1.0231 and - 0.00188 for ²⁰⁹Bi and ⁵¹V atoms, respectively. It is also observed that the bandgap, isotropic nuclear magnetic shielding, and chemical shifts increase with the change in Hubbard potentials (U) of 3, 4, 5, 6, and 7.

Infinitene as two fused helicoidal trails of fused rings: evaluation of the magnetic behavior of [12]infinitene and anionic species displaying global aromaticity and antiaromaticity

The unique formation of an infinity-shaped carbon backbone made exclusively from fused benzene rings has recently been achieved. The structure of [12]infinitene can be viewed as two fused [6]helicene structures with a central crossover section, depicting a global aromatic behavior along with the overall structure, with deshielding regions along both helicoidal axes. In addition, the ¹³C-NMR characteristics are discussed. The formation of a cumulative region involving the shielding regions from the aromatic rings is depicted along with the overall aesthetically pleasant structural backbone, which is enhanced at the crossover section. For the evaluated dianionic counterpart, the structure shows a deshielding region above the fused-ring trail and a helicoidal shielding region, ascribed to a global antiaromatic counterpart. The aromaticity is recovered and enhanced at the tetranionic state. Thus, the neutral and tetranionic states are able to build up a long-ranged shielding region, given by the global aromatic behavior, with an enhanced shielding region at the center of the crossover section displaying π-π stacked rings.

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.

Tracking the Structural Development of Amyloid Precursors in the Insulin B Chain and the Inhibition Effect by Fibrinogen

Amyloid fibrils are abnormal protein aggregates associated with several amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge before amyloid fibril formation, play an important role in structure formation. Therefore, to prevent fibril formation, the mechanisms underpinning the structural development of prefibrillar intermediates must be elucidated. An insulin-derived peptide, the insulin B chain, is known for its stable accumulation of prefibrillar intermediates. In this study, the structural development of B chain prefibrillar intermediates and their inhibition by fibrinogen (Fg) were monitored by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) combined with solid-state nuclear magnetic resonance spectroscopy (NMR) and size exclusion chromatography. TEM images obtained in a time-lapse manner demonstrated that prefibrillar intermediates were wavy rod-like structures emerging from initial non-rod-like aggregates, and their bundling was responsible for protofilament formation. Time-resolved SAXS revealed that the prefibrillar intermediates became thicker and longer as a function of time. Solid-state NMR measurement suggested a β-sheet formation around Ala14 residue was crucial for the structural conversion from prefibrillar intermediates to amyloid fibril. These observations suggested that prefibrillar intermediates serve as reaction fields for amyloid nucleation and its structural propagation. Time-resolved SAXS also demonstrated that Fg prevented elongation of the prefibrillar intermediates by forming specific complexes together, which implied that regulation of the length of prefibrillar intermediates upon Fg binding was the factor suppressing the prefibrillar intermediate elongation. The fibril formation mechanism and the inhibition strategy found in this study will be helpful in seeking appropriate methods against amyloid-related diseases.

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.

Investigation of the Influence of Various Functional Groups on the Dynamics of Glucocorticoids

The basic configuration of glucocorticoid consists of four-fused rings associated with one cyclohexadienone ring, two cyclohexane rings, and one cyclopentane ring. The ways the structure and dynamics of five glucocorticoids (prednisone, prednisolone, prednisolone acetate, methylprednisolone, and methylprednisolone acetate) are altered because of the substitution of various functional groups with these four-fused rings are studied thoroughly by applying sophisticated solid-state nuclear magnetic resonance (NMR) methodologies. The biological activities of these glucocorticoids are also changed because of the attachment of various functional groups with these four-fused rings. The substitution of the hydroxyl group (with the C11 atom of the cyclohexane ring) in place of the keto group enhances the potential of the glucocorticoid to cross the cellular membrane. As a result, the bioavailability of prednisolone (the hydroxyl group is attached with the C11 atom of the cyclohexane ring) is increased compared to prednisone (the keto group is attached with the C11 atom of cyclohexane rings). Another notable point is that the spin-lattice relaxation rate at crystallographically distinct carbon nuclei sites of prednisolone is increased compared to that of the prednisone, which implies that the motional degrees of freedom of glucocorticoid is increased because of the substitution of the hydroxyl group in place of the keto group of the cyclohexane ring. The attachment of the methyl group with the C6 atom of cyclohexane rings further reduces the spin-lattice relaxation time at crystallographically distinct carbon nuclei sites of glucocorticoid and its bioactivity is also increased. By comparing the spin-lattice relaxation time and the local correlation time at crystallographically different carbon nuclei sites of three steroids prednisone, prednisolone, and methylprednisolone, it is observed that both the spin-lattice relaxation time and the local correlation time gradually decrease at each crystallographically distinct carbon nuclei sites when we move from prednisone to prednisolone to methyl-prednisolone. On the other hand, if we compare the same for prednisolone, prednisolone acetate, and methylprednisolone acetate, then we also observe that both the spin-lattice relaxation time and the local-correlation time gradually decrease from prednisolone to prednisolone acetate to methylprednisolone acetate for all chemically different carbon nuclei. It is also noticeable that both the spin-lattice relaxation time and the local-correlation time gradually decrease from prednisone to prednisolone to prednisolone acetate to methylprednisolone to methylprednisolone acetate for most of the carbon nuclei sites. From in silico analysis, it is also revealed that the bioavailability and efficacy of the glucocorticoid increase from prednisone to prednisolone to prednisolone acetate to methylprednisolone to methylprednisolone acetate. Hence, it can be concluded that the biological activity and the motional degrees of freedom of the glucocorticoids are highly correlated. These types of studies provide a clear picture of the structure-activity relationship of the drug molecules, which will enlighten the path of developing highly potent glucocorticoids with minimum side effects. Another important aspect of these types of studies is to provide information about the electronics configuration and nuclear spin dynamics at crystallographically different carbon nuclei sites of five glucocorticoids, which will enrich the field of "NMR crystallography".

Mercurial possibilities: determining site distributions in Cu2HgSnS4 using 63/65Cu, 119Sn, and 199Hg solid-state NMR spectroscopy

Chalcogenides are an important class of materials that exhibit tailorable optoelectronic properties accessible through chemical modification. For example, the minerals kesterite, stannite, and velikite (Cu₂MSnS₄, where M = Zn, Cd, or Hg, respectively) are a series of Group 12 transition metal tin sulfides that readily exhibit optical bandgaps spanning the Shockley-Queisser limit; however, achieving consensus on their structure (space group I4̄ vs. I4̄2m) has been difficult. This study explores the average long-range and local structure of Cu₂HgSnS₄ and evaluates the parallels of M = Zn and Cd sister compounds using complementary X-ray diffraction and solid-state nuclear magnetic resonance (NMR) spectroscopy. The ^63/65Cu NMR spectra were acquired at multiple magnetic field strengths (B₀ = 7.05, 11.75, and 21.1 T) to assess the unique chemical shift anisotropy and quadrupolar coupling contributions. They reveal two inequivalent sets of Cu sites in Cu₂ZnSnS₄, in contrast to only one set of sites in Cu₂CdSnS₄ and Cu₂HgSnS₄, clarifying structural assignments previously proposed through X-ray diffraction methods. The presence of these Cu sites was further supported by DFT calculations. The ¹¹⁹Sn and ¹⁹⁹Hg NMR spectra suggest that an ordering phenomenon takes place in Cu₂HgSnS₄ when it undergoes annealing treatments. The trend in measured optical band gaps (1.5 eV for Cu₂ZnSnS₄, 1.2 eV for Cu₂CdSnS₄, and 0.9 eV for Cu₂HgSnS₄) was confirmed by electronic structure calculations, which show that the band gap narrows as the difference in electronegativity is diminished and that Hg-S bonds in Cu₂HgSnS₄ have greater covalent character.

Bonding and 13 C-NMR properties of coinage metal tris(ethylene) and tris(norbornene) complexes: Evaluation of the role of relativistic effects from DFT calculations

The π-complexes of cationic coinage metal ions (Cu(I), Ag(I), Au(I)) provide useful experimental support for understanding fundamental characteristics of bonding and ¹³ C-NMR patterns of the group 11 triad. Here, we account for the role of relativistic effects on olefin-coinage metal ion interaction for cationic, homoleptic tris-ethylene, and tris-norbornene complexes, [M(η² -C₂ H₄ )₃ ]⁺ and [M(η² -C₇ H₁₀ )₃ ]⁺ (M = Cu, Ag, Au), as representative case of studies. The M-(CC) bond strength in the cationic, tris-ethylene complexes is affected sizably for Au and to a lesser extent for Ag and Cu (48.6%, 16.7%, and 4.3%, respectively), owing to the influence on the different stabilizing terms accounting for the interaction energy in the formation of coinage metal cation-π complexes. The bonding elements provided by olefin → M σ-donation and olefin ← M π-backbonding are consequently affected, leading to a lesser covalent interaction going down in the triad if the relativistic effects are ignored. Analysis of the ¹³ C-NMR tensors provides further understanding of the observed experimental values, where the degree of backbonding charge donation to π₂ *-olefin orbital is the main influence on the observed high-field shifts in comparison to the free olefin. This donation is larger for ethylene complexes and lower for norbornene counterparts. However, the bonding energy in the later complexes is slightly stabilized given by the enhancement in the electrostatic character of the interaction. Thus, the theoretical evaluation of metal-alkene bonds, and other metal-bonding situations, benefits from the incorporation of relativistic effects even in lighter counterparts, which have an increasing role going down in the group.

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.

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.

Photo-and thermoresponsive N-salicylideneaniline derivatives: solid-state studies and structural aspects

Eight photo-and/or thermoresponsive salicylideneanilines were obtained by mechanosynthesis under solvent-free conditions and stabilized by external stimuli for their isolations in solid-state. Switching properties of these materials were investigated by various analytical techniques and spectroscopic data.

Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors

Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic 15N and 13C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes.

NMR Crystallography Enhanced by Quantum Chemical Calculations and Liquid State NMR Spectroscopy for the Investigation of Se-NHC Adducts*

N-heterocyclic carbene ligands (NHC) are widely utilized in catalysis and material science. They are characterized by their steric and electronic properties. Steric properties are usually quantified on the basis of their static structure, which can be determined by X-ray diffraction. The electronic properties are estimated in the liquid state; for example, via the ⁷⁷ Se liquid state NMR of Se-NHC adducts. We demonstrate that ⁷⁷ Se NMR crystallography can contribute to the characterization of the structural and electronic properties of NHC in solid and liquid states. Selected Se-NHC adducts are investigated via ⁷⁷ Se solid state NMR and X-ray crystallography, supported by quantum chemical calculations. This investigation reveals a correlation between the molecular structure of adducts and NMR parameters, including not only isotropic chemical shifts but also the other chemical shift tensor components. Afterwards, the liquid state ⁷⁷ Se NMR data is presented and interpreted in terms of the quantum chemistry modelling. The discrepancy between the structural and electronic properties, and in particular the π-accepting abilities of adducts in the solid and liquid states is discussed. Finally, the ¹³ C isotropic chemical shift from the liquid state NMR and the ¹³ C tensor components are also discussed, and compared with their ⁷⁷ Se counterparts. ⁷⁷ Se NMR crystallography can deliver valuable information about NHC ligands, and together with liquid state ⁷⁷ Se NMR can provide an in-depth outlook on the properties of NHC ligands.

Study of the Variation of the Electronic Distribution and Motional Dynamics of Two Independent Molecules of an Asymmetric Unit of Atorvastatin Calcium by Solid-State NMR Measurements

Significant changes in the spin-lattice time and chemical shift anisotropy (CSA) parameters are observed in two independent molecules of an asymmetric unit of atorvastatin calcium (ATC-I) (which is referred to as "a"- and "b"-type molecules by following Wang et al.). The longitudinal magnetization decay curve is fitted by two exponentials-one with longer relaxation time and another with shorter relaxation time for most of the carbon nuclei sites. The local correlation time also varies significantly. This is the experimental evidence of the coexistence of two different kinds of motional degrees of freedom within ATC-I molecule. The solubility and bioavailability of the drug molecule are enhanced due to the existence of two different kinds of dynamics. Hence, the macroscopic properties like solubility and bioavailability of a drug molecule are highly correlated with its microscopic properties. The motional degrees of freedom of "a"- and "b"-type molecules are also varied remarkably at certain carbon nuclei sites. This is the first time the change in the molecular dynamics of two independent molecules of an asymmetric unit of atorvastatin calcium is quantified using solid-state NMR methodology. These types of studies, in which the chemical shift anisotropy (CSA) parameters and spin-lattice relaxation time provide information about the change in electronic distribution and the spin dynamics at the various crystallographic location of the drug molecule, will enrich the field "NMR crystallography". It will also help us to understand the electronic distribution around a nucleus and the nuclear spin dynamics at various parts of the molecule, which is essential to develop the strategies for the administration of the drug.

Determination of the chemical shift tensor anisotropy and asymmetry of strongly dipolar coupled protons under fast MAS

Orientationally-dependent interactions such as dipolar coupling, quadrupolar coupling, and chemical shift anisotropy (CSA) contain a wealth of spatial information that can be used to elucidate molecular conformations and dynamics. To determine the sign of the chemical shift tensor anisotropy parameter (δ_aniso), both the |m| ​= ​1 and |m| ​= ​2 components of the CSA need to be symmetry allowed, while the recoupling of the |m| ​= ​1 term is accompanied with the reintroduction of homonuclear dipolar coupling components. Therefore, previously suggested sequences which solely recouple the |m| ​= ​2 term cannot determine the sign a ¹H's δ_aniso in a densely-coupled network. In this study, we demonstrate the CSA recoupling of strongly dipolar coupled ¹H spins using the Cn_n¹(90₀360₁₈₀540₀360₁₈₀90₀) sequence. This pulse scheme recouples both the |m| ​= ​1 and |m| ​= ​2 CSA terms but the scaling factors for the homonuclear dipolar coupling terms are zeroed. Consequently, the sequence is sensitive to the sign of δ_aniso but is not influenced by homonuclear dipolar interactions.

Ellagic Acid Inhibits α-Synuclein Aggregation at Multiple Stages and Reduces Its Cytotoxicity

α-Synuclein is a natively unfolded protein and its deposition in the Lewy body and Lewy neurites in the substantia nigra region of the brain is linked to Parkinson's disease (PD). The molecular mechanisms of α-synuclein aggregation and its clearance have not been well understood. Until now, several strategies have been designed to inhibit α-synuclein aggregation and related cytotoxicity. Polyphenols, small molecules, synthetic peptides, and peptide-derived molecules have been considered as potential candidates that inhibit α-synuclein oligomerization and its fibrillation, and a few of them are in clinical trials. We have identified a polyphenolic compound ellagic acid (EA) that inhibits α-synuclein aggregation. Our results demonstrated that EA inhibits primary nucleation, seeded aggregation, and membrane-induced aggregation. The cytotoxicity of α-synuclein oligomers and fibers treated with EA has been investigated and we found that EA treated oligomers and fibrils showed reduced cytotoxicity. Additionally, we also observed inhibition of membrane binding of α-synuclein by EA in SH-SY5Y cells. In conclusion, the present study suggests that small molecules such as ellagic acid have anti-amyloidogenic properties and may have therapeutic potential for Parkinson's disease and other proteinopathies.

Scaled recoupling of chemical shift anisotropies at high magnetic fields under MAS with interspersed C-elements

The power of chemical shift anisotropy (CSA) measurements for probing structure and dynamics of molecules has been long recognized. NMR pulse sequences that allow measurement of CSA values in an indirect dimension of a protein correlation spectrum have been employed for aliphatic groups, but for practical reasons, carbonyl functional groups have been little studied, despite the fact that carbonyls are expected to give particularly varied and informative CSA values. Specifically, the wide spectral widths of carbonyl tensors make their measurements difficult with typically attainable spectrometer settings. We present here an extended family of experiments that enable the recovery of static CSA lineshapes in an indirect dimension of magic angle spinning (MAS) solid-state NMR experiments, except for various real valued scaling factors. The experiment is suitable for uniformly labeled material, at moderate MAS rates (10 kHz-30 kHz) and at higher magnetic fields (ν_0H > 600 MHz). Specifically, the experiments are based on pulse sequence elements from a previous commonly used pulse sequence for CSA measurement, recoupling of chemical shift anisotropy (ROCSA), while modification of scaling factors is achieved by interspersing different blocks of C-elements of the same Cn_n ¹ cycle. Using experimental conditions similar to the parent ROCSA sequence, a CSA scaling factor between 0 and 0.272 can be obtained, thus allowing a useful practical range of possibilities in experimental conditions for measurement of larger CSA values. Using these blocks, it is also possible to make a constant-time CSA recoupling sequence. The effectiveness of this approach, fROCSA, is shown on model compounds 1-¹³C-Gly, U-¹³C,¹⁵N-l-His, and microcrystalline U-¹³C,¹⁵N-Ubiquitin.

Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals

In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the ¹³C and ¹H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For ¹³C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the ¹H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental ¹³C and ¹H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for ¹³C chemical shift calculations, but not for the ¹H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the ¹³C and ¹H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.

FEAST of biosensors: Food, environmental and agricultural sensing technologies (FEAST) in North America

We review the challenges and opportunities for biosensor research in North America aimed to accelerate translational research. We call for platform approaches based on: i) tools that can support interoperability between food, environment and agriculture, ii) open-source tools for analytics, iii) algorithms used for data and information arbitrage, and iv) use-inspired sensor design. We summarize select mobile devices and phone-based biosensors that couple analytical systems with biosensors for improving decision support. Over 100 biosensors developed by labs in North America were analyzed, including lab-based and portable devices. The results of this literature review show that nearly one quarter of the manuscripts focused on fundamental platform development or material characterization. Among the biosensors analyzed for food (post-harvest) or environmental applications, most devices were based on optical transduction (whether a lab assay or portable device). Most biosensors for agricultural applications were based on electrochemical transduction and few utilized a mobile platform. Presently, the FEAST of biosensors has produced a wealth of opportunity but faces a famine of actionable information without a platform for analytics.

Fibril Formation by Glucagon in Solution and in Membrane Environments

Glucagon is a 29-amino acid peptide hormone secreted by pancreatic α-cells and interacts with specific receptors located in various organs. Glucagon tends to form gel-like fibril aggregates that are cytotoxic because they activate apoptotic signaling pathways. First, fibril formation by glucagon in acidic solution is discussed in light of morphological and structural changes during elapsed time. Second, we provide kinetic analyses using a two-step autocatalytic reaction mechanism; the first step is a homogeneous nuclear formation process, and the second step is an autocatalytic heterogeneous fibril elongation process. Third, the processes of fibril formation by glucagon in a membrane environment are discussed based on the structural changes in the fibrils. In the presence of bicelles in acidic solution, glucagon interacts with the bicelles and forms fibril intermediates on the bicelle surface and grows into elongated fibrils. Glucagon-dimyristoylphosphatidylcholine (DMPC) bilayers in neutral solution mimic the environment for fibril formation by glucagon under near-physiological condition. Under these conditions, glucagon forms fibril intermediates that grow into elongated fibrils inside the lipid bilayer. Many days after preparing the glucagon-DMPC bilayer sample, the fibrils form networks inside and outside the bilayer. Furthermore, fibril intermediates strongly interact with lipid bilayers to form small particles.

A theoretical assessment of structure determination of multi-span membrane proteins by oriented sample solid-state NMR spectroscopy

Oriented sample solid state NMR (OS-ssNMR) spectroscopy allows direct determination of the structure and topology of membrane proteins reconstituted into aligned lipid bilayers. While OS-ssNMR theoretically has no upper size limit, its application to multi-span membrane proteins has not been established since most studies have been restricted to single or dual span proteins and peptides. Here, we present a critical assessment of the application of this method to multi-span membrane proteins. We used molecular dynamics simulations to back-calculate [¹⁵N-¹H] separated local field (SLF) spectra from a G protein-coupled receptor (GPCR) and show that fully resolved spectra can be obtained theoretically for a multi-span membrane protein with currently achievable resonance linewidths.

77Se NMR Probes the Protein Environment of Selenomethionine

Sulfur is critical for the correct structure and proper function of proteins. Yet, lacking a sensitive enough isotope, nuclear magnetic resonance (NMR) experiments are unable to deliver for sulfur in proteins the usual wealth of chemical, dynamic, and structural information. This limitation can be circumvented by substituting sulfur with selenium, which has similar physicochemical properties and minimal impact on protein structures but possesses an NMR compatible isotope (⁷⁷Se). Here we exploit the sensitivity of ⁷⁷Se NMR to the nucleus' chemical milieu and use selenomethionine as a probe for its proteinaceous environment. However, such selenium NMR spectra of proteins currently resist a reliable interpretation because systematic connections between variations of system variables and changes in ⁷⁷Se NMR parameters are still lacking. To start narrowing this knowledge gap, we report here on a biological ⁷⁷Se magnetic resonance data bank based on a systematically designed library of GB1 variants in which a single selenomethionine was introduced at different locations within the protein. We recorded the resulting isotropic ⁷⁷Se chemical shifts and relaxation times for six GB1 variants by solution-state ⁷⁷Se NMR. For four of the GB1 variants we were also able to determine the chemical shift anisotropy tensor of SeM by solid-state ⁷⁷Se NMR. To enable interpretation of the NMR data, the structures of five of the GB1 variants were solved by X-ray crystallography to a resolution of 1.2 Å, allowing us to unambiguously determine the conformation of the selenomethionine. Finally, we combine our solution- and solid-state NMR data with the structural information to arrive at general insights regarding the execution and interpretation of ⁷⁷Se NMR experiments that exploit selenomethionine to probe proteins.

Th@C86, Th@C82, Th@C80, and Th@C76: role of thorium encapsulation in determining spherical aromatic and bonding properties on medium-sized endohedral metallofullerenes

Thorium encapsulated metallofullerenes (Th-EMFs) with external C76, C80, C82, and C86 cages have been synthesized, with the 13C-NMR spectrum recorded for Th@C82. Here, we explore computationally the chemical bonding, NMR and spherical aromaticity of Th@C82 and related thorium-encapsulated metallofullerenes. Our results show that these Th-EMFs are new examples of spherical aromatic structures, representing interesting low-symmetry exceptions to the Hirsch 2(N + 1)2 rule of spherical aromaticity. Their electronic structures are based on π-electron counts of 80, 84, 86, and 90, respectively, with a shell structure ranging from S2P6D10F14G18H22I8 to S2P6D10F14G18H22I18, where the partially filled I-shell remains as a frontier orbital. Their behavior is comparable to that of the spherical aromatic alkali-C606- phases, which in addition to the favorable endohedral Th-fullerene bonding account for their particular abundance exhibiting the ability to sustain a long-range shielding cone as a result of the favorable metal-cage bonding. This rationalization of such species as neutral spherical aromatic EMFs suggests the possibility of an extensive series of aromatic fullerenes with nuclearity larger than C60 buckminsterfullerene as stable building blocks towards nanostructured metal-organic materials.

New silver (thio)semicarbazide derivatives: synthesis, structural features, and antimicrobial activity

New silver(i) (thio)semicarbazide coordination compounds were prepared, fully characterized, and tested as antimicrobial and antibiofilm agents.

Coexistence of three types of sodium motion in double molybdate Na9Sc(MoO4)6: 23Na and 45Sc NMR data and ab initio calculations

The rechargeable Na-ion batteries attract much attention as an alternative to the widely used but expensive Li-ion batteries. The search for materials with high sodium diffusion is important for the development of solid state electrolytes. We present the results of experimental and ab initio studies of the Na-ion diffusion mechanism in Na9Sc(MoO4)6. The ion conductivity reaches the value of 3.6 × 10-2 S cm-1 at T ∼ 850 K. The 23Na and 45Sc NMR data reveal the coexistence of three different types of Na-ion motion in the temperature range from 300 to 750 K. They are activated at different temperatures and are characterized by substantially different dynamics parameters. These features are confirmed by ab initio calculations of activation barriers for sodium diffusion along various paths.

Investigation of the internal structure and dynamics of cellulose by 13C-NMR relaxometry and 2DPASS-MAS-NMR measurements

Internal structure and dynamics of commercial and natural cellulose were studied by measuring chemical shift anisotropy (CSA) parameters, and spin-lattice relaxation rate (1/T₁) at each and every chemically different carbon nuclear site. CSA parameters were measured by ¹³C two-dimensional phase adjusted spinning sideband (2DPASS) cross-polarization magic angle spinning (CP-MAS) NMR experiment. Site specific spin-lattice relaxation time was measured by Torchia-CP method. Anisotropy parameters of C4 and C6 regions are higher than C1 and C235 regions and asymmetry of C4 line is lower than any other carbon site. The higher values of CSA parameters of C4 and C6 nuclei arise due to the rotation of O4-C4, C1-O4, O5-C5-C6-O6 and C4-C5-C6-O6 bonds at torsion angles ψ, Φ, χ and χ' respectively and the influence of interchain and intrachain hydrogen bondings. Two distinct peaks are also observed for C4 and C6 resonance line position-one peak arises primarily due to the nuclei in amorphous region and another one arises due to the same nuclei resides in paracrystalline region. The spin-lattice relaxation time and the CSA parameters are different at these two distinct peak positions of C4 and C6 line. Molecular correlation time of each and every chemically different carbon site was calculated with the help of CSA parameters and spin-lattice relaxation time. The molecular correlation time of the amorphous region is one order of magnitude less than the crystalline region. The distinction between amorphous and paracrystalline regions of cellulose is more vividly portrayed by determining spin-lattice relaxation time, CSA parameters, and molecular correlation time at each and every chemically different carbon site. This type of study correlating the structure and dynamics of cellulose will illuminate the path of inventing biomimetic materials.

A comprehensive and comparative study of the internal structure and dynamics of natural β-keratin and regeneratedβ-keratin by solid state NMR spectroscopy

Structure and dynamics of natural and regenerated chicken feather β-keratin were investigated by ¹³C cross-polarization (CP) magic angle spinning (MAS) solid state nuclear magnetic resonance (SSNMR) spectral analysis, ¹³C and ¹H spin-lattice relaxation time measurements, and ¹³C two dimensional phase adjusted spinning sidebands (2DPASS) MAS SSNMR measurements. Chemical shift anisotropy (CSA) parameters of both natural and regenerated chicken feather β-keratin were extracted by using 2DPASS MAS SSNMR experiment. The beauty of 2DPASS MAS SSNMR experiment is it can correlate the isotropic and anisotropic dimension with the help of shearing transformation and two dimensional Fourier Transformation. Molecular correlation time at each and every magnetically inequivalent carbon site of both natural and regenerated chicken feather β-keratin were also determined. The change in molecular dynamics of structural protein after pretreatment was monitored by 2DPASS MAS SSNMR and ¹³C relaxation measurement. This type of comprehensive study will provide the information about the interrelation between the structure and dynamics of structural protein and will also shed light in the way of developing methods for conversion of animal by-products to novel product.

Retinal Configuration of ppR Intermediates Revealed by Photoirradiation Solid-State NMR and DFT

Pharanois phoborhodopsin (ppR) from Natronomonas pharaonis is a transmembrane photoreceptor protein involved in negative phototaxis. Structural changes in ppR triggered by photoisomerization of the retinal chromophore are transmitted to its cognate transducer protein (pHtrII) through a cyclic photoreaction pathway involving several photointermediates. This pathway is called the photocycle. It is important to understand the detailed configurational changes of retinal during the photocycle. We previously observed one of the photointermediates (M-intermediates) by in situ photoirradiation solid-state NMR experiments. In this study, we further observed the ¹³C cross-polarization magic-angle-spinning NMR signals of late photointermediates such as O- and N'-intermediates by illumination with green light (520 nm). Under blue-light (365 nm) irradiation of the M-intermediates, ¹³C cross-polarization magic-angle-spinning NMR signals of 14- and 20-¹³C-labeled retinal in the O-intermediate appeared at 115.4 and 16.4 ppm and were assigned to the 13-trans, 15-syn configuration. The signals caused by the N'-intermediate appeared at 115.4 and 23.9 ppm and were assigned to the 13-cis configuration, and they were in an equilibrium state with the O-intermediate during thermal decay of the M-intermediates at -60°C. Thus, photoirradiation NMR studies revealed the photoreaction pathways from the M- to O-intermediates and the equilibrium state between the N'- and O-intermediate. Further, we evaluated the detailed retinal configurations in the O- and N'-intermediates by performing a density functional theory chemical shift calculation. The results showed that the N'-intermediate has a 63° twisted retinal state due to the 13-cis configuration. The retinal configurations of the O- and N'-intermediates were determined to be 13-trans, 15-syn, and 13-cis, respectively, based on the chemical shift values of [20-¹³C] and [14-¹³C] retinal obtained by photoirradiation solid-state NMR and density functional theory calculation.

Validation of protein backbone structures calculated from NMR angular restraints using Rosetta

Multidimensional solid-state NMR spectra of oriented membrane proteins can be used to infer the backbone torsion angles and hence the overall protein fold by measuring dipolar couplings and chemical shift anisotropies, which depend on the orientation of each peptide plane with respect to the external magnetic field. However, multiple peptide plane orientations can be consistent with a given set of angular restraints. This ambiguity is further exacerbated by experimental uncertainty in obtaining and interpreting such restraints. The previously developed algorithms for structure calculations using angular restraints typically involve a sequential walkthrough along the backbone to find the torsion angles between the consecutive peptide plane orientations that are consistent with the experimental data. This method is sensitive to experimental uncertainty in interpreting the peak positions of as low as ± 10 Hz, often yielding high structural RMSDs for the calculated structures. Here we present a significantly improved version of the algorithm which includes the fitting of several peptide planes at once in order to prevent propagation of error along the backbone. In addition, a protocol has been devised for filtering the structural solutions using Rosetta scoring functions in order to find the structures that both fit the spectrum and satisfy bioinformatics restraints. The robustness of the new algorithm has been tested using synthetic angular restraints generated from the known structures for two proteins: a soluble protein 2gb1 (56 residues), chosen for its diverse secondary structure elements, i.e. an alpha-helix and two beta-sheets, and a membrane protein 4a2n, from which the first two transmembrane helices (having a total of 64 residues) have been used. Extensive simulations have been performed by varying the number of fitted planes, experimental error, and the number of NMR dimensions. It has been found that simultaneously fitting two peptide planes always shifted the distribution of the calculated structures toward lower structural RMSD values as compared to fitting a single torsion-angle pair. For each protein, irrespective of the simulation parameters, Rosetta was able to distinguish the most plausible structures, often having structural RMSDs lower than 2 Å with respect to the original structure. This study establishes a framework for de-novo protein structure prediction using a combination of solid-state NMR angular restraints and bioinformatics.

Conformational Changes in the Cytoplasmic Region of KIR3DL1 upon Interaction with SHP-2

KIR3DL1 is an inhibitory killer cell immunoglobulin-like receptor (KIR) that negatively regulates natural killer cell cytotoxicity. The KIR3DL1 cytoplasmic region (3DL1-cyto) is disordered and can be dissected into three segments: (I) H340-V351; (II) M352-D371; and (III) P372-P423. NMR studies indicate that segment II can dynamically adopt a loop-like conformation, and segments I and III can form dynamic helices that may mediate binding to membranes, particularly in the region around the N-terminal (N) immunoreceptor tyrosine-based inhibitory motif (ITIM), consistent with its role in signaling. Furthermore, individual SH2 domains of SHP-2 strongly engage with the unphosphorylated N-ITIM of 3DL1-cyto, while binding of the tandem SHP-2 SH2 domains to the bis-phosphorylated ITIMs results in more extensive conformational changes in segments I and III. The findings enhance our understanding of KIR function and how ITIMs in a target receptor operate in concert to engage the tandem SH2 domains of SHP-2.

Elucidating the internal structure and dynamics of α-chitin by 2DPASS-MAS-NMR and spin-lattice relaxation measurements

The structure and dynamics of the second most abundant biopolymer α-chitin were studied by high resolution solid state ¹³C cross-polarization magic angle spinning nuclear magnetic resonance (CP-MAS-NMR) spectral analysis, ¹³C relaxation measurements at eight chemically different carbon sites and chemical shift anisotropy measurement by two-dimensional phase-adjusted spinning sidebands (2DPASS) magic angle spinning (MAS) solid state NMR method.¹³C spin-lattice relaxation time was measured by high resolution Torchia CP method. Spin-lattice relaxation rate (1/T₁) of side chain carbon nuclei were remarkably high, because those nuclei possess higher degree of motional freedom. Chemical shift anisotropy parameters of eight chemically different carbon nuclei were determined by 2DPASS-MAS-NMR experiment. Large value of chemical shift anisotropy was observed for carbonyl group carbon (C₇) nuclei, because of electrostatic effect, hydrogen bonding and molecular magnetic susceptibility. ¹³C relaxation mechanism is mainly governed by chemical shift anisotropy interaction, especially at high value of external magnetic field (11.74 T). Thus, the correlation time at different carbon sites were also calculated by using the spin-lattice relaxation times and chemical shift anisotropy values. The correlation time of side chain carbon (C₈) was two orders of magnitude less than the carbonyl group carbon. These types of investigations would enlighten the correlation between the structure and dynamics of long polysaccharide chain compound.

Accurate 13-C and 15-N molecular crystal chemical shielding tensors from fragment-based electronic structure theory

Standard nuclear magnetic resonance (NMR) spectroscopy experiments measure isotropic chemical shifts, but measuring the chemical shielding anisotropy (CSA) tensor can provide additional insights into solid state chemical structures. Interpreting the principal components of these tensors is facilitated by first-principles chemical shielding tensor predictions. Here, the ability to predict molecular crystal CSA tensor components for ¹³C and ¹⁵N nuclei with fragment-based electronic structure techniques is explored. Similar to what has been found previously for isotropic chemical shifts, the benchmarking demonstrates that fragment-based techniques can accurately reproduce CSA tensor components. The use of hybrid density functionals like PBE0 or B3LYP provide higher accuracy than generalized gradient approximation functionals like PBE. Unlike for planewave density functional techniques, hybrid density functionals can be employed routinely with modest computational cost in fragment approaches. Finally, good consistency between the regression parameters used to map either isotropic shieldings or CSA tensor components is demonstrated, providing further evidence for the quality of the models and highlighting that models trained for isotropic shifts can also be applied to CSA tensor components.

An Evaluation of the Potential of NMR Spectroscopy and Computational Modelling Methods to Inform Biopharmaceutical Formulations

Protein-based therapeutics are considered to be one of the most important classes of pharmaceuticals on the market. The growing need to prolong stability of high protein concentrations in liquid form has proven to be challenging. Therefore, significant effort is being made to design formulations which can enable the storage of these highly concentrated protein therapies for up to 2 years. Currently, the excipient selection approach involves empirical high-throughput screening, but does not reveal details on aggregation mechanisms or the molecular-level effects of the formulations under storage conditions. Computational modelling approaches have the potential to elucidate such mechanisms, and rapidly screen in silico prior to experimental testing. Nuclear Magnetic Resonance (NMR) spectroscopy can also provide complementary insights into excipient–protein interactions. This review will highlight the underpinning principles of molecular modelling and NMR spectroscopy. It will also discuss the advancements in the applications of computational and NMR approaches in investigating excipient–protein interactions.