Zero-quantum frequency-selective recoupling of homonuclear dipole-dipole interactions in solid state nuclear magnetic resonance

Great Offset Difference Internuclear Selective Transfer

Carbon-carbon dipolar recoupling sequences are frequently used building blocks in routine magic-angle spinning NMR experiments. While broadband homonuclear first-order dipolar recoupling sequences mainly excite intra-residue correlations, selective methods can detect inter-residue transfers and long-range correlations. Here, we present the great offset difference internuclear selective transfer (GODIST) pulse sequence optimized for selective carbonyl or aliphatic recoupling at fast magic-angle spinning, here, 55 kHz. We observe a 3- to 5-fold increase in intensities compared with broadband RFDR recoupling for perdeuterated microcrystalline SH3 and for the membrane protein influenza A M2 in lipid bilayers. In 3D (H)COCO(N)H and (H)CO(CO)NH spectra, inter-residue carbonyl-carbonyl correlations up to about 5 Å are observed in uniformly ¹³C-labeled proteins.

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.

Theory of frequency-selective homonuclear dipolar recoupling in solid-state NMR

In solid-state nuclear magnetic resonance, frequency-selective homonuclear dipolar recoupling is key to quantitative distance measurement or selective enhancement of correlations between atoms of interest in multiple-spin systems, which are not amenable to band-selective or broadband recoupling. Previous frequency-selective recoupling is mostly based on the so-called rotational resonance (R²) condition that restricts the application to spin pairs with resonance frequencies differing in integral multiples of the magic-angle spinning (MAS) frequency. Recently, we have proposed a series of frequency-selective homonuclear recoupling sequences called SPR (short for Selective Phase-optimized Recoupling), which have been successfully applied for selective ¹H-¹H or ¹³C-¹³C recoupling under from moderate (∼10 kHz) to ultra-fast (150 kHz) MAS frequencies. In this study, we fully analyze the average Hamiltonian theory of SPR sequences and reveal the origin of frequency selectivity in recoupling. The theoretical description, as well as numerical simulations and experiments, demonstrates that the frequency selectivity can be easily controlled by the flip angle (p) in the (p)_ϕk(p)_ϕk+π unit in the pSPR-N_n sequences. Small flip angles lead to frequency-selective recoupling, while large flip angles may lead to broadband recoupling in principle. The result shall shed new light on the design of homonuclear recoupling sequences with arbitrary frequency bandwidths.

Spectral editing of alanine, serine, and threonine in uniformly labeled proteins based on frequency-selective homonuclear recoupling in solid-state NMR

Spectral editing is crucial to simplify the crowded solid-state NMR spectra of proteins. New techniques are introduced to edit ¹³C-¹³C correlations of uniformly labeled proteins under moderate magic-angle spinning (MAS), based on our recent frequency-selective homonuclear recoupling sequences [Zhang et al., J. Phys. Chem. Lett. 2020, 11, 8077-8083]. The signals of alanine, serine, or threonine residues are selected out by selective ¹³Cα-¹³Cβ double-quantum filtering (DQF). The ¹³Cα-¹³Cβ correlations of alanine residues are selectively established with efficiency up to ~ 1.8 times that by dipolar-assisted rotational resonance (DARR). The techniques are shown in 2D/3D NCCX experiments and applied to the uniformly ¹³C, ¹⁵N labeled Aquaporin Z (AqpZ) membrane protein, demonstrating their potential to simplify spectral analyses in biological solid-state NMR.

Can proton-proton recoupling in fully protonated solids provide quantitative, selective and efficient polarization transfer?

Dipolar recoupling sequences have been used to probe spatial proximity of nuclear spins and were traditionally designed to probe rare spins such as ¹³C and/or ¹⁵N nuclei. The multi-spin dipolar-coupling network of the rare spins is weak due to smaller couplings and large chemical shift dispersion. Therefore, the recoupling approaches were tailored to design offset compensated or broadband sequences. In contrast, protons have a substantially stronger dipolar-coupling network and much narrower chemical shift range. Broadband recoupling sequences such as radio-frequency driven recoupling (RFDR), back-to-back (BABA), and lab frame proton-proton spin diffusion have been routinely used to characterize the structures of protein/macromolecules and small molecules. Recently selective ¹H-¹H recoupling sequences have been proposed that combine chemical shift offset of the resolved proton spectrum (at fast MAS) with first- and second-order dipolar recoupling Hamiltonians to obtain quantitative and qualitative proton distances, respectively. Herein, we evaluate the performances of broadband and selective proton recoupling sequences such as finite pulse RFDR (fp-RFDR), band-selective spectral spin diffusion (BASS-SD), second-order cross-polarization (SOCP), and selective recoupling of proton (SERP) in terms of the selectivity and efficiency of ¹H-¹H polarization transfers in a dense network of proton spins and explore the possibility of measuring ¹H-¹H distances. We use theoretical considerations, numerical simulations, and experiments to support the distinct advantages and disadvantages of each recoupling sequence. Experiments were performed on L-histidine.HCl.H₂O at a MAS frequency of 71.43 kHz. This study rationalizes the proper selection of ¹H-¹H recoupling sequences when working with fully protonated solids.

Quantitative 1H-1H Distances in Protonated Solids by Frequency-Selective Recoupling at Fast Magic Angle Spinning NMR

Nuclear magnetic resonance (NMR) spectroscopy of protons in protonated solids is challenging. Fast magic angle spinning (MAS) and homonuclear decoupling schemes, in conjunction, with high magnetic fields have improved the proton resolution. However, experiments to quantitatively measure ¹H-¹H distances still remain elusive due to the dense proton-proton dipolar coupling network. A novel MAS solid-state NMR pulse sequence is proposed to selectively recouple and measure interproton distances in protonated samples. The phase-modulated sequence combined with a judicious choice of transmitter frequency is used to measure quantitative ¹H-¹H distances on the order of 3 Å in l-histidine·HCl·H₂O, despite the presence of other strongly coupled protons. This method provides a major boost to NMR crystallography approaches for structural determination of pharmaceutical molecules by directly measuring ¹H-¹H distances. The band-selective nature of the sequence also enables observation of selective ¹H-¹H correlations (e.g., H^N-H^N/H^N-H^α/Η^Ν-Η^Methyl) in peptides and proteins, which should serve as useful restraints in structure determination.

Measurement of homonuclear magnetic dipole-dipole interactions in multiple 1/2-spin systems using constant-time DQ-DRENAR NMR

A new pulse sequence entitled DQ-DRENAR (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. As described in the present manuscript, the efficiency and performance of this sequence can be significantly improved, if the measurement is done in the constant-time mode. We describe both the theoretical analysis of this method and its experimental validation of a number of crystalline model compounds, considering both symmetry-based and back-to-back (BABA) DQ-coherence excitation schemes. Based on the combination of theoretical analysis and experimental results we discuss the effect of experimental parameters such as the chemical shift anisotropy (CSA), the spinning rate, and the radio frequency field inhomogeneity upon its performance. Our results indicate that constant-time (CT-) DRENAR is a method of high efficiency and accuracy for compounds with multiple homonuclear spin systems with particular promise for the analysis of stronger-coupled and short T2 spin systems.

DQ-DRENAR with back-to-back (BABA) excitation: Measuring homonuclear dipole-dipole interactions in multiple spin-1/2 systems

A new pulse sequence entitled DQ-DRENAR, (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. The double quantum coherences were created via a windowless symmetry-based pulse sequence (POST-C7). The present contribution evaluates the performance of the "Back-to-Back" excitation pulse scheme BABA-xy16 in such DRENAR experiments. Using SIMPSON simulations, special attention is given to finite pulse length effects, dipolar truncation, and chemical shift anisotropy interference. Experimental results on model compounds demonstrate good stability up to long mixing times (>10 ms) as well as high accuracy. As its dipolar coupling efficiency is relatively high (the dipolar coupling scaling factor is 4.24 times as high as that of POST-C7), DQ-DRENAR-BABA-xy16 is most appropriate for the measurement of relatively weak dipolar coupling strengths (<400 Hz). Different from POST-C7, for which the spinning rate is limited to 1/7 of the nutation frequency, DQ-DRENAR-BABA-xy16 experiments can take full advantage of ultrafast MAS experiments.

Membrane proteins structure and dynamics by nuclear magnetic resonance

Membrane proteins represent a challenging class of biological systems to study. They are extremely difficult to crystallize and in most cases they retain their structure and functions only in membrane environments. Therefore, commonly used diffraction methods fail to give detailed molecular structure and other approaches have to be utilized to obtain biologically relevant information. Nuclear magnetic resonance (NMR) spectroscopy, however, can provide powerful structural and dynamical constraints on these complicated systems. Solution- and solid-state NMR are powerful methods for investigating membrane proteins studies. In this work, we briefly review both solution and solid-state NMR techniques for membrane protein studies and illustrate the applications of these methods to elucidate proteins structure, conformation, topology, dynamics, and function. Recent advances in electronics, biological sample preparation, and spectral processing provided opportunities for complex biological systems, such as membrane proteins inside lipid vesicles, to be studied faster and with outstanding quality. New analysis methods therefore have emerged, that benefit from the combination of sample preparation and corresponding specific high-end NMR techniques, which give access to more structural and dynamic information.

Zero-quantum stochastic dipolar recoupling in solid state nuclear magnetic resonance

We present the theoretical description and experimental demonstration of a zero-quantum stochastic dipolar recoupling (ZQ-SDR) technique for solid state nuclear magnetic resonance (NMR) studies of (13)C-labeled molecules, including proteins, under magic-angle spinning (MAS). The ZQ-SDR technique combines zero-quantum recoupling pulse sequence blocks with randomly varying chemical shift precession periods to create randomly amplitude- and phase-modulated effective homonuclear magnetic dipole-dipole couplings. To a good approximation, couplings between different (13)C spin pairs become uncorrelated under ZQ-SDR, leading to spin dynamics (averaged over many repetitions of the ZQ-SDR sequence) that are fully described by an orientation-dependent N × N polarization transfer rate matrix for an N-spin system, with rates that are inversely proportional to the sixth power of internuclear distances. Suppression of polarization transfers due to non-commutivity of pairwise couplings (i.e., dipolar truncation) does not occur under ZQ-SDR, as we show both analytically and numerically. Experimental demonstrations are reported for uniformly (13)C-labeled L-valine powder (at 14.1 T and 28.00 kHz MAS), uniformly (13)C-labeled protein GB1 in microcrystalline form (at 17.6 T and 40.00 kHz MAS), and partially labeled (13)C-labeled protein GB1 (at 14.1 T and 40.00 kHz MAS). The experimental results verify that spin dynamics under ZQ-SDR are described accurately by rate matrices and suggest the utility of ZQ-SDR in structural studies of (13)C-labeled solids.

Restraints on backbone conformations in solid state NMR studies of uniformly labeled proteins from quantitative amide 15N-15N and carbonyl 13C-13C dipolar recoupling data

Recent structural studies of uniformly (15)N, (13)C-labeled proteins by solid state nuclear magnetic resonance (NMR) rely principally on two sources of structural restraints: (i) restraints on backbone conformation from isotropic (15)N and (13)C chemical shifts, based on empirical correlations between chemical shifts and backbone torsion angles; (ii) restraints on inter-residue proximities from qualitative measurements of internuclear dipole-dipole couplings, detected as the presence or absence of inter-residue crosspeaks in multidimensional spectra. We show that site-specific dipole-dipole couplings among (15)N-labeled backbone amide sites and among (13)C-labeled backbone carbonyl sites can be measured quantitatively in uniformly-labeled proteins, using dipolar recoupling techniques that we call (15)N-BARE and (13)C-BARE (BAckbone REcoupling), and that the resulting data represent a new source of restraints on backbone conformation. (15)N-BARE and (13)C-BARE data can be incorporated into structural modeling calculations as potential energy surfaces, which are derived from comparisons between experimental (15)N and (13)C signal decay curves, extracted from crosspeak intensities in series of two-dimensional spectra, with numerical simulations of the (15)N-BARE and (13)C-BARE measurements. We demonstrate this approach through experiments on microcrystalline, uniformly (15)N, (13)C-labeled protein GB1. Results for GB1 show that (15)N-BARE and (13)C-BARE restraints are complementary to restraints from chemical shifts and inter-residue crosspeaks, improving both the precision and the accuracy of calculated structures.

1H-13C/1H-15N heteronuclear dipolar recoupling by R-symmetry sequences under fast magic angle spinning for dynamics analysis of biological and organic solids

Fast magic angle spinning (MAS) NMR spectroscopy is becoming increasingly important in structural and dynamics studies of biological systems and inorganic materials. Superior spectral resolution due to the efficient averaging of the dipolar couplings can be attained at MAS frequencies of 40 kHz and higher with appropriate decoupling techniques, while proton detection gives rise to significant sensitivity gains, therefore making fast MAS conditions advantageous across the board compared with the conventional slow- and moderate-MAS approaches. At the same time, many of the dipolar recoupling approaches that currently constitute the basis for structural and dynamics studies of solid materials and that are designed for MAS frequencies of 20 kHz and below, fail above 30 kHz. In this report, we present an approach for (1)H-(13)C/(1)H-(15)N heteronuclear dipolar recoupling under fast MAS conditions using R-type symmetry sequences, which is suitable even for fully protonated systems. A series of rotor-synchronized R-type symmetry pulse schemes are explored for the determination of structure and dynamics in biological and organic systems. The investigations of the performance of the various RN(n)(v)-symmetry sequences at the MAS frequency of 40 kHz experimentally and by numerical simulations on [U-(13)C,(15)N]-alanine and [U-(13)C,(15)N]-N-acetyl-valine, revealed excellent performance for sequences with high symmetry number ratio (N/2n > 2.5). Further applications of this approach are presented for two proteins, sparsely (13)C/uniformly (15)N-enriched CAP-Gly domain of dynactin and U-(13)C,(15)N-Tyr enriched C-terminal domain of HIV-1 CA protein. Two-dimensional (2D) and 3D R16(3)(2)-based DIPSHIFT experiments carried out at the MAS frequency of 40 kHz, yielded site-specific (1)H-(13)C/(1)H-(15)N heteronuclear dipolar coupling constants for CAP-Gly and CTD CA, reporting on the dynamic behavior of these proteins on time scales of nano- to microseconds. The R-symmetry-based dipolar recoupling under fast MAS is expected to find numerous applications in studies of protein assemblies and organic solids by MAS NMR spectroscopy.

Broad-band homo-nuclear correlations assisted by 1H irradiation for bio-molecules in very high magnetic field at fast and ultra-fast MAS frequencies

We propose a new broadband second-order proton-assisted (13)C-(13)C correlation experiment, SHANGHAI. The (13)C-(13)C magnetization transfer is promoted by (1)H irradiation with interspersed four phases super-cycling. This through-space homo-nuclear sequence only irradiates on the proton channel during the mixing time. SHANGHAI benefits from a large number of modulation sidebands, hence leading to a large robustness with respect to chemical shift differences, which permits its use in a broad MAS frequency range. At ultra-fast MAS (ν(R) 60 kHz), SHANGHAI is only efficient when the amplitude of (1)H recoupling rf-field is close to half the spinning speed (ν(1) ≈ ν(R)/2). However, at moderate to fast MAS (ν(R)=20-35 kHz), SHANGHAI is efficient at any rf-power level larger than ν(1) ≈ 10 kHz, which simultaneously permits avoiding excessive heating of bio-molecules, and using large sample volumes. We show that SHANGHAI can be employed at the very high magnetic field of 23.5 T and then allows the observation of correlation between (13)C nuclei, even if their resonance frequencies differ by more than 38 kHz.

Solid-state NMR studies of amyloid fibril structure

Current interest in amyloid fibrils stems from their involvement in neurodegenerative and other diseases and from their role as an alternative structural state for many peptides and proteins. Solid-state nuclear magnetic resonance (NMR) methods have the unique capability of providing detailed structural constraints for amyloid fibrils, sufficient for the development of full molecular models. In this article, recent progress in the application of solid-state NMR to fibrils associated with Alzheimer's disease, prion fibrils, and related systems is reviewed, along with relevant developments in solid-state NMR techniques and technology.

Solid-state NMR techniques for the structural determination of amyloid fibrils

This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.

Dipolar-coupling-mediated total correlation spectroscopy in solid-state 13C NMR: selection of individual 13C-13C dipolar interactions

Herein is described a useful approach in solid-state NMR, for selecting homonuclear (13)C-(13)C spin pairs in a multiple-(13)C homonuclear dipolar coupled spin system. This method builds upon the zero-quantum (ZQ) dipolar recoupling method introduced by Levitt and coworkers (Marin-Montesinos et al., 2006) by extending the originally introduced one-dimensional (1D) experiment into a two-dimensional (2D) method with selective irradiation scheme, while moving the (13)C-(13)C mixing scheme from the transverse to the longitudinal mode, together with a dramatic improvement in the proton decoupling efficiency. Selective spin-pair recoupling experiments incorporating Gaussian and cosine-modulated Gaussian pulses for inverting specific spins were performed, demonstrating the ability to detect informative, simplified/individualized, long-range (13)C-(13)C homonuclear dipolar coupling interactions more accurately by removing less informative, stronger, short-range (13)C-(13)C interactions from 2D correlation spectra. The capability of this new approach was demonstrated experimentally on uniformly (13)C-labeled Glutamine and a tripeptide sample, GAL.