Microsecond motions probed by near-rotary-resonance R1ρ15N MAS NMR experiments: the model case of protein overall-rocking in crystals

Dipolar Recoupling in Rotating Solids

Magic angle spinning (MAS) nuclear magnetic resonance (NMR) has evolved significantly over the past three decades and established itself as a vital tool for the structural analysis of biological macromolecules and materials. This review delves into the development and application of dipolar recoupling techniques in MAS NMR, which are crucial for obtaining detailed structural and dynamic information. We discuss a variety of homonuclear and heteronuclear recoupling methods which are essential for measuring spatial restraints and explain in detail the spin dynamics that these sequences generate. We also explore recent developments in high spinning frequency MAS, proton detection, and dynamic nuclear polarization, underscoring their importance in advancing biomolecular NMR. Our aim is to provide a comprehensive account of contemporary dipolar recoupling methods, their principles, and their application to structural biology and materials, highlighting significant contributions to the field and emerging techniques that enhance resolution and sensitivity in MAS NMR spectroscopy.

Slow global motions in biosolids studied by the deuteron stimulated echo NMR experiment

Recent 15N R1ρ-relaxation studies have shown that proteins in the solid state undergo slow, low amplitude global motion in the sub-millisecond time range. This range is at the edge of the time window for R1ρ experiments and, therefore, the motional parameters obtained by this method are not precise or reliable. In this paper, we present a 2H stimulated echo study of this type of molecular dynamics. The 2H stimulated echo experiments on a static sample allow for direct measurement of the correlation function in the time range of 10-6-10-1 s, making them well suited to study this type of molecular mobility. We have conducted a detailed analytical and numerical comparison of the correlation functions obtained from the relaxation and stimulated echo experiments, which are generally different. We have identified conditions and algorithms that enable a direct comparison of the relaxation and stimulated echo experimental results. Using the protein GB1 in the form of a lyophilized powder, we have demonstrated that 15N R1ρ-relaxation and 2H stimulated echo experiments yield essentially the same slow-motion correlation function. Surprisingly, this type of motion is observed not only in the protein sample but also in the tripeptide and single amino acid solid samples. The comparison of data measured in these three samples at different temperatures led us to conclude that this slow motion is, in fact, ultrasonic phonons, which seem to be inherent to all rigid biological solids.

NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function

Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.

Carbon-detected deuterium solid-state NMR rotating frame relaxation measurements for protein methyl groups under magic angle spinning

Deuterium rotating frame solid-state NMR relaxation measurements (2H R1ρ) are important tools in quantitative studies of molecular dynamics. We demonstrate how 2H to 13C cross-polarization (CP) approaches under 10-40 kHz magic angle spinning rates can be combined with the 2H R1ρ blocks to allow for extension of deuterium rotating frame relaxation studies to methyl groups in biomolecules. This extension permits detection on the 13C nuclei and, hence, for the achievement of site-specific resolution. The measurements are demonstrated using a nine-residue low complexity peptide with the sequence GGKGMGFGL, in which a single selective -13CD3 label is placed at the methionine residue. Carbon-detected measurements are compared with the deuterium direct-detection results, which allows for fine-tuning of experimental approaches. In particular, we show how the adiabatic respiration CP scheme and the double adiabatic sweep on the 2H and 13C channels can be combined with the 2H R1ρ relaxation rates measurement. Off-resonance 2H R1ρ measurements are investigated in addition to the on-resonance condition, as they extent the range of effective spin-locking field.

Protein dynamics detected by magic-angle spinning relaxation dispersion NMR

Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

We demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.

Exploring Molecular Dynamics of Adsorbed CO2 Species in Amine-Modified Porous Silica by Solid-State NMR Relaxation

Previous studies on CO2 adsorbents have mainly addressed the identification and quantification of adsorbed CO2 species in amine-modified porous materials. Investigation of molecular motion of CO2 species in confinement has not been explored in depth yet. This work entails a comprehensive study of molecular dynamics of the different CO2 species chemi- and physisorbed at amine-modified silica materials through the determination of the rotating frame spin-lattice relaxation times (T 1ρ) by solid-state NMR. Rotational correlation times (τC) were also estimated using spin relaxation models based on the Bloch, Wangsness, and Redfield and the Bloembergen-Purcell-Pound theories. As expected, the τC values for the two physisorbed CO2 species are considerably shorter (32 and 20 μs) than for the three identified chemisorbed CO2 species (162, 62, and 123 μs). The differences in molecular dynamics between the different chemisorbed species correlate well with the structures previously proposed. In the case of the physisorbed CO2 species, the τC values of the CO2 species displaying faster molecular dynamics falls in the range of viscous liquids, whereas the species presenting slower dynamics exhibit T 1ρ and τC values compatible with a CO2 layer of weakly interacting molecules with the silica surface. The values for chemical shift anisotropy (CSA) and 1H-13C heteronuclear dipolar couplings have also been estimated from T 1ρ measurements, for each adsorbed CO2 species. The CSA tensor parameters obtained from fitting the relaxation data agree with the experimentally measured CSA values, thus showing that the theories are well suited to study CO2 dynamics in silica surfaces.

Deuteron rotating frame relaxation for the detection of slow motions in rotating solids

We demonstrate experimental and computational approaches for measuring 2H rotating frame NMR relaxation for solid samples under magic angle spinning (MAS) conditions. The relaxation properties of the deuterium spin-1 system are dominated by the reorientation of the anisotropic quadrupolar tensors, with the effective quadrupolar coupling constant around 55 kHz for methyl groups. The technique is demonstrated using the model compound dimethyl-sulfone at MAS rates of 10 and 60 kHz as well as for an amyloid fibril sample comprising an amyloid-β (1-40) protein with a selective methyl group labeled in the disordered domain of the fibrils, at an MAS rate of 8 kHz. For both systems, the motional parameters fall well within the ranges determined by other techniques, thus validating its feasibility. Experimental and computational factors such as i) the probe's radio frequency inhomogeneity profiles, ii) rotary resonances at conditions for which the spin-lock field strength matches the half- or full-integer of the MAS rate, iii) the choice of MAS rates and spin-lock field strengths, and iv) simulations that account for the interconversion of multiple coherences for the spin-1 system under MAS and deviations from the analytical Redfield treatment are thoroughly considered.

Solid-State NMR: Methods for Biological Solids

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

A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR

Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B₀ field in a perdeuterated environment are compiled.

Model-Free or Not?

Relaxation in nuclear magnetic resonance is a powerful method for obtaining spatially resolved, timescale-specific dynamics information about molecular systems. However, dynamics in biomolecular systems are generally too complex to be fully characterized based on NMR data alone. This is a familiar problem, addressed by the Lipari-Szabo model-free analysis, a method that captures the full information content of NMR relaxation data in case all internal motion of a molecule in solution is sufficiently fast. We investigate model-free analysis, as well as several other approaches, and find that model-free, spectral density mapping, LeMaster's approach, and our detector analysis form a class of analysis methods, for which behavior of the fitted parameters has a well-defined relationship to the distribution of correlation times of motion, independent of the specific form of that distribution. In a sense, they are all "model-free." Of these methods, only detectors are generally applicable to solid-state NMR relaxation data. We further discuss how detectors may be used for comparison of experimental data to data extracted from molecular dynamics simulation, and how simulation may be used to extract details of the dynamics that are not accessible via NMR, where detector analysis can be used to connect those details to experiments. We expect that combined methodology can eventually provide enough insight into complex dynamics to provide highly accurate models of motion, thus lending deeper insight into the nature of biomolecular dynamics.

Deuterium solid-state NMR quadrupolar order rotating frame relaxation with applications to amyloid-β fibrils

We describe a new method for measuring molecular dynamics based on the deuterium solid-state nuclear magnetic resonance (NMR) quadrupolar order rotating frame relaxation rate R1ρ,Q under static conditions. The observed quadrupolar order coherence is created using the broad-band Jeener-Broekaert excitation and is locked with a weak radio frequency (RF) field. We describe the experimental and theoretical approaches and show applications to a selectively deuterated valine side chain of the phosphorylated amyloid-β (1-40) fibrils phosphorylated at the serine-8 position. The R1ρ,Q rate is sensitive to the rotameric exchange mode. For biological samples, the low spin-lock field in the 5- to 10-kHz range has the advantage of avoiding sample heating and dehydration. Thus, it provides an alternative to approaches based on single-quantum coherence, which require larger spin-lock fields.

Deuteron Chemical Exchange Saturation Transfer for the Detection of Slow Motions in Rotating Solids

We utilized the ²H Chemical Exchange Saturation Transfer (CEST) technique under magic angle spinning (MAS) conditions to demonstrate the feasibility of the method for studies of slow motions in the solid state. For the quadrupolar anisotropic interaction, the essence of CEST is to scan the saturation pattern over a range of offsets corresponding to the entire spectral region(s) for all conformational states involved, which translates into a range of −60–+ 60 kHz for methyl groups. Rotary resonances occur when the offsets are at half-and full-integer of the MAS rates. The choice of the optimal MAS rate is governed by the condition to reduce the number of rotary resonances in the CEST profile patterns and retain a sufficiently large quadrupolar interaction active under MAS to maintain sensitivity to motions. As examples, we applied this technique to a well-known model compound dimethyl-sulfone (DMS) as well as amyloid-β fibrils selectively deuterated at a single methyl group of A2 belonging to the disordered domain. It is demonstrated that the obtained exchange rate between the two rotameric states of DMS at elevated temperatures fell within known ranges and the fitted model parameters for the fibrils agree well with the previously obtained value using static ²H NMR techniques. Additionally, for the fibrils we have observed characteristic broadening of rotary resonances in the presence of conformational exchange, which provides implications for model selection and refinement. This work sets the stage for future potential extensions of the ²H CEST under MAS technique to multiple-labeled samples in small molecules and proteins.

Recent developments in deuterium solid-state NMR for the detection of slow motions in proteins

Slow timescale dynamics in proteins are essential for a variety of biological functions spanning ligand binding, enzymatic catalysis, protein folding and misfolding regulations, as well as protein-protein and protein-nucleic acid interactions. In this review, we focus on the experimental and theoretical developments of 2H static NMR methods applicable for studies of microsecond to millisecond motional modes in proteins, particularly rotating frame relaxation dispersion (R1ρ), quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation dispersion, and quadrupolar chemical exchange saturation transfer NMR experiments (Q-CEST). With applications chosen from amyloid-β fibrils, we show the complementarity of these approaches for elucidating the complexities of conformational ensembles in disordered domains in the non-crystalline solid state, with the employment of selective deuterium labels. Combined with recent advances in relaxation dispersion backbone measurements for 15N/13C/1H nuclei, these techniques provide powerful tools for studies of biologically relevant timescale dynamics in disordered domains in the solid state.

Relaxation-induced dipolar exchange with recoupling (RIDER) distortions in CODEX experiments

Chemical shift anisotropy (CSA) and dipolar CODEX (Cenralband Only Detection of EXchange) experiments enable abundant quantitative information on the reorientation of the CSA and dipolar tensors to be obtained on millisecond-second timescales. At the same time, proper performance of the experiments and data analysis can often be a challenge since CODEX is prone to some interfering effects that may lead to incorrect interpretation of the experimental results. One of the most important such effects is RIDER (relaxation-induced dipolar exchange with recoupling). It appears due to the dipolar interaction of the observed X nuclei with some other nuclei, which causes an apparent decay in the mixing time dependence of the signal intensity reflecting not molecular motion, but spin flips of the adjacent nuclei. This may hamper obtaining correct values of the parameters of molecular mobility. In this contribution we consider in detail the reasons why the RIDER distortions remain even under decoupling conditions and propose measures to eliminate them. That is, we suggest (1) using an additional Z filter between the cross-polarization (CP) section and the CODEX recoupling blocks that suppresses the interfering anti-phase coherence responsible for the X -H RIDER and (2) recording only the cosine component of the CODEX signal since it is less prone to the RIDER distortions in comparison to the sine component. The experiments were conducted on rigid model substances as well as microcrystalline 2 H /  15 N-enriched proteins (GB1 and SH3) with a partial back-exchange of labile protons. Standard CSA and dipolar CODEX experiments reveal a fast-decaying component in the mixing time dependence of 15 N nuclei in proteins, which can be misinterpreted as a slow overall protein rocking motion. However, the RIDER-free experimental setup provides flat mixing time dependences, meaning that the studied proteins do not undergo global motions on the millisecond timescale.

Recent advances in solid-state relaxation dispersion techniques

This review describes two rotating-frame (R_1ρ) relaxation dispersion methods, namely the Bloch-McConnell Relaxation Dispersion and the Near-rotary Resonance Relaxation Dispersion, which enable the study of microsecond time-scale conformational fluctuations in the solid state using magic-angle-spinning nuclear magnetic resonance spectroscopy. The goal is to provide the reader with key ideas, experimental descriptions, and practical considerations associated with R_1ρ measurements that are needed for analyzing relaxation dispersion and quantifying conformational exchange. While the focus is on protein motion, many presented concepts can be equally well adapted to study the microsecond time-scale dynamics of other bio- (e.g. lipids, polysaccharides, nucleic acids), organic (e.g. pharmaceutical compounds), or inorganic molecules (e.g., metal organic frameworks). This article summarizes the essential contributions made by recent theoretical and experimental solid-state NMR studies to our understanding of protein motion. Here we discuss recent advances in fast MAS applications that enable the observation and atomic level characterization of sparsely populated conformational states which are otherwise inaccessible for other experimental methods. Such high-energy states are often associated with protein functions such as molecular recognition, ligand binding, or enzymatic catalysis, as well as with disease-related properties such as misfolding and amyloid formation.

Effect of Post-Translational Modifications and Mutations on Amyloid-β Fibrils Dynamics at N Terminus

We investigate the variability in the dynamics of the disordered N-terminal domain of amyloid-β fibrils (Aβ), comprising residues 1-16 of Aβ1-40, due to post-translational modifications and mutations in the β-bend regions known to modulate aggregation properties. Using 2H static solid-state NMR approaches, we compare the dynamics in the wild-type Aβ fibrils in the threefold symmetric polymorph with the fibrils from three post-translational modification sequences: isoaspartate-D7, the phosphorylation of S8, and an N-terminal truncation ΔE3. Additional comparisons are made with the mutants in the β-bend region (residues 21-23) corresponding to the familial Osaka E22Δ deletion and D23N Iowa mutation. We also include the aggregates induced by Zn2+ ions. The dynamics are probed at the F4 and G9 positions. The main motional model involves two free states undergoing diffusion and conformational exchanges with the bound state in which the diffusion is quenched because of transient interactions involving fibril core and other intrastrand contacts. The fraction of the bound state increases in a sigmoidal fashion with a decrease in temperature. There is clear variability in the dynamics: the phosphorylation of S8 variant is the most rigid at the G9 site in line with structural studies, the ΔE3 fibrils are more flexible at the G9 site in line with the morphological fragmentation pattern, the Zn-induced aggregates are the most mobile, and the two β-bend mutants have the strongest changes at the F4 site toward higher rigidity. Overall, the changes underlie the potential role of conformational ensembles in setting the stage for aggregation-prone states.

Quantifying Microsecond Exchange in Large Protein Complexes with Accelerated Relaxation Dispersion Experiments in the Solid State

Solid state NMR is a powerful method to obtain information on the structure and dynamics of protein complexes that, due to solubility and size limitations, cannot be achieved by other methods. Here, we present an approach that allows the quantification of microsecond conformational exchange in large protein complexes by using a paramagnetic agent to accelerate ¹⁵N R_1ρ relaxation dispersion measurements and overcome sensitivity limitations. The method is validated on crystalline GB1 and then applied to a >300 kDa precipitated complex of GB1 with full length human immunoglobulin G (IgG). The addition of a paramagnetic agent increased the signal to noise ratio per time unit by a factor of 5, which allowed full relaxation dispersion curves to be recorded on a sample containing less than 50 μg of labelled material in 5 and 10 days on 850 and 700 MHz spectrometers, respectively. We discover a similar exchange process across the β-sheet in GB1 in crystals and in complex with IgG. However, the slow motion observed for a number of residues in the α-helix of crystalline GB1 is not detected in the complex.

Reducing bias in the analysis of solution-state NMR data with dynamics detectors

Nuclear magnetic resonance (NMR) is sensitive to dynamics on a wide range of correlation times. Recently, we have shown that analysis of relaxation rates via fitting to a correlation function with a small number of exponential terms could yield a biased characterization of molecular motion in solid-state NMR due to limited sensitivity of experimental data to certain ranges of correlation times. We introduced an alternative approach based on "detectors" in solid-state NMR, for which detector responses characterize motion for a range of correlation times and reduce potential bias resulting from the use of simple models for the motional correlation functions. Here, we show that similar bias can occur in the analysis of solution-state NMR relaxation data. We have thus adapted the detector approach to solution-state NMR, specifically separating overall tumbling motion from internal motions and accounting for contributions of chemical exchange to transverse relaxation. We demonstrate that internal protein motions can be described with detectors when the overall motion and the internal motions are statistically independent. We illustrate the detector analysis on ubiquitin with typical relaxation data sets recorded at a single high magnetic field or at multiple high magnetic fields and compare with results of model-free analysis. We also compare our methodology to LeMaster's method of dynamics analysis.

Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation

Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross-correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer-range correlated motion. Similar trends on ns- and μs-timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.

Deuteron Solid-State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N-Terminal Domain of Amyloid-β Fibrils

We employed deuterium solid-state NMR techniques under static conditions to discern the details of the μs-ms timescale motions in the flexible N-terminal subdomain of Aβ1-40 amyloid fibrils, which spans residues 1-16. In particular, we utilized a rotating frame (R1ρ ) and the newly developed time domain quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation measurements at the selectively deuterated side chains of A2, H6, and G9. The two experiments are complementary in terms of probing somewhat different timescales of motions, governed by the tensor parameters and the sampling window of the magnetization decay curves. The results indicated two mobile "free" states of the N-terminal domain undergoing global diffusive motions, with isotropic diffusion coefficients of 0.7-1 ⋅ 108 and 0.3-3 ⋅ 106 ad2  s-1 . The free states are also involved in the conformational exchange with a single bound state, in which the diffusive motions are quenched, likely due to transient interactions with the structured hydrophobic core. The conformational exchange rate constants are 2-3 ⋅ 105  s-1 and 2-3 ⋅ 104  s-1 for the fast and slow diffusion free states, respectively.

Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. While static structures of capsids from several viruses are now accessible with near-atomic-level resolution, atomic-level understanding of functionally important motions in assembled capsids is lacking. We observed up to 64-fold signal enhancements by DNP, which permitted in-depth analysis of these assemblies. For the HIV-1 CA assemblies, a remarkably high spectral resolution in the 3D and 2D heteronuclear data sets permitted the assignment of a significant fraction of backbone and side-chain resonances. Using an integrated DNP MAS NMR and molecular dynamics (MD) simulation approach, the conformational space sampled by the assembled capsid at cryogenic temperatures was mapped. Qualitatively, a remarkable agreement was observed for the experimental ¹³C/¹⁵N chemical shift distributions and those calculated from substructures along the MD trajectory. Residues that are mobile at physiological temperatures are frozen out in multiple conformers at cryogenic conditions, resulting in broad experimental and calculated chemical shift distributions. Overall, our results suggest that DNP MAS NMR measurements in combination with MD simulations facilitate a thorough understanding of the dynamic signatures of viral capsids.

Solid-state NMR reveals a comprehensive view of the dynamics of the flexible, disordered N-terminal domain of amyloid-β fibrils

Amyloid fibril deposits observed in Alzheimer's disease comprise amyloid-β (Aβ) protein possessing a structured hydrophobic core and a disordered N-terminal domain (residues 1-16). The internal flexibility of the disordered domain is likely essential for Aβ aggregation. Here, we used ²H static solid-state NMR methods to probe the dynamics of selected side chains of the N-terminal domain of Aβ_1-40 fibrils. Line shape and relaxation data suggested a two-state model in which the domain's free state undergoes a diffusive motion that is quenched in the bound state, likely because of transient interactions with the structured C-terminal domain. At 37 °C, we observed freezing of the dynamics progressively along the Aβ sequence, with the fraction of the bound state increasing and the rate of diffusion decreasing. We also found that without solvation, the diffusive motion is quenched. The solvent acted as a plasticizer reminiscent of its role in the onset of global dynamics in globular proteins. As the temperature was lowered, the fraction of the bound state exhibited sigmoidal behavior. The midpoint of the freezing curve coincided with the bulk solvent freezing for the N-terminal residues and increased further along the sequence. Using ²H R _1ρ measurements, we determined the conformational exchange rate constant between the free and bound states under physiological conditions. Zinc-induced aggregation leads to the enhancement of the dynamics, manifested by the faster conformational exchange, faster diffusion, and lower freezing-curve midpoints.

Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR

Studying protein dynamics on microsecond-to-millisecond (μs-ms) time scales can provide important insight into protein function. In magic-angle-spinning (MAS) NMR, μs dynamics can be visualized by R 1 ρ rotating-frame relaxation dispersion experiments in different regimes of radio-frequency field strengths: at low RF field strength, isotropic-chemical-shift fluctuation leads to "Bloch-McConnell-type" relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R 1 ρ rate constants ("Near-Rotary-Resonance Relaxation Dispersion", NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical-shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.

Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques

NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (¹H and ¹⁵N) and different relaxation dispersion techniques (Bloch-McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains.

Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR

Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using ¹⁵ N rotating frame (R_1ρ ) relaxation dispersion solid-state nuclear magnetic resonance spectroscopy over a wide range of spin-lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two-state exchange process with a common exchange rate of 1000 s^-1 , corresponding to protein backbone motion on the timescale of 1 ms, and an excited-state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited-state populations (∼5-15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100-300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.

Refocusing CSA during magic angle spinning rotating-frame relaxation experiments

We examine coherent evolution of spin-locked magnetization during magic-angle spinning (MAS), in the context of relaxation experiments designed to probe chemical exchange (rotating-frame relaxation (R_1ρ)). Coherent evolution is expected in MAS based rotating-frame relaxation decay experiments if matching conditions are met (such as, ω₁ = nω_r) and if the chemical shielding anisotropy (CSA) is substantial. We show here using numerical simulations and experiments that even when such matching requirements are avoided (e.g., ω₁ < 0.5ω_r, ∼1.5ω_r, >2.5ω_r), coherent evolution of spin-locked magnetization with large CSA is still considerable. The coherent evolution has important consequences on the analysis of relaxation decay and the ability to extract accurate information of interest about dynamics. We present a pulse sequence that employs rotary echoes and refocuses CSA contributions, allowing for more sensitive measurement of rotating-frame relaxation with less interference from coherent evolution. In practice, the proposed pulse sequence, REfocused CSA Rotating-frame Relaxation (RECRR) is robust to carrier frequency offset, B₁-field inhomogeneity, and slight miscalibrations of the refocusing pulses.