Solid-state NMR measurement of Ψ in peptides: a NCCN 2Q-heteronuclear local field experiment

Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures

While low-temperature Nuclear Magnetic Resonance (NMR) holds great promise for the analysis of unstable samples and for sensitizing NMR detection, spectral broadening in frozen protein samples is a common experimental challenge. One hypothesis explaining the additional linewidth is that a variety of conformations are in rapid equilibrium at room temperature and become frozen, creating an inhomogeneous distribution at cryogenic temperatures. Here, we investigate conformational heterogeneity by measuring the backbone torsion angle (Ψ) in Escherichia coli Dihydrofolate Reductase (DHFR) at 105 K. Motivated by the particularly broad N chemical shift distribution in this and other examples, we modified an established NCCN Ψ experiment to correlate the chemical shift of Ni+1 to Ψi. With selective 15N and 13C enrichment of Ile, only the unique I60-I61 pair was expected to be detected in 13C'-15N correlation spectrum. For this unique amide, we detected three different conformation basins based on dispersed chemical shifts. Backbone torsion angles Ψ were determined for each basin: 114 ± 7° for the major peak and 150 ± 8° and 164 ± 16° for the minor peaks as contrasted with 118° for the X-ray crystal structure (and 118° to 130° for various previously reported structures). These studies support the hypothesis that inhomogeneous distributions of protein backbone torsion angles contribute to the lineshape broadening in low-temperature NMR spectra.

Solid-State NMR Double-Quantum Dipolar Recoupling Enhanced by Additional Phase Modulation

Additional phase modulation (APM) is proposed to generally enhance the theoretical efficiency of homonuclear double-quantum (DQ) recoupling in solid-state NMR. APM applies an additional phase list to DQ recoupling in steps of an entire block. The sine-based phase list can enhance the theoretical efficiency by 15-30 %, from 0.52 to 0.68 (non-γ-encoded recoupling) or from 0.73 to 0.84 (γ-encoded recoupling), with doubled recoupling time. The genetic-algorithm (GA) optimized APM can adiabatically enhance the efficiency to ∼1.0 at longer times. The concept of APM has been tested on SPR-51 , BaBa, and SPR-31 , which represent γ-encoded recoupling, non-γ-encoded recoupling, and another kind beyond the former two, respectively. Simulations reveal that enhancements from APM are due to the activation of more crystallites in the powder. Experiments on 2,3-13 C labeled alanine are used to validate the APM recoupling. This new concept shall shed light on developing more efficient homonuclear recoupling methods.

The Structure of Boron Monoxide

Boron monoxide (BO), prepared by the thermal condensation of tetrahydroxydiboron, was first reported in 1955; however, its structure could not be determined. With the recent attention on boron-based two-dimensional materials, such as borophene and hexagonal boron nitride, there is renewed interest in BO. A large number of stable BO structures have been computationally identified, but none are supported by experiments. The consensus is that the material likely forms a boroxine-based two-dimensional material. Herein, we apply advanced 11B NMR experiments to determine the relative orientations of B(B)O2 centers in BO. We find that the material is composed of D2h-symmetric O2B-BO2 units that organize to form larger B4O2 rings. Further, powder diffraction experiments additionally reveal that these units organize to form two-dimensional layers with a random stacking pattern. This observation is in agreement with earlier density functional theory (DFT) studies that showed B4O2-based structures to be the most stable.

Discovering the Solid-State Secrets of Lorlatinib by NMR Crystallography: To Hydrogen Bond or not to Hydrogen Bond

Lorlatinib is an active pharmaceutical ingredient (API) used in the treatment of lung cancer. Here, an NMR crystallography analysis is presented whereby the single-crystal X-ray diffraction structure (CSD: 2205098) determination is complemented by multinuclear (1H, 13C, 14/15N, 19F) magic-angle spinning (MAS) solid-state NMR and gauge-including projector augmented wave (GIPAW) calculation of NMR chemical shifts. Lorlatinib crystallises in the P21 space group, with two distinct molecules in the asymmetric unit cell, Z' = 2. Three of the four NH2 hydrogen atoms form intermolecular hydrogen bonds, N30-H…N15 between the two distinct molecules and N30-H…O2 between two equivalent molecules. This is reflected in one of the NH21H chemical shifts being significantly lower, 4.0 ppm compared to 7.0 ppm. Two-dimensional 1H-13C, 14N-1H and 1H (double-quantum, DQ)-1H (single-quantum, SQ) MAS NMR spectra are presented. The 1H resonances are assigned and specific HH proximities corresponding to the observed DQ peaks are identified. The resolution enhancement at a 1H Larmor frequency of 1 GHz as compared to 500 or 600 MHz is demonstrated.

Comparison of methods for 14N-1H recoupling in 14N-1H HMQC MAS NMR

¹H-detected ¹⁴N heteronuclear multiple-quantum coherence (HMQC) magic-angle-spinning (MAS) NMR experiments performed at fast magic-angle spinning (≥50 kHz) are finding increasing application, e.g., to pharmaceuticals. Of importance to the efficacy of these techniques is the recoupling technique applied to reintroduce the ¹H-¹⁴N dipolar coupling. In this paper, we compare, by experiment and 2-spin density matrix simulations, two classes of recoupling scheme: first, those based on n = 2 rotary resonance, namely R³ and spin-polarisation inversion SPI-R³, and the symmetry based SR4₁² method and, second, the TRAPDOR method. Both classes require optimisation depending on the magnitude of the quadrupolar interaction, and thus there is a compromise choice for samples with more than one nitrogen site, as is the case for the studied dipeptide β-AspAla that contains two nitrogen sites with a small and large quadrupolar coupling constant. Considering this, we observe better sensitivity for the TRAPDOR method, though noting the marked sensitivity of TRAPDOR to the ¹⁴N transmitter offset, with both SPI-R³ and SR4₁² giving similar recoupling performance.

Asynchronising five-fold symmetry sequence for better homonuclear polarisation transfer in magic-angle-spinning solid-state NMR

Recoupling, decoupling, and multidimensional correlation experiments in magic-angle-spinning (MAS) solid-state NMR can be designed by exploiting the symmetry of internal spin interactions. One such scheme, namely, C5₂¹, and its supercycled version SPC5₂¹, notated as a five-fold symmetry sequence, is widely used for double-quantum dipole-dipole recoupling. Such schemes are generally rotor synchronised by design. We demonstrate an asynchronous implementation of the SPC5₂¹ sequence leading to higher double-quantum homonuclear polarisation transfer efficiency compared to the normal synchronous implementation. Rotor-synchronisation is broken in two different ways: lengthening the duration of one of the pulses, denoted as pulse-width variation (PWV), and mismatching the MAS frequency denoted as MAS variation (MASV). The application of this asynchronous sequence is shown on three different samples, namely, U-¹³C-alanine and 1,4-¹³C-labelled ammonium phthalate which include ¹³C_α-¹³C_β, ¹³C_α-¹³C_o, and ¹³C_o-¹³C_o spin systems, and adenosine 5'- triphosphate disodium salt trihydrate (ATP⋅3H₂O). We show that the asynchronous version performs better for spin pairs with small dipole-dipole couplings and large chemical-shift anisotropies, for example, ¹³C_o-¹³C_o. Simulations and experiments are shown to corroborate the results.

Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures

While low temperature NMR holds great promise for the analysis of unstable samples and for sensitizing NMR detection, spectral broadening in frozen protein samples is a common experimental challenge. One hypothesis explaining the additional linewidth is that a variety of conformations are in rapid equilibrium at room temperature and become frozen, creating an inhomogeneous distribution at cryogenic temperatures. Here we investigate conformational heterogeneity by measuring the backbone torsion angle (Ψ) in E. coli DHFR at 105K. Motivated by the particularly broad N chemical shift distribution in this and other examples, we modified an established NCCN Ψ experiment to correlate the chemical shift of N i+1 to Ψ i . With selective 15 N and 13 C enrichment of Ile, only the unique I60-I61 pair was expected to be detected in 13 C'- 15 N correlation spectrum. For this unique amide we detected three different conformation basins based on dispersed chemical shifts. Backbone torsion angles Ψ were determined for each basin 114 ± 7 for the major peak, and 150 ± 8 and 164 ± 16° for the minor peak as contrasted with 118 for the X-ray crystal structure (and 118-130 for various previously reported structures). These studies support the hypothesis that inhomogeneous distributions of protein backbone torsion angles contribute to the lineshape broadening in low temperature NMR spectra.

Significance Statement

Understanding protein conformational flexibility is essential for insights into the molecular basis of protein function and the thermodynamics of proteins. Here we investigate the ensemble of protein backbone conformations in a frozen protein freezing, which is likely a close representation for the ensemble in rapid equilibrium at room temperature. Various conformers are spectrally resolved due to the exquisite sensitivity of NMR shifts to local conformations, and NMR methods allow us to directly probe the torsion angles corresponding to each band of chemical shifts.

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.

Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy

In structural studies of immobilized, aggregated and self-assembled biomolecules, solid-state NMR (ssNMR) spectroscopy can provide valuable high-resolution structural information. Among the structural restraints provided by magic angle spinning (MAS) ssNMR the canonical focus is on inter-atomic distance measurements. In the current review, we examine the utility of ssNMR measurements of angular constraints, as a complement to distance-based structure determination. The focus is on direct measurements of angular restraints via the judicious recoupling of multiple anisotropic ssNMR parameters, such as dipolar couplings and chemical shift anisotropies. Recent applications are highlighted, with a focus on studies of nanocrystalline polypeptides, aggregated peptides and proteins, receptor-substrate interactions, and small molecule interactions with amyloid protein fibrils. The review also examines considerations of when and where ssNMR torsion angle experiments are (most) effective, and discusses challenges and opportunities for future applications.

Drug-Polymer Interactions in Acetaminophen/Hydroxypropylmethylcellulose Acetyl Succinate Amorphous Solid Dispersions Revealed by Multidimensional Multinuclear Solid-State NMR Spectroscopy

The bioavailability of insoluble crystalline active pharmaceutical ingredients (APIs) can be enhanced by formulation as amorphous solid dispersions (ASDs). One of the key factors of ASD stabilization is the formation of drug-polymer interactions at the molecular level. Here, we used a range of multidimensional and multinuclear nuclear magnetic resonance (NMR) experiments to identify these interactions in amorphous acetaminophen (paracetamol)/hydroxypropylmethylcellulose acetyl succinate (HPMC-AS) ASDs at various drug loadings. At low drug loading (<20 wt %), we showed that 1H-13C through-space heteronuclear correlation experiments identify proximity between aromatic protons in acetaminophen with cellulose backbone protons in HPMC-AS. We also show that 14N-1H heteronuclear multiple quantum coherence (HMQC) experiments are a powerful approach in probing spatial interactions in amorphous materials and establish the presence of hydrogen bonds (H-bond) between the amide nitrogen of acetaminophen with the cellulose ring methyl protons in these ASDs. In contrast, at higher drug loading (40 wt %), no acetaminophen/HPMC-AS spatial proximity was identified and domains of recrystallization of amorphous acetaminophen into its crystalline form I, the most thermodynamically stable polymorph, and form II are identified. These results provide atomic scale understanding of the interactions in the acetaminophen/HPMC-AS ASD occurring via H-bond interactions.

35 Cl-1 H Heteronuclear correlation magic-angle spinning nuclear magnetic resonance experiments for probing pharmaceutical salts

Heteronuclear multiple-quantum coherence (HMQC) pulse sequences for establishing heteronuclear correlation in solid-state nuclear magnetic resonance (NMR) between ³⁵ Cl and ¹ H nuclei in chloride salts under fast (60 kHz) magic-angle spinning (MAS) and at high magnetic field (a ¹ H Larmor frequency of 850 MHz) are investigated. Specifically, recoupling of the ³⁵ Cl-¹ H dipolar interaction using rotary resonance recoupling with phase inversion every rotor period or the symmetry-based SR4² ₁ pulse sequences are compared. In our implementation of the population transfer (PT) dipolar (D) HMQC experiment, the satellite transitions of the ³⁵ Cl nuclei are saturated with an off-resonance WURST sweep, at a low nutation frequency, over the second spinning sideband, whereby the WURST pulse must be of the same duration as the recoupling time. Numerical simulations of the ³⁵ Cl-¹ H MAS D-HMQC experiment performed separately for each crystallite orientation in a powder provide insight into the orientation dependence of changes in the second-order quadrupolar-broadened ³⁵ Cl MAS NMR lineshape under the application of dipolar recoupling. Two-dimensional ³⁵ Cl-¹ H PT-D-HMQC MAS NMR spectra are presented for the amino acids glycine·HCl and l-tyrosine·HCl and the pharmaceuticals cimetidine·HCl, amitriptyline·HCl and lidocaine·HCl·H₂ O. Experimentally observed ³⁵ Cl lineshapes are compared with those simulated for ³⁵ Cl chemical shift and quadrupolar parameters as calculated using the gauge-including projector-augmented wave (GIPAW) method: the calculated quadrupolar product (P_Q ) values exceed those measured experimentally by a factor of between 1.3 and 1.9.

Through-space 11 B-27 Al correlation: Influence of the recoupling channel

Through-space heteronuclear correlation (D-HETCOR) experiments based on heteronuclear multiple-quantum correlation (D-HMQC) and refocused insensitive nuclei enhanced by polarization transfer (D-RINEPT) sequences have been proven to be useful approaches for the detection of the spatial proximity between half-integer quadrupolar nuclei in solids under magic-angle spinning (MAS) conditions. The corresponding pulse sequences employ coherence transfers mediated by heteronuclear dipolar interactions, which are reintroduced under MAS by radiofrequency irradiation of only one of the two correlated nuclei. We investigate herein using numerical simulations of spin dynamics and solid-state NMR experiments on magnesium aluminoborate glass how the choice of the channel to which the heteronuclear dipolar recoupling is applied affects the transfer efficiency of D-HMQC and D-RINEPT sequences between ¹¹ B and ²⁷ Al nuclei. Experimental results show that maximum transfer efficiency is achieved when the recoupling scheme is applied to the channel, for which the spin magnetization is parallel to the B₀ axis in average.

14N–1H HMQC solid-state NMR as a powerful tool to study amorphous formulations – an exemplary study of paclitaxel loaded polymer micelles

¹⁴N–¹H HMQC experiments are powerful experiments to characterize amorphous drug–polymer formulations of paclitaxel yielding well-separated signals in the ¹⁴N dimension as well as information on the symmetry of ¹⁴N and ¹⁴N–¹H interactions.

Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR

Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.

Efficient dipolar double quantum filtering under magic angle spinning without a (1)H decoupling field

We present a systematic study of dipolar double quantum (DQ) filtering in (13)C-labeled organic solids over a range of magic-angle spinning rates, using the SPC-n recoupling sequence element with a range of n symmetry values from 3 to 11. We find that efficient recoupling can be achieved for values n⩾7, provided that the (13)C nutation frequency is on the order of 100kHz or greater. The decoupling-field dependence was investigated and explicit heteronuclear decoupling interference conditions identified. The major determinant of DQ filtering efficiency is the decoupling interference between (13)C and (1)H fields. For (13)C nutation frequencies greater than 75kHz, optimal performance is observed without an applied (1)H field. At spinning rates exceeding 20kHz, symmetry conditions as low as n=3 were found to perform adequately.

Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies

The HIV-1 capsid protein (CA) forms the capsid shell that encloses RNA within a mature HIV-1 virion. Previous studies by electron microscopy have shown that the capsid shell is primarily a triangular lattice of CA hexamers, with variable curvature that destroys the ideal symmetry of a planar lattice. The mature CA lattice depends on CA dimerization, which occurs through interactions between helix 9 segments of the C-terminal domain (CTD) of CA. Several high-resolution structures of the CTD-CTD dimerization interface have been reported, based on X-ray crystallography and multidimensional solution nuclear magnetic resonance (NMR), with significant differences in amino acid side chain conformations and helix 9-helix 9 orientations. In a structural model for tubular CA assemblies based on cryogenic electron microscopy (cryoEM) [Zhao et al. Nature, 2013, 497, 643-646], the dimerization interface is substantially disordered. The dimerization interface structure in noncrystalline CA assemblies and the extent to which this interface is structurally ordered within a curved lattice have therefore been unclear. Here we describe solid state NMR measurements on the dimerization interface in tubular CA assemblies, which contain the curved triangular lattice of a mature virion, including quantitative measurements of intermolecular and intramolecular distances using dipolar recoupling techniques, solid state NMR chemical shifts, and long-range side chain-side chain contacts. When combined with restraints on the distance and orientation between helix 9 segments from the cryoEM study, the solid state NMR data lead to a unique high-resolution structure for the dimerization interface in the noncrystalline lattice of CA tubes. These results demonstrate that CA lattice curvature is not dependent on disorder or variability in the dimerization interface. This work also demonstrates the feasibility of local structure determination within large noncrystalline assemblies formed by high-molecular-weight proteins, using modern solid state NMR methods.

Huntingtin exon 1 fibrils feature an interdigitated β-hairpin-based polyglutamine core

Polyglutamine expansion within the exon1 of huntingtin leads to protein misfolding, aggregation, and cytotoxicity in Huntington's disease. This incurable neurodegenerative disease is the most prevalent member of a family of CAG repeat expansion disorders. Although mature exon1 fibrils are viable candidates for the toxic species, their molecular structure and how they form have remained poorly understood. Using advanced magic angle spinning solid-state NMR, we directly probe the structure of the rigid core that is at the heart of huntingtin exon1 fibrils and other polyglutamine aggregates, via measurements of long-range intramolecular and intermolecular contacts, backbone and side-chain torsion angles, relaxation measurements, and calculations of chemical shifts. These experiments reveal the presence of β-hairpin-containing β-sheets that are connected through interdigitating extended side chains. Despite dramatic differences in aggregation behavior, huntingtin exon1 fibrils and other polyglutamine-based aggregates contain identical β-strand-based cores. Prior structural models, derived from X-ray fiber diffraction and computational analyses, are shown to be inconsistent with the solid-state NMR results. Internally, the polyglutamine amyloid fibrils are coassembled from differently structured monomers, which we describe as a type of "intrinsic" polymorphism. A stochastic polyglutamine-specific aggregation mechanism is introduced to explain this phenomenon. We show that the aggregation of mutant huntingtin exon1 proceeds via an intramolecular collapse of the expanded polyglutamine domain and discuss the implications of this observation for our understanding of its misfolding and aggregation mechanisms.

An NMR crystallography study of the hemihydrate of 2', 3'-O-isopropylidineguanosine

An NMR crystallography study of the hemihydrate of 2', 3'-O-isopropylidineguanosine (Gace) is presented, together with powder X-ray diffraction and thermogravimetric analysis. (1)H double-quantum and (14)N-(1)H HMQC spectra recorded at 850MHz and 75kHz MAS (using a JEOL 1mm probe) are presented together with a (1)H-(13)C refocused INEPT spectrum recorded at 500MHz and 12.5kHz MAS using eDUMBO-122(1)H homonuclear decoupling. NMR chemical shieldings are calculated using the GIPAW (gauge-including projector augmented wave) method; good two-dimensional agreement between calculation and experiment is observed for (13)C and (1)H chemical shifts for directly bonded CH and CH3 peaks. There are two Gace molecules in the asymmetric unit cell: differences in specific (1)H chemical shifts are rationalised in terms of the strength of CH-π and intermolecular hydrogen bonding interactions.

Recent advances in magic angle spinning solid state NMR of membrane proteins

Membrane proteins mediate many critical functions in cells. Determining their three-dimensional structures in the native lipid environment has been one of the main objectives in structural biology. There are two major NMR methodologies that allow this objective to be accomplished. Oriented sample NMR, which can be applied to membrane proteins that are uniformly aligned in the magnetic field, has been successful in determining the backbone structures of a handful of membrane proteins. Owing to methodological and technological developments, Magic Angle Spinning (MAS) solid-state NMR (ssNMR) spectroscopy has emerged as another major technique for the complete characterization of the structure and dynamics of membrane proteins. First developed on peptides and small microcrystalline proteins, MAS ssNMR has recently been successfully applied to large membrane proteins. In this review we describe recent progress in MAS ssNMR methodologies, which are now available for studies of membrane protein structure determination, and outline a few examples, which highlight the broad capability of ssNMR spectroscopy.

A 3D experiment that provides isotropic homonuclear correlations of half-integer quadrupolar nuclei

Two 3D experiments, capable of producing enhanced resolution two-spin double-quantum (DQ) homonuclear correlations for half-integer quadrupolar nuclei, are described. The first uses a split-t1 MQMAS sequence followed by a sandwiched oR(3) symmetry-based dipolar recoupling sequence to directly excite DQ coherences. In this case an isotropic single-quantum (SQ) coherence starts the homonuclear DQ excitation. In the second experiment a single strong pulse is used to create triple quantum (TQ) coherence followed by a further single pulse conversion to zero-order before a non-sandwiched oR(3) DQ sequence. The first experiment is demonstrated using (87)Rb in RbNO3, with three Rb sites in a ∼5ppm range, and the second to (11)B in caesium triborate, CsB3O5, with two three-coordinated sites separated by ∼2ppm and one four-coordinated boron site. In both cases, all sites are clearly resolved and their connections observed. The second experiment has higher sensitivity and a good signal to noise is obtained in a reasonable time despite the long T1 relaxation time of (11)B in this material.

Constant time tensor correlation experiments by non-gamma-encoded recoupling pulse sequences

Constant-time tensor correlation under magic-angle spinning conditions is an important technique in solid-state nuclear magnetic resonance spectroscopy for the measurements of backbone or side-chain torsion angles of polypeptides and proteins. We introduce a general method for the design of constant-time tensor correlation experiments under magic-angle spinning. Our method requires that the amplitude of the average Hamiltonian must depend on all the three Euler angles bringing the principal axis system to the rotor-fixed frame, which is commonly referred to as non-gamma encoding. We abbreviate this novel approach as COrrelation of Non-Gamma-Encoded Experiment (CONGEE), which exploits the orientation-dependence of non-gamma-encoded sequences with respect to the magic-angle rotation axis. By manipulating the relative orientation of the average Hamiltonians created by two non-gamma-encoded sequences, one can obtain a modulation of the detected signal, from which the structural information can be extracted when the tensor orientations relative to the molecular frame are known. CONGEE has a prominent feature that the number of rf pulses and the total pulse sequence duration can be maintained to be constant so that for torsion angle determination the effects of systematic errors owing to the experimental imperfections and/or T(2) effects could be minimized. As a proof of concept, we illustrate the utility of CONGEE in the correlation between the C' chemical shift tensor and the C(α)-H(α) dipolar tensor for the backbone psi angle determination. In addition to a detailed theoretical analysis, numerical simulations and experiments measured for [U-(13)C, (15)N]-L-alanine and N-acetyl-[U-(13)C, (15)N]-D,L-valine are used to validate our approach at a spinning frequency of 20 kHz.

14N–1H Heteronuclear Multiple-Quantum Correlation Magic-Angle Spinning NMR Spectroscopy of Organic Solids

14N–1H heteronuclear multiple-quantum correlation (HMQC) solid-state magic-angle spinning (MAS) NMR spectra recorded at a 1H Larmor frequency of 850 MHz are presented for the dipeptide β-AspAla. A modified version of the pulse sequence presented by Gan et al. (Chem. Phys. Lett. 435 (2007) 163) that utilises rotary resonance recoupling (R3) at the n = 2 condition (ν 1 = 2ν R ) is employed. Spectra recorded with a short recoupling period (under 200 μs) show two correlation peaks corresponding to the NH and NH3 moieties in the dipeptide. The quadrupolar product, P Q = C Q √ [1 + (η Q 2/3)], is determined experimentally as 3.1 MHz (NH) and 1.0 MHz (NH3) by a comparison of the 14N and 15N isotropic chemical shifts which differ due to the isotropic second-order quadrupolar shift for the spin I = 1 14N nucleus. It is shown that the peak sensitivities increase markedly upon increasing the MAS frequency from 30 to 45 to 60 kHz due to a combination of the reduced residual dipolar broadening of the 1H resonances and a lengthening of the coherence lifetimes under R 3 recoupling. Increasing the recoupling period leads to the observation of additional peaks corresponding to longer range intra- and intermolecular NH proximities. Reasonable agreement is evident upon comparing the experimental build-up of correlation peak intensity to that observed for eight-spin density-matrix simulations.

Intramolecular 1H-13C distance measurement in uniformly 13C, 15N labeled peptides by solid-state NMR

A (1)H-(13)C frequency-selective REDOR (FS-REDOR) experiment is developed for measuring intramolecular (1)H-(13)C distances in uniformly (13)C, (15)N-labeled molecules. Theory and simulations show that the experiment removes the interfering homonuclear (1)H-(1)H, (13)C-(13)C and heteronuclear (1)H-(15)N, (13)C-(15)N dipolar interactions while retaining the desired heteronuclear (1)H-(13)C dipolar interaction. Our results indicate that this technique, combined with the numerical fitting, can be used to measure a (1)H-(13)C distance up to 5Å. We also demonstrate that the measured intramolecular (1)H-(13)C distances are useful to determine dihedral angles in proteins.

Membrane protein structure and dynamics from NMR spectroscopy

We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca(2+) pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.

Identifying guanosine self assembly at natural isotopic abundance by high-resolution 1H and 13C solid-state NMR spectroscopy

By means of the (1)H chemical shifts and the proton-proton proximities as identified in (1)H double-quantum (DQ) combined rotation and multiple-pulse spectroscopy (CRAMPS) solid-state NMR correlation spectra, ribbon-like and quartet-like self-assembly can be identified for guanosine derivatives without isotopic labeling for which it was not possible to obtain single crystals suitable for diffraction. Specifically, characteristic spectral fingerprints are observed for dG(C10)(2) and dG(C3)(2) derivatives, for which quartet-like and ribbon-like self-assembly has been unambiguously identified by (15)N refocused INADEQUATE spectra in a previous study of (15)N-labeled derivatives (Pham, T. N.; et al. J. Am. Chem. Soc.2005, 127, 16018). The NH (1)H chemical shift is observed to be higher (13-15 ppm) for ribbon-like self-assembly as compared to 10-11 ppm for a quartet-like arrangement, corresponding to a change from NH···N to NH···O intermolecular hydrogen bonding. The order of the two NH(2)(1)H chemical shifts is also inverted, with the NH(2) proton closest in space to the NH proton having a higher or lower (1)H chemical shift than that of the other NH(2) proton for ribbon-like as opposed to quartet-like self-assembly. For the dG(C3)(2) derivative for which a single-crystal diffraction structure is available, the distinct resonances and DQ peaks are assigned by means of gauge-including projector-augmented wave (GIPAW) chemical shift calculations. In addition, (14)N-(1)H correlation spectra obtained at 850 MHz under fast (60 kHz) magic-angle spinning (MAS) confirm the assignment of the NH and NH(2) chemical shifts for the dG(C3)(2) derivative and allow longer range through-space N···H proximities to be identified, notably to the N7 nitrogens on the opposite hydrogen-bonding face.

Site-specific ϕ- and ψ-torsion angle determination in a uniformly/extensively 13C- and 15N-labeled peptide

A solid-state rotational-echo double resonance (REDOR) NMR method was introduced to identify the ϕ- and ψ-torsion angle from a (1)H-(15)N or (1)H-(13)C' spin system of alanine-like residues in a selectively, uniformly, or extensively (15)N-/(13)C-labeled peptide. When a C(α)(i) or a (15)N peak is site-specifically obtainable in the NMR spectrum of a uniformly (15)N/(13)C-labeled sample system, the ψ- or ϕ-torsion angle specified by the conformational structure of peptide geometry involving (15)N(i)-(1)H(α)i-(15)N(i+1) or (13)C'(i-1)-(1)H(N)i-(13)C'(i) spin system can be identified based on (13)C(α)- or (15)N-detected (1)H(α)-(15)N or (1)H(N)-(13)C REDOR experiment. This method will conveniently be utilized to identify major secondary motifs, such as α-helix, β-sheet, and β-turn, from a uniformly (15)N-/(13)C-labled peptide sample system. When tested on a (13)C-/(15)N-labeled model system of a three amino acid peptide Gly-[U-(13)C, (15)N]Ala-[U-(13)C, (15)N]Leu, the ψ-angle of alanine obtained experimentally, ψ = -40 ± 30°, agreed reasonably well with the X-ray determined angle, ψ = -39°.

Structure and dynamics of cationic membrane peptides and proteins: insights from solid-state NMR

Many membrane peptides and protein domains contain functionally important cationic Arg and Lys residues, whose insertion into the hydrophobic interior of the lipid bilayer encounters significant energy barriers. To understand how these cationic molecules overcome the free energy barrier to insert into the lipid membrane, we have used solid-state NMR spectroscopy to determine the membrane-bound topology of these peptides. A versatile array of solid-state NMR experiments now readily yields the conformation, dynamics, orientation, depth of insertion, and site-specific protein-lipid interactions of these molecules. We summarize key findings of several Arg-rich membrane peptides, including β-sheet antimicrobial peptides, unstructured cell-penetrating peptides, and the voltage-sensing helix of voltage-gated potassium channels. Our results indicate the central role of guanidinium-phosphate and guanidinium-water interactions in dictating the structural topology of these cationic molecules in the lipid membrane, which in turn account for the mechanisms of this functionally diverse class of membrane peptides.

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.

Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR

Several human diseases are associated with the formation of amyloid aggregates, but experimental characterization of these amyloid fibrils and their oligomeric precursors has remained challenging. Experimental and computational analysis of simpler model systems has therefore been necessary, for instance, on the peptide fragment GNNQQNY7−13 of yeast prion protein Sup35p. Expanding on a previous publication, we report here a detailed structural characterization of GNNQQNY fibrils using magic angle spinning (MAS) NMR. On the basis of additional chemical shift assignments we confirm the coexistence of three distinct peptide conformations within the fibrillar samples, as reflected in substantial chemical shift differences. Backbone torsion angle measurements indicate that the basic structure of these coexisting conformers is an extended β-sheet. We structurally characterize a previously identified localized distortion of the β-strand backbone specific to one of the conformers. Intermolecular contacts are consistent with each of the conformers being present in its own parallel and in-register sheet. Overall the MAS NMR data indicate a substantial difference between the structure of the fibrillar and crystalline forms of these peptides, with a clearly increased complexity in the GNNQQNY fibril structure. These experimental data can provide guidance for future work, both experimental and theoretical, and provide insights into the distinction between fibril growth and crystal formation.

Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning NMR

Amyloid fibrils are structurally ordered aggregates of proteins whose formation is associated with many neurodegenerative and other diseases. For that reason, their high-resolution structures are of considerable interest and have been studied using a wide range of techniques, notably electron microscopy, X-ray diffraction, and magic angle spinning (MAS) NMR. Because of the excellent resolution in the spectra, MAS NMR is uniquely capable of delivering site-specific, atomic resolution information about all levels of amyloid structure: (1) the monomer, which packs into several (2) protofilaments that in turn associate to form a (3) fibril. Building upon our high-resolution structure of the monomer of an amyloid-forming peptide from transthyretin (TTR(105-115)), we introduce single 1-(13)C labeled amino acids at seven different sites in the peptide and measure intermolecular carbonyl-carbonyl distances with an accuracy of ~0.11 A. Our results conclusively establish a parallel, in register, topology for the packing of this peptide into a β-sheet and provide constraints essential for the determination of an atomic resolution structure of the fibril. Furthermore, the approach we employ, based on a combination of a double-quantum filtered variant of the DRAWS recoupling sequence and multispin numerical simulations in SPINEVOLUTION, is general and should be applicable to a wide range of systems.

3D (13)C-(13)C-(13)C correlation NMR for de novo distance determination of solid proteins and application to a human alpha-defensin

The de novo structure of an antimicrobial protein, human alpha-defensin 1 (HNP-1), is determined by combining a 3D (13)C-(13)C-(13)C (CCC) magic-angle spinning (MAS) correlation experiment with standard resonance assignment experiments. Using a short spin diffusion mixing time to assign intra-residue cross peaks and a long mixing time to detect inter-residue correlation peaks, we show that the 3D CCC experiment not only reduces the ambiguity of resonance assignment, but more importantly yields two orders of magnitude more long-range distances without recourse to existing crystal structures. Most of these distance constraints could not be obtained in a de novo fashion from 2D correlation spectra due to significant resonance overlap. Combining the distance constraints from the 3D CCC experiment and the chemical-shift-derived torsion angles, we obtained a de novo high-resolution NMR structure of HNP-1, with a heavy-atom RMSD of 3.4A from the crystal structure of the analogous HNP-3. The average energy of the minimum-energy ensemble is less than of 40kcal/mol. Thus, the 3D CCC experiment provides a reliable means of restraining the three-dimensional structure of insoluble proteins with unknown conformations.

Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR

Human alpha-defensins [human neutrophil peptides (HNPs)] are immune defense mini-proteins that act by disrupting microbial cell membranes. Elucidating the three-dimensional (3D) structures of HNPs in lipid membranes is important for understanding their mechanisms of action. Using solid-state NMR (SSNMR), we have determined the 3D structure of HNP-1 in a microcrystalline state outside the lipid membrane, which provides benchmarks for structure determination and comparison with the membrane-bound state. From a suite of two-dimensional and 3D magic-angle spinning experiments, (13)C and (15)N chemical shifts that yielded torsion angle constraints were obtained, while inter-residue distances were obtained to restrain the 3D fold. Together, these constraints led to the first high-resolution SSNMR structure of a human defensin. The SSNMR structure has close similarity to the crystal structures of the HNP family, with the exception of the loop region between the first and second beta-strands. The difference, which is partially validated by direct torsion angle measurements of selected loop residues, suggests possible conformational variation and flexibility of this segment of the protein, which may regulate HNP interaction with the phospholipid membrane of microbial cells.

Heteronuclear dipolar recoupling of half-integer quadrupole nuclei under fast magic angle spinning

An experimental method for the heteronuclear dipolar recoupling of half-integer quadrupole nuclei is proposed. The idea is to manipulate the central transition based on the recoupling technique of spin-polarization-inversion rotary resonance. This method allows the extraction of structural parameters under fast magic-angle spinning. Its validity has been examined by the average Hamiltonian theory and numerical simulations. The initial rotational-echo dephasing arising from the dipolar evolution can be approximated by a parabolic function, from which the heteronuclear van Vleck second moment can be estimated. A factor, estimated from two-spin simulations, is required to account for the effects of the quadrupolar coupling and is rather independent of the geometry and the orders of the spin systems. Our method can facilitate the structural characterization of materials containing half-integer quadrupole nuclei under high-resolution condition. Experimental verification has been carried out on two aluminophosphate systems, namely, AlPO(4)-5 and AlPO(4)-11.

High-resolution solid-state NMR structure of alanyl-prolyl-glycine

We present a de novo high-resolution structure of the peptide Alanyl-Prolyl-Glycine using a combination of sensitive solid-state NMR techniques that each yield precise structural constraints. High-quality (13)C-(13)C distance constraints are extracted by fitting rotational resonance width (R(2)W) experiments using Multimode Multipole Floquet Theory and experimental chemical shift anisotropy (CSA) orientations. In this strategy, a structure is first calculated using DANTE-REDOR and torsion angle measurements and the resulting relative CSA orientations are used as an input parameter in the (13)C-(13)C distance calculations. Finally, a refined structure is calculated using all the constraints. We investigate the effect of different structural constraints on structure quality, as determined by comparison to the crystal structure and also self-consistency of the calculated structures. Inclusion of all or subsets of these constraints into CNS calculations resulted in high-quality structures (0.02A backbone RMSD using all 11 constraints).

Structural analysis of uniformly (13)C-labelled solids from selective angle measurements at rotational resonance

We demonstrate that individual H-C-C-H torsional angles in uniformly labelled organic solids can be estimated by selective excitation of (13)C double-quantum coherences under magic-angle spinning at rotational resonance. By adapting a straightforward one-dimensional experiment described earlier [T. Karlsson, M. Eden, H. Luhman, M.H. Levitt, J. Magn. Reson. 145 (2000) 95-107], a double-quantum filtered spectrum selective for Calpha and Cbeta of uniformly labelled L-[(13)C,(15)N]valine is obtained with 25% efficiency. The evolution of Calpha-Cbeta double-quantum coherence under the influence of the dipolar fields of bonded protons is monitored to provide a value of the Halpha-Calpha-Cbeta-Hbeta torsional angle that is consistent with the crystal structure. In addition, double-quantum filtration selective for C6 and C1' of uniformly labelled [(13)C,(15)N]uridine is achieved with 12% efficiency for a (13)C-(13)C distance of 2.5A, yielding a reliable estimate of the C6-H and C1'-H projection angle defining the relative orientations of the nucleoside pyrimidine and ribose rings. This procedure will be useful, in favourable cases, for structural analysis of fully labelled small molecules such as receptor ligands that are not readily synthesised with labels placed selectively at structurally diagnostic sites.

Observation of a low-temperature, dynamically driven structural transition in a polypeptide by solid-state NMR spectroscopy

At reduced temperatures, proteins and other biomolecules are generally found to exhibit dynamic as well as structural transitions. This includes a so-called protein glass transition that is universally observed in systems cooled between 200 and 230 K, and which is generally attributed to interactions between hydrating solvent molecules and protein side chains. However, there is also experimental and theoretical evidence for a low-temperature transition in the intrinsic dynamics of the protein itself, absent any solvent. Here, we use low-temperature solid-state NMR to examine site-specific fluctuations in atomic structure and dynamics in the absence of solvents. In particular, we employ magic angle spinning NMR to examine a structural phase transition associated with dynamic processes in a solvent-free polypeptide, N-f-MLF-OH, lattice at temperatures as low as 90 K. This transition is characterized by the appearance of an extra set of lines in 1D (15)N spectra as well as additional cross peaks in 2D (13)C-(13)C and (13)C-(15)N spectra. Interestingly, the gradual, temperature-dependent appearance of the new spectral component is not accompanied by the line broadening typical of dynamic transitions. A direct comparison between the spectra of N-f-MLF-OH and the analog N-f-MLF-OMe, which does not display this transition, indicates a correlation of the structural transition to the temperature dependent motion of the aromatic phenylalanine side chain. Several quantitative solid state NMR experiments were employed to provide site-specific measurements of structural and motional features of the observed transition.

Combined NMR and computational study for azide binding to human manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the (15)N-labeled inhibitor azide ([(15)N(3)(-)]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy ((19)F-MAS and (15)N-CPMAS). Employing (19)F-(15)N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three (15)N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R(1)=4.85A between the (19)F-label of Tyf34 and the nearest (15)N of the azide and an azide-fluorotyrosine Tyf34 angle of 90 degrees were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide-Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-(19)F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.

Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR

Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.

Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel

The M2 protein of influenza A virus forms a transmembrane proton channel important for viral infection and replication. Amantadine blocks this channel, thus inhibiting viral replication. Elucidating the high-resolution structure of the M2 protein and its change upon amantadine binding is crucial for designing antiviral drugs to combat the growing resistance of influenza A viruses against amantadine. We used magic-angle-spinning solid-state NMR to determine the conformation and dynamics of the transmembrane domain of the protein M2TMP in the apo- and amantadine-bound states in lipid bilayers. (13)C chemical shifts and torsion angles of the protein in 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine (DLPC) bilayers indicate that M2TMP is alpha-helical in both states, but the average conformation differs subtly, especially at the G34-I35 linkage and V27 side chain. In the liquid-crystalline membrane, the complexed M2TMP shows dramatically narrower lines than the apo peptide. Analysis of the homogeneous and inhomogeneous line widths indicates that the apo-M2TMP undergoes significant microsecond-time scale motion, and amantadine binding alters the motional rates, causing line-narrowing. Amantadine also reduces the conformational heterogeneity of specific residues, including the G34/I35 pair and several side chains. Finally, amantadine causes the helical segment N-terminal to G34 to increase its tilt angle by 3 degrees , and the G34-I35 torsion angles cause a kink of 5 degrees in the amantadine-bound helix. These data indicate that amantadine affects the M2 proton channel mainly by changing the distribution and exchange rates among multiple low-energy conformations and only subtly alters the average conformation and orientation. Amantadine-resistant mutations thus may arise from binding-incompetent changes in the conformational equilibrium.