Asymmetric doublets in MAS NMR: coherent and incoherent mechanisms

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.

Microsecond Timescale Protein Dynamics: a Combined Solid-State NMR Approach

Conformational exchange in proteins is a major determinant in protein functionality. In particular, the μs-ms timescale is associated with enzymatic activity and interactions between biological molecules. We show here that a comprehensive data set of R1ρ relaxation dispersion profiles employing multiple effective fields and tilt angles can be easily obtained in perdeuterated, partly back-exchanged proteins at fast magic-angle spinning and further complemented with chemical-exchange saturation transfer NMR experiments. The approach exploits complementary sources of information and enables the extraction of multiple exchange parameters for μs-ms timescale conformational exchange, most notably including the sign of the chemical shift differences between the ground and excited states.

Microsecond Time Scale Proton Rotating-Frame Relaxation under Magic Angle Spinning

This paper deals with the theoretical foundation of proton magic angle spinning rotating-frame relaxation (R_1ρ) and establishes the range of validity and accuracy of the presented approach to describe low-amplitude microsecond time scale motion in the solid state. Beside heteronuclear dipolar and chemical shift anisotropy interactions, a major source of relaxation for protons is the homonuclear dipolar interaction. For this latter relaxation process, no general analytical equation has been published until now, which would describe the R_1ρ relaxation at any spinning speed, spin-lock field, or tilt angle. To validate the derived equations, we compared the analytical relaxation rates, obtained by solving the master equation within the framework of Redfield theory, with numerically simulated relaxation rates. We found that for small opening angles (∼10°), the relaxation rates obtained with stochastic Liouville simulations agree well with the analytical Redfield relaxation rates for a large range of motional correlation times. However, deviations around the rotary-resonance conditions highlight the fact that Redfield treatment of the solid-state relaxation rates can only provide qualitative insights into the microsecond time scale motion.

Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements

Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns-ms) time scales. The measurement of heteronuclear ((13)C, (15)N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns-ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.

Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules

Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.

Characterization of fibril dynamics on three timescales by solid-state NMR

A multi-timescale analysis of the backbone dynamics of HET-s (218-289) fibrils is described based on multiple site-specific R 1 and R 1ρ data sets and S (2) measurements via REDOR for most backbone (15)N and (13)Cα nuclei. (15)N and (13)Cα data are fitted with motions at three timescales. Slow motion is found, indicating a global fibril motion. We further investigate the effect of (13)C-(13)C transfer in measurement of (13)Cα R 1. Finally, we show that it is necessary to go beyond the Redfield approximation for slow motions in order to obtain accurate numerical values for R 1ρ.

Restoring Resolution in Biological Solid-State NMR under Conditions of Off-Magic-Angle Spinning

Spin-state-selective excitation (S3E) experiments allow the selection of individual transitions in a coupled two spin system. We show that in the solid state, the dipole-dipole interaction (DD) between (15)N and (1)H in a (1)H-(15)N bond and the chemical shift anisotropy (CSA) of (15)N in an amide moiety mutually cancel each other for a particular multiplet component at high field, when the sample is spun off the magic angle (Arctan [√2] = 54.74°). The accuracy of the adjustment of the spinning angle is crucial in conventional experiments. We demonstrate that for S3E experiments, the requirement to spin the sample exactly at the magic angle is not mandatory. Applications of solid state NMR in narrow bore magnets will be facilitated where the adjustment of the magic angle is often difficult. The method opens new perspectives for the development of schemes to determine distances and to quantify dynamics in the solid state.

Observing the overall rocking motion of a protein in a crystal

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Small-amplitude overall motion of molecules in crystals limits the achievable resolution in X-ray diffraction, yet little is known about its exact nature. Here, the authors obtain NMR, XRD and MD data from three different crystal forms of a protein (ubiquitin) to gain insight into amplitude and timescale of such motions.

Access to Cα backbone dynamics of biological solids by 13C T1 relaxation and molecular dynamics simulation

We introduce a labeling scheme for magic angle spinning (MAS) solid-state NMR that is based on deuteration in combination with dilution of the carbon spin system. The labeling strategy achieves spectral editing by simplification of the HαCα and aliphatic side chain spectral region. A reduction in both proton and carbon spin density in combination with fast spinning (≥50 kHz) is essential to retrieve artifact-free (13)C-R1 relaxation data for aliphatic carbons. We obtain good agreement between the NMR experimental data and order parameters extracted from a molecular dynamics (MD) trajectory, which indicates that carbon based relaxation parameters can yield complementary information on protein backbone as well as side chain dynamics.

Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes

Aggregates formed by amyloidogenic peptides and proteins and reconstituted membrane protein preparations differ significantly in terms of the spectral quality that they display in solid-state NMR experiments. Structural heterogeneity and dynamics can both in principle account for that observation. This perspectives article aims to point out challenges and limitations, but also potential opportunities in the investigation of these systems.

Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy

We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr-Purcell-Meiboom-Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.

Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: implications for structure and dynamics

High resolution proton spectra are obtained in MAS solid-state NMR in case samples are prepared using perdeuterated protein and D(2)O in the recrystallization buffer. Deuteration reduces drastically (1)H, (1)H dipolar interactions and allows to obtain amide proton line widths on the order of 20 Hz. Similarly, high-resolution proton spectra of aliphatic groups can be obtained if specifically labeled precursors for biosynthesis of methyl containing side chains are used, or if limited amounts of H(2)O in the bacterial growth medium is employed. This review summarizes recent spectroscopic developments to access structure and dynamics of biomacromolecules in the solid-state, and shows a number of applications to amyloid fibrils and membrane proteins.

Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR

Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.

Accurate determination of order parameters from 1H,15N dipolar couplings in MAS solid-state NMR experiments

A reliable site-specific estimate of the individual N-H bond lengths in the protein backbone is the fundamental basis of any relaxation experiment in solution and in the solid-state NMR. The N-H bond length can in principle be influenced by hydrogen bonding, which would result in an increased N-H distance. At the same time, dynamics in the backbone induces a reduction of the experimental dipolar coupling due to motional averaging. We present a 3D dipolar recoupling experiment in which the (1)H,(15)N dipolar coupling is reintroduced in the indirect dimension using phase-inverted CP to eliminate effects from rf inhomogeneity. We find no variation of the N-H dipolar coupling as a function of hydrogen bonding. Instead, variations in the (1)H,(15)N dipolar coupling seem to be due to dynamics of the protein backbone. This is supported by the observed correlation between the H(N)-N dipolar coupling and the amide proton chemical shift. The experiment is demonstrated for a perdeuterated sample of the alpha-spectrin SH3 domain. Perdeuteration is a prerequisite to achieve high accuracy. The average error in the analysis of the H-N dipolar couplings is on the order of +/-370 Hz (+/-0.012 A) and can be as small as 150 Hz, corresponding to a variation of the bond length of +/-0.005 A.

Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy

We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include (15)N T (1) relaxation times measured at two different magnetic fields as well as (1)H-(15)N dipole, (15)N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T (2) in the solid-state. In addition, global order parameters are included from a (1)H,(15)N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore-Lipari-Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10 degrees for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken alpha-spectrin SH3 domain.

Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent

In solution, the correlation time of the overall protein tumbling, tau(R), plays a role of a natural dynamics cutoff-internal motions with correlation times on the order of tau ( R ) or longer cannot be reliably identified on the basis of spin relaxation data. It has been proposed some time ago that the 'observation window' of solution experiments can be expanded by changing the viscosity of solvent to raise the value of tau(R). To further explore this concept, we prepared a series of samples of alpha-spectrin SH3 domain in solvent with increasing concentration of glycerol. In addition to the conventional (15)N labeling, the protein was labeled in the Val, Leu methyl positions ((13)CHD(2) on a deuterated background). The collected relaxation data were used in asymmetric fashion: backbone (15)N relaxation rates were used to determine tau(R) across the series of samples, while methyl (13)C data were used to probe local dynamics (side-chain motions). In interpreting the results, it has been initially suggested that addition of glycerol leads only to increases in tau(R), whereas local motional parameters remain unchanged. Thus the data from multiple samples can be analyzed jointly, with tau(R) playing the role of experimentally controlled variable. Based on this concept, the extended model-free model was constructed with the intent to capture the effect of ns time-scale rotameric jumps in valine and leucine side chains. Using this model, we made a positive identification of nanosecond dynamics in Val-23 where ns motions were already observed earlier. In several other cases, however, only tentative identification was possible. The lack of definitive results was due to the approximate character of the model-contrary to what has been assumed, addition of glycerol led to a gradual 'stiffening' of the protein. This and other observations also shed light on the interaction of the protein with glycerol, which is one of the naturally occurring osmoprotectants. In particular, it has been found that the overall protein tumbling is controlled by the bulk solvent, and not by a thin solvation layer which contains a higher proportion of water.

Sensitivity enhancement in static solid-state NMR experiments via single- and multiple-quantum dipolar coherences

We present a new method for enhancing the sensitivity in static solid-state NMR experiments for a gain in signal-to-noise ratio of up to 40%. This sensitivity enhancement is different from the corresponding solution NMR sensitivity enhancement schemes and is achieved by combining single- and multiple-quantum dipolar coherences. While this new approach is demonstrated for the polarization inversion spin exchange at magic angle (PISEMA) experiment, it can be generalized to the other separated local field experiments for solid-state NMR spectroscopy. This method will have a direct impact on solid-state NMR spectroscopy of liquid crystals as well as of membrane proteins aligned in lipid membranes.