¹³C- and ¹H-detection under fast MAS for the study of poorly available proteins: application to sub-milligram quantities of a 7 trans-membrane protein

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.

Multiplexing experiments in NMR and multi-nuclear MRI

Multiplexing NMR experiments by direct detection of multiple free induction decays (FIDs) in a single experiment offers a dramatic increase in the spectral information content and often yields significant improvement in sensitivity per unit time. Experiments with multi-FID detection have been designed with both homonuclear and multinuclear acquisition, and the advent of multiple receivers on commercial spectrometers opens up new possibilities for recording spectra from different nuclear species in parallel. Here we provide an extensive overview of such techniques, designed for applications in liquid- and solid-state NMR as well as in hyperpolarized samples. A brief overview of multinuclear MRI is also provided, to stimulate cross fertilization of ideas between the two areas of research (NMR and MRI). It is shown how such techniques enable the design of experiments that allow structure elucidation of small molecules from a single measurement. Likewise, in biomolecular NMR experiments multi-FID detection allows complete resonance assignment in proteins. Probes with multiple RF microcoils routed to multiple NMR receivers provide an alternative way of increasing the throughput of modern NMR systems, effectively reducing the cost of NMR analysis and increasing the information content at the same time. Solid-state NMR experiments have also benefited immensely from both parallel and sequential multi-FID detection in a variety of multi-dimensional pulse schemes. We are confident that multi-FID detection will become an essential component of future NMR methodologies, effectively increasing the sensitivity and information content of NMR measurements.

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

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

Collective exchange processes reveal an active site proton cage in bacteriorhodopsin

Proton translocation across membranes is vital to all kingdoms of life. Mechanistically, it relies on characteristic proton flows and modifications of hydrogen bonding patterns, termed protonation dynamics, which can be directly observed by fast magic angle spinning (MAS) NMR. Here, we demonstrate that reversible proton displacement in the active site of bacteriorhodopsin already takes place in its equilibrated dark-state, providing new information on the underlying hydrogen exchange processes. In particular, MAS NMR reveals proton exchange at D85 and the retinal Schiff base, suggesting a tautomeric equilibrium and thus partial ionization of D85. We provide evidence for a proton cage and detect a preformed proton path between D85 and the proton shuttle R82. The protons at D96 and D85 exchange with water, in line with ab initio molecular dynamics simulations. We propose that retinal isomerization makes the observed proton exchange processes irreversible and delivers a proton towards the extracellular release site.

Daniel Friedrich et al. show that reversible proton translocation occurs in the dark–state of bacteriorhodopsin, involving the retinal Schiff base and D85 exchanging protons with H₂O. They find evidence of an active site proton cage and possible proton transfer via R82.

1H magic-angle spinning NMR evolves as a powerful new tool for membrane proteins

Building on a decade of continuous advances of the community, the recent development of very fast (60 kHz and above) magic-angle spinning (MAS) probes has revolutionised the field of solid-state NMR. This new spinning regime reduces the ¹H-¹H dipolar couplings, so that direct detection of the larger magnetic moment available from ¹H is now possible at high resolution, not only in deuterated molecules but also in fully-protonated substrates. Such capabilities allow rapid "fingerprinting" of samples with a ten-fold reduction of the required sample amounts with respect to conventional approaches, and permit extensive, robust and expeditious assignment of small-to-medium sized proteins (up to ca. 300 residues), and the determination of inter-nuclear proximities, relative orientations of secondary structural elements, protein-cofactor interactions, local and global dynamics. Fast MAS and ¹H detection techniques have nowadays been shown to be applicable to membrane-bound systems. This paper reviews the strategies underlying this recent leap forward in sensitivity and resolution, describing its potential for the detailed characterization of membrane proteins.

Interaction of Monomeric Interleukin-8 with CXCR1 Mapped by Proton-Detected Fast MAS Solid-State NMR

The human chemokine interleukin-8 (IL-8; CXCL8) is a key mediator of innate immune and inflammatory responses. This small, soluble protein triggers a host of biological effects upon binding and activating CXCR1, a G protein-coupled receptor, located in the cell membrane of neutrophils. Here, we describe ¹H-detected magic angle spinning solid-state NMR studies of monomeric IL-8 (1-66) bound to full-length and truncated constructs of CXCR1 in phospholipid bilayers under physiological conditions. Cross-polarization experiments demonstrate that most backbone amide sites of IL-8 (1-66) are immobilized and that their chemical shifts are perturbed upon binding to CXCR1, demonstrating that the dynamics and environments of chemokine residues are affected by interactions with the chemokine receptor. Comparisons of spectra of IL-8 (1-66) bound to full-length CXCR1 (1-350) and to N-terminal truncated construct NT-CXCR1 (39-350) identify specific chemokine residues involved in interactions with binding sites associated with N-terminal residues (binding site-I) and extracellular loop and helical residues (binding site-II) of the receptor. Intermolecular paramagnetic relaxation enhancement broadening of IL-8 (1-66) signals results from interactions of the chemokine with CXCR1 (1-350) containing Mn²⁺ chelated to an unnatural amino acid assists in the characterization of the receptor-bound form of the chemokine.

Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure

Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.

Pharmaceutical cocrystals, salts and polymorphs: Advanced characterization techniques

The main goal of a novel drug development is to obtain it with optimal physiochemical, pharmaceutical and biological properties. Pharmaceutical companies and scientists modify active pharmaceutical ingredients (APIs), which often are cocrystals, salts or carefully selected polymorphs, to improve the properties of a parent drug. To find the best form of a drug, various advanced characterization methods should be used. In this review, we have described such analytical methods, dedicated to solid drug forms. Thus, diffraction, spectroscopic, thermal and also pharmaceutical characterization methods are discussed. They all are necessary to study a solid API in its intrinsic complexity from bulk down to the molecular level, gain information on its structure, properties, purity and possible transformations, and make the characterization efficient, comprehensive and complete. Furthermore, these methods can be used to monitor and investigate physical processes, involved in the drug development, in situ and in real time. The main aim of this paper is to gather information on the current advancements in the analytical methods and highlight their pharmaceutical relevance.

Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy

In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.

Five decades of homonuclear dipolar decoupling in solid-state NMR: Status and outlook

It has been slightly more than fifty years since the first homonuclear spin decoupling scheme, Lee-Goldburg decoupling, was proposed for removing homonuclear dipolar interactions in solid-state nuclear magnetic resonance. A family of such schemes has made observation of high-resolution NMR spectra of abundant spins possible in various applications in solid state. This review outlines the strategies used in this field and the future prospects of homonuclear spin decoupling in solid-state NMR.

Dynamic Nuclear Polarization enhanced NMR at 187 GHz/284 MHz using an Extended Interaction Klystron amplifier

A Dynamic Nuclear Polarisation (DNP) enhanced solid-state Magic Angle Spinning (MAS) NMR spectrometer which uses a 187 GHz (corresponding to (1)H NMR frequency of 284 MHz) Extended Interaction Klystron (EIK) amplifier as the microwave source is briefly described. Its performance is demonstrated for a biomolecule (bacteriorhodopsin), a pharmaceutical, and surface functionalised silica. The EIK is very compact and easily incorporated into an existing spectrometer. The bandwidth of the amplifier is sufficient that it obviates the need for a sweepable magnetic field, once set, for all commonly used radicals. The variable power (CW or pulsed) output from the EIK is transmitted to the DNP-NMR probe using a quasi-optic system with a high power isolator and a corrugated waveguide which feeds the microwaves into the DNP-NMR probe. Curved mirrors inside the probe project the microwaves down the axis of the MAS rotor, giving a very efficient system such that maximum DNP enhancement is achieved with less than 3 W output from the microwave source. The DNP-NMR probe operates with a sample temperature down to 90K whilst spinning at 8 kHz. Significant enhancements, in excess of 100 for bacteriorhodopsin in purple membrane (bR in PM), are shown along with spectra which are enhanced by ≈25 with respect to room temperature, for both the pharmaceutical furosemide and surface functionalised silica. These enhancements allow hitherto prohibitively time consuming experiments to be undertaken. The power at which the DNP enhancement in bR in PM saturates does not change significantly between 90K and 170 K even though the enhancement drops by a factor of ≈11. As the DNP build up time decreases by a factor 3 over this temperature range, the reduction in T1n is presumably a significant contribution to the drop in enhancement.

Proton-detected solid-state NMR spectroscopy of fully protonated proteins at slow to moderate magic-angle spinning frequencies

(1)H-detection offers a substitute to the sensitivity-starved experiments often used to characterize biomolecular samples using magic-angle spinning solid-state NMR spectroscopy (MAS-ssNMR). To mitigate the effects of the strong (1)H-(1)H dipolar coupled network that would otherwise severely broaden resonances, high MAS frequencies (>40kHz) are often employed. Here, we have explored the alternative of stroboscopic (1)H-detection at moderate MAS frequencies of 5-30kHz using windowed version of supercycled-phase-modulated Lee-Goldburg homonuclear decoupling. We show that improved resolution in the (1)H dimension, comparable to that obtainable at high spinning frequencies of 40-60kHz without homonuclear decoupling, can be obtained in these experiments for fully protonated proteins. Along with detailed analysis of the performance of the method on the standard tri-peptide f-MLF, experiments on micro-crystalline GB1 and amyloid-β aggregates are used to demonstrate the applicability of these pulse-sequences to challenging biomolecular systems. With only two parameters to optimize, broadbanded performance of the homonuclear decoupling sequence, linear dependence of the chemical-shift scaling factor on resonance offset and a straightforward implementation under experimental conditions currently used for many biomolecular studies (viz. spinning frequencies and radio-frequency amplitudes), we expect these experiments to complement the current (13)C-detection based methods in assignments and characterization through chemical-shift mapping.

Proton detection for signal enhancement in solid-state NMR experiments on mobile species in membrane proteins

Direct proton detection is becoming an increasingly popular method for enhancing sensitivity in solid-state nuclear magnetic resonance spectroscopy. Generally, these experiments require extensive deuteration of the protein, fast magic angle spinning (MAS), or a combination of both. Here, we implement direct proton detection to selectively observe the mobile entities in fully-protonated membrane proteins at moderate MAS frequencies. We demonstrate this method on two proteins that exhibit different motional regimes. Myelin basic protein is an intrinsically-disordered, peripherally membrane-associated protein that is highly flexible, whereas Anabaena sensory rhodopsin is composed of seven rigid transmembrane α-helices connected by mobile loop regions. In both cases, we observe narrow proton linewidths and, on average, a 10× increase in sensitivity in 2D insensitive nuclear enhancement of polarization transfer-based HSQC experiments when proton detection is compared to carbon detection. We further show that our proton-detected experiments can be easily extended to three dimensions and used to build complete amino acid systems, including sidechain protons, and obtain inter-residue correlations. Additionally, we detect signals which do not correspond to amino acids, but rather to lipids and/or carbohydrates which interact strongly with membrane proteins.