Measurement of dipole-coupled lineshapes in a many-spin system by constant-time two-dimensional solid state NMR with high-speed magic-angle spinning

Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications

Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.

Recent progress in dipolar recoupling techniques under fast MAS in solid-state NMR spectroscopy

With the recent advances in NMR hardware and probe design technology, magic-angle spinning (MAS) rates over 100 ​kHz are accessible now, even on commercial solid NMR probes. Under such fast MAS conditions, excellent spectral resolution has been achieved by efficient suppression of anisotropic interactions, which also opens an avenue to the proton-detected NMR experiments in solids. Numerous methods have been developed to take full advantage of fast MAS during the last decades. Among them, dipolar recoupling techniques under fast MAS play vital roles in the determination of the molecular structure and dynamics, and are also key elements in multi-dimensional correlation NMR experiments. Herein, we review the dipolar recoupling techniques, especially those developed in the past two decades for fast-to-ultrafast MAS conditions. A major focus for our discussion is the ratio of RF field strength (in frequency) to MAS frequency, ν₁/ν_r, in different pulse sequences, which determines whether these dipolar recoupling techniques are suitable for NMR experiments under fast MAS conditions. Systematic comparisons are made among both heteronuclear and homonuclear dipolar recoupling schemes. In addition, the schemes developed specially for proton-detection NMR experiments under ultrafast MAS conditions are highlighted as well.

NMR-based site-resolved profiling of β-amyloid misfolding reveals structural transitions from pathologically relevant spherical oligomer to fibril

Increasing evidence highlights the central role of neurotoxic oligomers of the 42-residue-long β-amyloid (Aβ42) in Alzheimer's disease (AD). However, very limited information is available on the structural transition from oligomer to fibril, particularly for pathologically relevant amyloids. To the best of our knowledge, we present here the first site-specific structural characterization of Aβ42 misfolding, from toxic oligomeric assembly yielding a similar conformation to an AD-associated Aβ42 oligomer, into a fibril. Transmission EM (TEM) analysis revealed that a spherical amyloid assembly (SPA) of Aβ42 with a 15.6 ± 2.1-nm diameter forms in a ∼30-μm Aβ42 solution after a ∼10-h incubation at 4 °C, followed by a slow conversion into fibril at ∼180 h. Immunological analysis suggested that the SPA has a surface structure similar to that of amylospheroid (ASPD), a patient-derived toxic Aβ oligomer, which had a diameter of 10-15 nm in negative-stain TEM. Solid-state NMR analyses indicated that the SPA structure involves a β-loop-β motif, which significantly differed from the triple-β motif observed for the Aβ42 fibril. The comparison of the ¹³C chemical shifts of SPA with those of the fibril prepared in the above conditions and interstrand distance measurements suggested a large conformational change involving rearrangements of intermolecular β-sheet into in-register parallel β-sheet during the misfolding. A comparison of the SPA and ASPD ¹³C chemical shifts indicated that SPA is structurally similar to the ASPD relevant to AD. These observations provide insights into the architecture and key structural transitions of amyloid oligomers relevant for AD pathology.

Homonuclear dipolar recoupling of arbitrary pairs in multi-spin systems under magic angle spinning: A double-frequency-selective ZQ-SEASHORE experiment

We describe a useful method for measuring the internuclear distances within arbitrarily selected pairs of like nuclei in dipolar-coupled multi-spin systems. The method uses a combination of the zero-quantum shift-evolution-assisted selective homonuclear recoupling (ZQ-SEASHORE) technique developed by Hu and Tycko [J. Chem. Phys. 2009, 131, 045101] and double-frequency-selective radio-frequency pulse. The double-frequency-selective pulse inverts polarizations of two spins simultaneously, and thus applications of the method presented here are only limited by the spectral resolution, and not by the number of interacting spins. Our experiments demonstrate the validity of the method and present analytical expressions for the dephasing curve.

Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels

For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.

Solid-State NMR Studies of Amyloid Materials: A Protocol to Define an Atomic Model of Aβ(1-42) in Amyloid Fibrils

Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015). Despite great biological and clinical interest in Aβ(1-42) fibrils, their structural details have been long-elusive until this study. The protocol is divided into four sections. First, the solid-phase peptide synthesis (SPPS) and purification of monomeric Aβ(1-42) is described. We illustrate a controlled incubation method to prompt misfolding of Aβ(1-42) into homogeneous amyloid fibrils in an aqueous solution with fragmented Aβ(1-42) fibrils as seeds. Next, we detail analysis of Aβ(1-42) fibrils by SSNMR to obtain structural restraints. Finally, we describe methods to construct atomic models of Aβ(1-42) fibrils based on SSNMR results through two-stage molecular dynamics calculations.

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.

REDOR NMR for drug discovery

Rotational-echo double-resonance (REDOR) NMR is a powerful and versatile solid-state NMR measurement that has been recruited to elucidate drug modes of action and to drive the design of new therapeutics. REDOR has been implemented to examine composition, structure, and dynamics in diverse macromolecular and whole-cell systems, including taxol-bound microtubules, enzyme-cofactor-inhibitor ternary complexes, and antibiotic-whole-cell complexes. The REDOR approach involves the integrated design of specific isotopic labeling strategies and the selection of appropriate REDOR experiments. By way of example, this digest illustrates the versatility of the REDOR approach, with an emphasis on the practical considerations of experimental design and data interpretation.

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.

Solid-State NMR of a Large Membrane Protein by Paramagnetic Relaxation Enhancement

Membrane proteins play an important role in many biological functions. Solid-state NMR spectroscopy is uniquely suited for studying structure and dynamics of membrane proteins in a membranous environment. The major challenge to obtain high quality solid-state NMR spectra of membrane proteins is sensitivity, due to limited quantities of labeled high-molecular-weight proteins. Here we demonstrate the incorporation of paramagnetic metal (Cu(2+)) ions, through either EDTA or a chelator lipid, into membrane protein samples for rapid data collection under fast magic-angle spinning (MAS) and low power (1)H decoupling. Spectral sensitivity of DsbB (20 kDa), an integral membrane protein, more than doubles in the same experimental time due to (1)H T(1) relaxation enhancement by Cu(2+) ions, with DsbB native fold and active site intact. This technique can be implemented to acquire multidimensional solid-state NMR spectra for chemical shift assignments and structure elucidation of large membrane proteins with small sample quantities.

Steric zipper formed by hydrophobic peptide fragment of Syrian hamster prion protein

Steric zippers, where the residues of two neighboring β-sheet layers are tightly interdigitated, have been proposed as fundamental structural units of amyloid fibrils by Eisenberg and co-workers. The steric zipper formed by polypeptides containing the palindromic sequence AGAAAAGA has a distinctive feature that the distance between two interdigitated β-sheet layers is comparable to the interstrand distance of the individual β-sheet. This structural motif is of great interest in the study of prion disease because the AGAAAAGA sequence is highly conserved in prion proteins of different species. In this work, the amyloid fibrils formed by the polypeptides of PrP(113-127), viz. Ac-AGAAAAGAVVGGLGG-NH(2), are taken as the model compound to investigate the biophysical principles governing the steric zipper formation. The target fibrils adopt the structural motif of class 7 steric zipper, which is formed by stacking of antiparallel β-sheet layers with residue 117 + k forming backbone hydrogen bonds to residue 120 - k. Implication of our results in the infectivity of scrapie prion is briefly discussed.

Phase transformation of calcium phosphates in the presence of glutamic acid

This work describes a phase-transformation pathway of calcium phosphate in the presence of glutamic acid. The route follows the order starting from amorphous calcium phosphate and brushite, then octacalcium phosphate (OCP), and finally hydroxyapatite (HAp). The preferred growth direction of the intermediate OCP and the final HAp phases lies along the c axis. On the basis of our scanning electron microscopy, X-ray powder diffraction, and 31P solid-state NMR data, we suggest that the transformation is via the dissolution–reprecipitation process, which is facilitated in the presence of glutamic acid. The effect on the transformation kinetics is rationalized by the disruption of the water layer bound on the crystal surface.

New insights into Keggin-type 12-tungstophosphoric acid from 31P MAS NMR analysis of absorbed trimethylphosphine oxide and DFT calculations

The acid and transport properties of the anhydrous Keggin-type 12-tungstophosphoric acid (H(3)PW(12)O(40); HPW) have been studied by solid-state (31)P magic-angle spinning NMR of absorbed trimethylphosphine oxide (TMPO) in conjunction with DFT calculations. Accordingly, (31)P NMR resonances arising from various protonated complexes, such as TMPOH(+) and (TMPO)(2)H(+) adducts, could be unambiguously identified. It was found that thermal pretreatment of the sample at elevated temperatures (≥423 K) is a prerequisite for ensuring complete penetration of the TMPO guest probe molecule into HPW particles. Transport of the TMPO absorbate into the matrix of the HPW adsorbent was found to invoke a desorption/absorption process associated with the (TMPO)(2)H(+) adducts. Consequently, three types of protonic acid sites with distinct superacid strengths, which correspond to (31)P chemical shifts of 92.1, 89.4, and 87.7 ppm, were observed for HPW samples loaded with less than three molecules of TMPO per Keggin unit. Together with detailed DFT calculations, these results support the scenario that the TMPOH(+) complexes are associated with protons located at three different terminal oxygen (O(d)) sites of the PW(12)O(40)(3-) polyanions. Upon increasing the TMPO loading to >3.0 molecules per Keggin unit, abrupt decreases in acid strength and the corresponding structural variations were attributed to the change in secondary structure of the pseudoliquid phase of HPW in the presence of excessive guest absorbate.

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.

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.

Rotational echo double resonance without proton decoupling under fast spinning condition

We show that rotational echo double resonance (REDOR) experiments can be carried out without proton decoupling under the conditions of fast spinning and strong rf field. Numerical simulations on a five-spin systems show that no significant attenuation of the reference signal (S(0)) is observed at a spin rate of 25 kHz, provided that the rf power is larger than 100 kHz. This approach has been validated by (31)P{(13)C} REDOR measurements on isotopically labeled glyphosate. The obtained van Vleck's second moment is in favorable agreement with the value calculated based on the crystal structure.

Solid-state P-31 NMR study of octacalcium phosphate incorporated with succinate

Octacalcium phosphate (OCP) is an important model compound in the study of biomineralization. The octacalcium phosphate-succinate (OCPS) compound is prepared and characterized by (31)P solid-state NMR spectroscopy. Taking advantage of the fact that the crystal structures of OCP and OCPS are very similar, an NMR strategy based on the (31)P homonuclear double-quantum spectroscopy is developed to assign all the peaks observed in the (31)P magic-angle spinning spectrum of OCPS. On the basis of our experimental data, the molecular formula of OCPS is determined to be Ca(7.81)(HPO(4))(1.82)(PO(4))(3.61)(succinate)(0.56).zH(2)O, where z<or= 0.5. We find that mainly the phosphorus species at the P5 site will be displaced when succinate ions are incorporated to form the OCPS lattice. The stability of OCPS is significantly higher than OCP with respect to the hydrolysis reaction at high pH conditions. We conclude that the hydration layer of OCP is playing the key role in the structural transformation of OCP.

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

We describe a method for measuring magnetic dipole-dipole interactions, and hence distances, between pairs of like nuclear spins in a many-spin system under magic-angle spinning (MAS). This method employs a homonuclear dipolar recoupling sequence that creates an average dipole-dipole coupling Hamiltonian under MAS with full zero-quantum symmetry, including both secular and flip-flop terms. Flip-flop terms are then attenuated by inserting rotor-synchronized periods of chemical shift evolution between recoupling blocks, leaving an effective Hamiltonian that contains only secular terms to a good approximation. Couplings between specific pairs of nuclear spins can then be selected with frequency-selective pi pulses. We demonstrate this technique, which we call zero-quantum shift evolution assisted homonuclear recoupling, in a series of one-dimensional and two-dimensional (13)C NMR experiments at 17.6 T and 40.00 kHz MAS frequency on uniformly (13)C-labeled L-threonine powder and on the helix-forming peptide MB(i+4)EK, synthesized with a pair of uniformly (13)C-labeled L-alanine residues. Experimental demonstrations include measurements of distances between (13)C sites that are separated by three bonds, placing quantitative constraints on both sidechain and backbone torsion angles in polypeptides.

Double-quantum NMR spectroscopy of 31P species submitted to very large CSAs

We introduce an original pulse sequence, BR2(2)(1)(taupitau), which is a block super-cycled R2(2)(1) sequence employing as basic element a pi pulse sandwiched by 'window' intervals. This homonuclear dipolar recoupling method allows the efficient excitation of double-quantum coherences between spin-1/2 nuclei submitted to very large chemical shift anisotropy. We demonstrate that this technique can be employed in double-quantum<-->single-quantum (31)P homonuclear correlation experiment at high magnetic field (B(0)>or=14 T) and high MAS frequencies (nu(R)>or=30 kHz). The performances of BR2(2)(1)(taupitau) are compared to those of the double-quantum recoupling methods, such as BABA and bracketed fp-RFDR, which were already employed at fast MAS rates. The BR2(2)(1)(taupitau) sequence displays a higher robustness to CSA and offset than the other existing techniques.

The functional curli amyloid is not based on in-register parallel beta-sheet structure

The extracellular curli proteins of Enterobacteriaceae form fibrous structures that are involved in biofilm formation and adhesion to host cells. These curli fibrils are considered a functional amyloid because they are not a consequence of misfolding, but they have many of the properties of protein amyloid. We confirm that fibrils formed by CsgA and CsgB, the primary curli proteins of Escherichia coli, possess many of the hallmarks typical of amyloid. Moreover we demonstrate that curli fibrils possess the cross-beta structure that distinguishes protein amyloid. However, solid state NMR experiments indicate that curli structure is not based on an in-register parallel beta-sheet architecture, which is common to many human disease-associated amyloids and the yeast prion amyloids. Solid state NMR and electron microscopy data are consistent with a beta-helix-like structure but are not sufficient to establish such a structure definitively.

Evidence for novel beta-sheet structures in Iowa mutant beta-amyloid fibrils

Asp23-to-Asn mutation within the coding sequence of beta-amyloid, called the Iowa mutation, is associated with early onset, familial Alzheimer's disease and cerebral amyloid angiopathy, in which patients develop neuritic plaques and massive vascular deposition predominantly of the mutant peptide. We examined the mutant peptide, D23N-Abeta40, by electron microscopy, X-ray diffraction, and solid-state NMR spectroscopy. D23N-Abeta40 forms fibrils considerably faster than the wild-type peptide (k = 3.77 x 10(-3) min(-1) and 1.07 x 10(-4) min(-1) for D23N-Abeta40 and the wild-type peptide WT-Abeta40, respectively) and without a lag phase. Electron microscopy shows that D23N-Abeta40 forms fibrils with multiple morphologies. X-ray fiber diffraction shows a cross-beta pattern, with a sharp reflection at 4.7 A and a broad reflection at 9.4 A, which is notably smaller than the value for WT-Abeta40 fibrils (10.4 A). Solid-state NMR measurements indicate molecular level polymorphism of the fibrils, with only a minority of D23N-Abeta40 fibrils containing the in-register, parallel beta-sheet structure commonly found in WT-Abeta40 fibrils and most other amyloid fibrils. Antiparallel beta-sheet structures in the majority of fibrils are indicated by measurements of intermolecular distances through (13)C-(13)C and (15)N-(13)C dipole-dipole couplings. An intriguing possibility exists that there is a relationship between the aberrant structure of D23N-Abeta40 fibrils and the unusual vasculotropic clinical picture in these patients.

Radio frequency-driven recoupling at high magic-angle spinning frequencies: homonuclear recoupling sans heteronuclear decoupling

We describe solid-state NMR homonuclear recoupling experiments at high magic-angle spinning (MAS) frequencies using the radio frequency-driven recoupling (RFDR) scheme. The effect of heteronuclear decoupling interference during RFDR recoupling at high spinning frequencies is investigated experimentally and via numerical simulations, resulting in the identification of optimal decoupling conditions. The effects of MAS frequency, RF field amplitude, bandwidth, and chemical shift offsets are examined. Most significantly, it is shown that broadband homonuclear correlation spectra can be efficiently obtained using RFDR without decoupling during the mixing period in fully protonated samples, thus considerably reducing the rf power requirements for acquisition of (13)C-(13)C correlation spectra. The utility of RFDR sans decoupling is demonstrated with broadband correlation spectra of a peptide and a model protein at high MAS frequencies and high magnetic field.

Investigation of finite-pulse radiofrequency-driven recoupling methods for measurement of intercarbonyl distances in polycrystalline and membrane-associated HIV fusion peptide samples

Two finite-pulse radiofrequency-driven recoupling (RFDR) methods were compared and applied to the measurement of 3-6 Å (13)CO-(13)CO distances in polycrystalline and membrane-associated HIV fusion peptide (HFP) samples. The RFDR methods were based on π pulses and were relatively straightforward to implement and insensitive to pulse imperfections. The two tested methods were: (i) constant-time double-quantum buildup with finite pulses (fpCTDQBU) for which the pulse sequence maintained a constant transverse relaxation period while allowing a variable period of dipolar dephasing; and (ii) constant-time finite-pulse rf-driven recoupling (fpRFDR-CT) for which the duration of transverse relaxation increased with increasing dephasing period. The fpRFDR-CT method yielded higher signal-to-noise and an accurate determination of a ~5 Å intercarbonyl distance was made in a crystalline peptide which had T(2) ≈ 55 ms. In some contrast, the HFP samples had T(2) ≈ 15 ms and the fpRFDR-CT data were dominated by transverse relaxation. Examination of the fpCTDQBU sequence showed: (i) the most rapid signal buildup was obtained with application of one (13) C π pulse per rotor period rather than one (13)C π pulse per multiple rotor periods and (ii) the data were insensitive to ~15 ppm transmitter offset and to ~5° variation of π pulse nutation angle. For HFP samples which were (13)CO labeled at a single residue, analyses of the fpCTDQBU data were interpreted with a model of mixed parallel and antiparallel β-strand arrangements in the N-terminal region of HFP and loss of parallel β-sheet structure in the C-terminal region of HFP.

Symmetry-based constant-time homonuclear dipolar recoupling in solid state NMR

Constant-time dipolar recoupling pulse sequences are advantageous in structural studies by solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) because they yield experimental data that are relatively insensitive to radio-frequency pulse imperfections and nuclear spin relaxation processes. A new approach to the construction of constant-time homonuclear dipolar recoupling sequences is described, based on symmetry properties of the recoupled dipole-dipole interaction Hamiltonian under cyclic displacements in time with respect to the MAS sample rotation period. A specific symmetry-based pulse sequence called PITHIRDS-CT is introduced and demonstrated experimentally. (13)C NMR data for singly-(13)C-labeled amino acid powders and amyloid fibrils indicate the effectiveness of PITHIRDS-CT in measurements of intermolecular distances in solids. (15)N-detected and (13)C-detected measurements of intramolecular (15)N-(15)N distances in peptides with alpha-helical and beta-sheet structures indicate the utility of PITHIRDS-CT in studies of molecular conformations, especially measurements of backbone psi torsion angles in peptides containing uniformly (15)N- and (13)C-labeled amino acids.

Double-quantum filtered heteronuclear correlation spectroscopy under magic angle spinning

We present a simple experimental method to extract the van Vleck second moment of a multiple-spin system under high-resolution condition. The idea is to incorporate a double-quantum (DQ) filter into the pulse sequence of heteronuclear correlation spectroscopy so that a DQ excitation profile can be obtained by measuring a series of 2D spectra. The effects of spinning frequency and proton decoupling are demonstrated on the measurements of two model compounds, viz. hydroxyapatite and brushite. Based on the results obtained for the model compounds, the P-31 homonuclear second moment of the apatite component in rat dentin is characterized. The method is generally suited for the study of bone, enamel and dentin.

Amyloid of the prion domain of Sup35p has an in-register parallel beta-sheet structure

The [PSI(+)] prion of Saccharomyces cerevisiae is a self-propagating amyloid form of Sup35p, a subunit of the translation termination factor. Using solid-state NMR we have examined the structure of amyloid fibrils formed in vitro from purified recombinant Sup35(1-253), consisting of the glutamine- and asparagine-rich N-terminal 123-residue prion domain (N) and the adjacent 130-residue highly charged M domain. Measurements of magnetic dipole-dipole couplings among (13)C nuclei in a series of Sup35NM fibril samples, (13)C-labeled at backbone carbonyl sites of Tyr, Leu, or Phe residues or at side-chain methyl sites of Ala residues, indicate intermolecular (13)C-(13)C distances of approximately 0.5 nm for nearly all sites in the N domain. Certain sites in the M domain also exhibit intermolecular distances of approximately 0.5 nm. These results indicate that an in-register parallel beta-sheet structure underlies the [PSI(+)] prion phenomenon.

Molecular alignment within beta-sheets in Abeta(14-23) fibrils: solid-state NMR experiments and theoretical predictions

We report investigations of the molecular structure of amyloid fibrils formed by residues 14-23 of the beta-amyloid peptide associated with Alzheimer's disease (Abeta(14-23)), using solid-state nuclear magnetic resonance (NMR) techniques in conjunction with electron microscopy and atomic force microscopy. The NMR measurements, which include two-dimensional proton-mediated (13)C-(13)C exchange and two-dimensional relayed proton-mediated (13)C-(13)C exchange spectra, show that Abeta(14-23) fibrils contain antiparallel beta-sheets with a registry of backbone hydrogen bonds that aligns residue 17+k of each peptide molecule with residue 22-k of neighboring molecules in the same beta-sheet. We compare these results, as well as previously reported experimental results for fibrils formed by other beta-amyloid fragments, with theoretical predictions of molecular alignment based on databases of residue-specific alignments in antiparallel beta-sheets in known protein structures. While the theoretical predictions are not in exact agreement with the experimental results, they facilitate the design of experiments by suggesting a small number of plausible alignments that are readily distinguished by solid-state NMR.

Theory and applications of supercycled symmetry-based recoupling sequences in solid-state nuclear magnetic resonance

We present the theoretical principles of supercycled symmetry-based recoupling sequences in solid-state magic-angle-spinning NMR. We discuss the construction procedure of the SR26 pulse sequence, which is a particularly robust sequence for double-quantum homonuclear dipole-dipole recoupling. The supercycle removes destructive higher-order average Hamiltonian terms and renders the sequence robust over long time intervals. We demonstrate applications of the SR26 sequence to double-quantum spectroscopy, homonuclear spin counting, and determination of the relative orientations of chemical shift anisotropy tensors.

Effective dipolar couplings determined by dipolar dephasing of double-quantum coherences

It is shown how homonuclear distances and homonuclear dipolar lattice sums between spin-1/2 nuclei can be measured by a pulsed solid-state NMR experiment under magic-angle spinning conditions. The presented technique is based on double-quantum coherence filtering. Instead of measuring a build-up of double-quantum coherence the pulse sequence is designed to dephase double-quantum coherence. This is achieved by exciting double-quantum coherence either with the help of the through-space dipolar coupling or the through-bond dipolar coupling while the dephasing relies on the through-space dipolar coupling as selected by a gamma-encoded pulse sequence from the C/R symmetry class. Since dephasing curves can be normalized on zero dephasing, it is possible to analyze the initial dephasing regime and hence determine dipolar lattice sums (effective dipolar couplings) in multiple-spin systems. A formula for the effective dipolar coupling is derived theoretically and validated by numerical calculations and experiments on crystalline model compounds for (13)C and (31)P spin systems. The double-quantum dephasing experiment can be combined with constant-time data sampling to compensate for relaxation effects, consequently only two experimental data points are necessary for a single distance measurement. The phase cycling overhead for the constant-time experiment is minimal because a short cogwheel phase cycle exists. A 2D implementation is demonstrated on [(13)C(3)]alanine.

Characterization of amyloid structures at the molecular level by solid state nuclear magnetic resonance spectroscopy

Solid state nuclear magnetic resonance (NMR) spectroscopy is particularly useful in structural studies of amyloid fibrils because solid state NMR techniques have unique capabilities as site-specific, molecular-level structural probes of noncrystalline materials. These techniques provide experimental data that strongly constrain the secondary, tertiary, and quaternary structures of amyloid fibrils, permitting the development of experimentally based structural models. Examples of techniques that are applicable to amyloid samples prepared with isotopic labeling of specific sites and to samples prepared with uniform isotopic labeling of selected residues are presented, illustrating the utility of the various techniques and labeling schemes. Information regarding the preparation of amyloid samples for solid state NMR measurements is also included.

Double-quantum NMR spectroscopy based on finite pulse RFDR

We demonstrate that the finite pulse RFDR sequence (J. Chem. Phys. 114 (2001) 8473) can be used effectively for 31P double-quantum NMR spectroscopy at a spinning frequency of 10 kHz. The 31P NMR data measured for hydroxyapatite and octacalcium phosphate show that sizable double-quantum excitation efficiency can be obtained with the ratio of the recoupling field to spinning frequency set equal to 1.67.

Amyloidosis of Alzheimer's Abeta peptides: solid-state nuclear magnetic resonance, electron paramagnetic resonance, transmission electron microscopy, scanning transmission electron microscopy and atomic force microscopy studies

Aggregation cascade for Alzheimer's amyloid-beta peptides, its relevance to neurotoxicity in the course of Alzheimer's disease and experimental methods useful for these studies are discussed. Details of the solid-phase peptide synthesis and sample preparation procedures for Alzheimer's beta-amyloid fibrils are given. Recent progress in obtaining structural constraints on Abeta-fibrils from solid-state NMR and scanning transmission electron microscopy (STEM) data is discussed. Polymorphism of amyloid fibrils and oligomers of the 'Arctic' mutant of Abeta(1-40) was studied by (1)H,(13)C solid-state NMR, transmission electron microscopy (TEM) and atomic force microscopy (AFM), and a real-time aggregation of different polymorphs of the peptide was observed with the aid of in situ AFM. Recent results on binding of Cu(II) ions and Al-citrate and Al-ATP complexes to amyloid fibrils, as studied by electron paramagnetic resonance (EPR) and solid-state (27)Al NMR techniques, are also presented.

Solid state NMR reveals a pH-dependent antiparallel beta-sheet registry in fibrils formed by a beta-amyloid peptide

We report solid state nuclear magnetic resonance (NMR) measurements that probe the supramolecular organization of beta-sheets in the cross-beta motif of amyloid fibrils formed by residues 11-25 of the beta-amyloid peptide associated with Alzheimer's disease (Abeta(11-25)). Fibrils were prepared at pH 7.4 and pH 2.4. The solid state NMR data indicate that the central hydrophobic segment of Abeta(11-25) (sequence LVFFA) adopts a beta-strand conformation and participates in antiparallel beta-sheets at both pH values, but that the registry of intermolecular hydrogen bonds is pH-dependent. Moreover, both registries determined for Abeta(11-25) fibrils are different from the hydrogen bond registry in the antiparallel beta-sheets of Abeta(16-22) fibrils at pH 7.4 determined in earlier solid state NMR studies. In all three cases, the hydrogen bond registry is highly ordered, with no detectable "registry-shift" defects. These results suggest that the supramolecular organization of beta-sheets in amyloid fibrils is determined by a sensitive balance of multiple side-chain-side-chain interactions. Recent structural models for Abeta(11-25) fibrils based on X-ray fiber diffraction data are inconsistent with the solid state NMR data at both pH values.

Increasing the amphiphilicity of an amyloidogenic peptide changes the beta-sheet structure in the fibrils from antiparallel to parallel

Solid-state NMR measurements have been reported for four peptides derived from beta-amyloid peptide Abeta(1-42): Abeta(1-40), Abeta(10-35), Abeta(16-22), and Abeta(34-42). Of these, the first two are predicted to be amphiphilic and were reported to form parallel beta-sheets, whereas the latter two peptides appear nonamphiphilic and adopt an antiparallel beta-sheet organization. These results suggest that amphiphilicity may be significant in determining fibril structure. Here, we demonstrate that acylation of Abeta(16-22) with octanoic acid increases its amphiphilicity and changes the organization of fibrillar beta-sheet from antiparallel to parallel. Electron microscopy, Congo Red binding, and one-dimensional 13C NMR measurements demonstrate that octanoyl-Abeta(16-22) forms typical amyloid fibrils. Based on the stability of monolayers at the air-water interface, octanoyl-Abeta(16-22) is more amphiphilic than Abeta(16-22). Measurements of 13C-13C and 15N-13C nuclear magnetic dipole-dipole couplings in isotopically labeled fibril samples, using the constant-time finite-pulse radiofrequency-driven recoupling (fpRFDR-CT) and rotational echo double resonance (REDOR) solid-state NMR techniques, demonstrate that octanoyl-Abeta(16-22) fibrils are composed of parallel beta-sheets, whereas Abeta(16-22) fibrils are composed of antiparallel beta-sheets. These data demonstrate that amphiphilicity is critical in determining the structural organization of beta-sheets in the amyloid fibril. This work also shows that all amyloid fibrils do not share a common supramolecular structure, and suggests a method for controlling the structure of amyloid fibrils.

Site-specific identification of non-beta-strand conformations in Alzheimer's beta-amyloid fibrils by solid-state NMR

The most well-established structural feature of amyloid fibrils is the cross-beta motif, an extended beta-sheet structure formed by beta-strands oriented perpendicular to the long fibril axis. Direct experimental identification of non-beta-strand conformations in amyloid fibrils has not been reported previously. Here we report the results of solid-state NMR measurements on amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)), prepared synthetically with pairs of (13)C labels at consecutive backbone carbonyl sites. The measurements probe the peptide backbone conformation in residues 24-30, a segment where a non-beta-strand conformation has been suggested by earlier sequence analysis, cross-linking experiments, and molecular modeling. Data obtained with the fpRFDR-CT, DQCSA, and 2D MAS exchange solid-state NMR techniques, which provide independent constraints on the phi and psi backbone torsion angles between the labeled carbonyl sites, indicate non-beta-strand conformations at G25, S26, and G29. These results represent the first site-specific identification and characterization of non-beta-strand peptide conformations in an amyloid fibril.

A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR

We present a structural model for amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)), based on a set of experimental constraints from solid state NMR spectroscopy. The model additionally incorporates the cross-beta structural motif established by x-ray fiber diffraction and satisfies constraints on Abeta(1-40) fibril dimensions and mass-per-length determined from electron microscopy. Approximately the first 10 residues of Abeta(1-40) are structurally disordered in the fibrils. Residues 12-24 and 30-40 adopt beta-strand conformations and form parallel beta-sheets through intermolecular hydrogen bonding. Residues 25-29 contain a bend of the peptide backbone that brings the two beta-sheets in contact through sidechain-sidechain interactions. A single cross-beta unit is then a double-layered beta-sheet structure with a hydrophobic core and one hydrophobic face. The only charged sidechains in the core are those of D23 and K28, which form salt bridges. Fibrils with minimum mass-per-length and diameter consist of two cross-beta units with their hydrophobic faces juxtaposed.

Supramolecular structure in full-length Alzheimer's beta-amyloid fibrils: evidence for a parallel beta-sheet organization from solid-state nuclear magnetic resonance

We report constraints on the supramolecular structure of amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (A beta(1-40)) obtained from solid-state nuclear magnetic resonance (NMR) measurements of intermolecular dipole-dipole couplings between (13)C labels at 11 carbon sites in residues 2 through 39. The measurements are carried out under magic-angle spinning conditions, using the constant-time finite-pulse radiofrequency-driven recoupling (fpRFDR-CT) technique. We also present one-dimensional (13)C magic-angle spinning NMR spectra of the labeled A beta(1-40) samples. The fpRFDR-CT data reveal nearest-neighbor intermolecular distances of 4.8 +/- 0.5 A for carbon sites from residues 12 through 39, indicating a parallel alignment of neighboring peptide chains in the predominantly beta-sheet structure of the amyloid fibrils. The one-dimensional NMR spectra indicate structural order at these sites. The fpRFDR-CT data and NMR spectra also indicate structural disorder in the N-terminal segment of A beta(1-40), including the first nine residues. These results place strong constraints on any molecular-level structural model for full-length beta-amyloid fibrils.

Homonuclear zero-quantum recoupling in fast magic-angle spinning nuclear magnetic resonance

Solid-state magic-angle-spinning NMR pulse sequences which implement zero-quantum homonuclear dipolar recoupling are designed with the assistance of symmetry theory. The pulse sequences are compensated on a short time scale by the use of composite pulses and on a longer time scale by the use of supercycles. (13)C dipolar recoupling is demonstrated in powdered organic solids at high spinning frequencies. The new sequences are compared to existing pulse sequences by means of numerical simulations. Experimental two-dimensional magnetization exchange spectra are shown for [U-(13)C]-L-tyrosine.

Sensitivity enhancement in structural measurements by solid state NMR through pulsed spin locking

Free induction decay (FID) signals in solid state NMR measurements performed with magic angle spinning can often be extended in time by factors on the order of 10 by a simple pulsed spin locking technique. The sensitivity of a structural measurement in which the structural information is contained in the dependence of the integrated FID amplitude on a preceding evolution period can therefore be enhanced substantially by pulsed spin locking in the signal detection period. We demonstrate sensitivity enhancements in a variety of solid state NMR techniques that are applicable to selectively isotopically labeled samples, including 13C-15N rotational echo double resonance (REDOR), 13C-13C dipolar recoupling measurements using the constant-time finite-pulse radio-frequency-driven recoupling (fpRFDR-CT) and constant-time double-quantum-filtered dipolar recoupling (CTDQFD) techniques, and torsion angle measurements using the double quantum chemical shift anisotropy (DQCSA) technique. Further, we demonstrate that the structural information in the solid state NMR data is not distorted by pulsed spin locking in the detection period.