Multidimensional Heteronuclear Correlation Spectroscopy of a Uniformly 15N- and 13C-Labeled Peptide Crystal: Toward Spectral Resolution, Assignment, and Structure Determination of Oriented Molecules in Solid-State NMR

Oxidative Nitrogen Insertion into Silyl Enol Ether C═C Bonds

Here, we demonstrate a fundamentally new reactivity of the silyl enol ether functionality utilizing an in situ-generated iodonitrene-like species. The present transformation inserts a nitrogen atom between the silyl enol ether olefinic carbons with the concomitant cleavage of the C═C bond. Overall, this facile transformation converts a C-nucleophilic silyl enol ether to the corresponding C-electrophilic N-acyl-N,O-acetal. This unprecedented access to α-amido alkylating agents enables modular derivatization with carbon and heteroatom nucleophiles and the unique late-stage editing of carbon frameworks. The reaction efficiency of this transformation is well correlated with enol ether nucleophilicity as described by the Mayr N scale. Applications presented herein include late-stage nitrogen insertion into carbon skeletons of natural products with previously unattainable regioselectivity as well as modified conditions for 15N labeling of amides and lactams.

Structural Arrangement within a Peptide Fibril Derived from the Glaucoma-Associated Myocilin Olfactomedin Domain

Myocilin-associated glaucoma is a new addition to the list of diseases linked to protein misfolding and amyloid formation. Single point variants of the ∼257-residue myocilin olfactomedin domain (mOLF) lead to mutant myocilin aggregation. Here, we analyze the 12-residue peptide P1 (GAVVYSGSLYFQ), corresponding to residues 326-337 of mOLF, previously shown to form amyloid fibrils in vitro and in silico. We applied solid-state NMR structural measurements to test the hypothesis that P1 fibrils adopt one of three predicted structures. Our data are consistent with a U-shaped fibril arrangement for P1, one that is related to the U-shape predicted previously in silico. Our data are also consistent with an antiparallel fibril arrangement, likely driven by terminal electrostatics. Our proposed structural model is reminiscent of fibrils formed by the Aβ(1-40) Iowa mutant peptide, but with a different arrangement of molecular turn regions. Taken together, our results strengthen the connection between mOLF fibrils and the broader amylome and contribute to our understanding of the fundamental molecular interactions governing fibril architecture and stability.

1H/13C/15N triple-resonance experiments for structure determinaton of membrane proteins by oriented-sample NMR

The benefits of triple-resonance experiments for structure determination of macroscopically oriented membrane proteins by solid-state NMR are discussed. While double-resonance ¹H/¹⁵N experiments are effective for structure elucidation of alpha-helical domains, extension of the method of oriented samples to more complex topologies and assessing side-chain conformations necessitates further development of triple-resonance (¹H/¹³C/¹⁵N) NMR pulse sequences. Incorporating additional spectroscopic dimensions involving ¹³C spin-bearing nuclei, however, introduces essential complications arising from the wide frequency range of the ¹H-¹³C dipolar couplings and ¹³C CSA (>20 ​kHz), and the presence of the ¹³C-¹³C homonuclear dipole-dipole interactions. The recently reported ROULETTE-CAHA pulse sequence, in combination with the selective z-filtering, can be used to evolve the structurally informative ¹H-¹³C dipolar coupling arising from the aliphatic carbons while suppressing the signals from the carbonyl and methyl regions. Proton-mediated magnetization transfer under mismatched Hartman-Hahn conditions (MMHH) can be used to correlate ¹³C and ¹⁵N nuclei in such triple-resonance experiments for the subsequent ¹⁵N detection. The recently developed pulse sequences are illustrated for n-acetyl Leucine (NAL) single crystal and doubly labeled Pf1 coat protein reconstituted in magnetically aligned bicelles. An interesting observation is that in the case of ¹⁵N-labeled NAL measured at ¹³C natural abundance, the triple (¹H/¹³C/¹⁵N) MMHH scheme predominantly gives rise to long-range intermolecular magnetization transfers from ¹³C to ¹⁵N spins; whereas direct Hartmann-Hahn ¹³C/¹⁵N transfer is entirely intramolecular. The presented developments advance NMR of oriented samples for structure determination of membrane proteins and liquid crystals.

Paramagnetic NMR in solution and the solid state

The field of paramagnetic NMR has expanded considerably in recent years. This review addresses both the theoretical description of paramagnetic NMR, and the way in which it is currently practised. We provide a review of the theory of the NMR parameters of systems in both solution and the solid state. Here we unify the different languages used by the NMR, EPR, quantum chemistry/DFT, and magnetism communities to provide a comprehensive and coherent theoretical description. We cover the theory of the paramagnetic shift and shift anisotropy in solution both in the traditional formalism in terms of the magnetic susceptibility tensor, and using a more modern formalism employing the relevant EPR parameters, such as are used in first-principles calculations. In addition we examine the theory first in the simple non-relativistic picture, and then in the presence of spin-orbit coupling. These ideas are then extended to a description of the paramagnetic shift in periodic solids, where it is necessary to include the bulk magnetic properties, such as magnetic ordering at low temperatures. The description of the paramagnetic shift is completed by describing the current understanding of such shifts due to lanthanide and actinide ions. We then examine the paramagnetic relaxation enhancement, using a simple model employing a phenomenological picture of the electronic relaxation, and again using a more complex state-of-the-art theory which incorporates electronic relaxation explicitly. An additional important consideration in the solid state is the impact of bulk magnetic susceptibility effects on the form of the spectrum, where we include some ideas from the field of classical electrodynamics. We then continue by describing in detail the solution and solid-state NMR methods that have been deployed in the study of paramagnetic systems in chemistry, biology, and the materials sciences. Finally we describe a number of case studies in paramagnetic NMR that have been specifically chosen to highlight how the theory in part one, and the methods in part two, can be used in practice. The systems chosen include small organometallic complexes in solution, solid battery electrode materials, metalloproteins in both solution and the solid state, systems containing lanthanide ions, and multi-component materials used in pharmaceutical controlled-release formulations that have been doped with paramagnetic species to measure the component domain sizes.

Solid-state NMR methods for oriented membrane proteins

Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.

A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers

We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unassigned signals, and assignment gaps. Examination of a set of high-scoring assignments from a large number of independent runs allows one to determine whether a unique assignment exists for the entire sequence or parts thereof. We demonstrate the MCSA algorithm using two-dimensional (2D) and three-dimensional (3D) solid state NMR spectra of several model protein samples (α-spectrin SH3 domain and protein G/B1 microcrystals, HET-s(218-289) fibrils), obtained with magic-angle spinning and standard polarization transfer techniques. The MCSA algorithm and MCASSIGN2 program can accommodate arbitrary combinations of NMR spectra with arbitrary dimensionality, and can therefore be applied in many areas of solid state and solution NMR.

On the performance of spin diffusion NMR techniques in oriented solids: prospects for resonance assignments and distance measurements from separated local field experiments

NMR spin diffusion experiments have the potential to provide both resonance assignment and internuclear distances for protein structure determination in oriented solid-state NMR. In this paper, we compared the efficiencies of three spin diffusion experiments: proton-driven spin diffusion (PDSD), cross-relaxation-driven spin diffusion (CRDSD), and proton-mediated proton transfer (PMPT). As model systems for oriented proteins, we used single crystals of N-acetyl-L-(15)N-leucine (NAL) and N-acetyl-L-(15)N-valyl-L-(15)N-leucine (NAVL) to probe long and short distances, respectively. We demonstrate that, for short (15)N/(15)N distances such as those found in NAVL (3.3 Å), the PDSD mechanism gives the most intense cross-peaks, while, for longer distances (>6.5 Å), the CRDSD and PMPT experiments are more efficient. The PDSD was highly inefficient for transferring magnetization across distances greater than 6.5 Å (NAL crystal sample), due to small (15)N/(15)N dipolar couplings (<4.5 Hz). Interestingly, the mismatched Hartmann-Hahn condition present in the PMPT experiment gave more intense cross-peaks for lower (1)H and (15)N RF spinlock amplitudes (32 and 17 kHz, respectively) rather than higher values (55 and 50 kHz), suggesting a more complex magnetization transfer mechanism. Numerical simulations are in good agreement with the experimental findings, suggesting a combined PMPT and CRDSD effect. We conclude that, in order to assign SLF spectra and measure short- and long-range distances, the combined use of homonuclear correlation spectra, such as the ones surveyed in this work, are necessary.

1H-13C separated local field spectroscopy of uniformly 13C labeled peptides and proteins

By incorporating homonuclear decoupling on both the (1)H and (13)C channels it is feasible to obtain high-resolution two-dimensional separated local field spectra of peptides and proteins that are 100% labeled with (13)C. Dual-PISEMO (Polarization Inversion Spin Exchange Modulated Observation) can be performed as a conventional two-dimensional experiment, or with windowed detection as a one-dimensional experiment that offers flexibility as a building block for shiftless and other multidimensional triple-resonance experiments with the inclusion of (15)N irradiation. The triple-resonance MAGC probe used to perform these experiments at 500 MHz is described.

Sensitivity enhanced heteronuclear correlation spectroscopy in multidimensional solid-state NMR of oriented systems via chemical shift coherences

We present new sensitivity enhanced schemes for heteronuclear correlation spectroscopy (HETCOR) in solid-state NMR of oriented systems. These schemes will enhance the sensitivity of the HETCOR by 40% for the two-dimensional experiments (SE-HETCOR) and up to 180% for the 3D HETCOR-separated local field version (SE-PISEMAI-HETCOR). The signal enhancement is demonstrated for a single crystal of ((15)N)N-acetylleucine and the integral membrane protein sarcolipin oriented in lipid bicelles. These methods will significantly reduce the time needed to acquire multidimensional experiments for membrane proteins oriented in magnetically or mechanically aligned lipid bilayers as well as liquid crystalline materials.

(1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins

(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples.

Labeling strategies for 13C-detected aligned-sample solid-state NMR of proteins

(13)C-detected solid-state NMR experiments have substantially higher sensitivity than the corresponding (15)N-detected experiments on stationary, aligned samples of isotopically labeled proteins. Several methods for tailoring the isotopic labeling are described that result in spatially isolated (13)C sites so that dipole-dipole couplings among the (13)C are minimized, thus eliminating the need for homonuclear (13)C-(13)C decoupling in either indirect or direct dimensions of one- or multi-dimensional NMR experiments that employ (13)C detection. The optimal percentage for random fractional (13)C labeling is between 25% and 35%. Specifically labeled glycerol and glucose can be used at the carbon sources to tailor the isotopic labeling, and the choice depends on the resonances of interest for a particular study. For investigations of the protein backbone, growth of the bacteria on [2-(13)C]-glucose-containing media was found to be most effective.

Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins

Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.

Trungapeptins A-C, cyclodepsipeptides from the marine cyanobacterium Lyngbya majuscula

Trungapeptins A-C (1-3) were isolated from the marine cyanobacterium Lyngbya majuscula collected from Trung Province, Thailand. Their gross structures were elucidated by interpretation of spectroscopic data. The absolute configurations of the amino acids and phenyllactic acid were determined by Marfey's and chiral HPLC analyses, respectively. The relative stereochemistry of 3-hydroxy-2-methyl-7-octynoic acid (Hmoya) of trungapeptin A was elucidated by application of the J-based configuration analysis, and its absolute stereochemistry was established to be 2S, 3R by Mosher's method. The structures of compounds 1-3 are closely related to the antanapeptins, a series of depsipeptides isolated from a Madagascan collection of L. majuscula.

Determination of the residue-specific 15N CSA tensor principal components using multiple alignment media

The individual components of the backbone (15)N CSA tensor, sigma(11), sigma(22), sigma(33), and the orientation of sigma(11) relative to the NH bond described by the angle beta have been determined for uniformly labeled (15)N, (13)C ubiquitin from partial alignment in phospholipid bicelles, Pf1 phage, and poly(ethylene glycol) by measuring the residue-specific residual dipolar couplings and chemical shift deviations. No strong correlation between any of the CSA tensor components is observed with any single structural feature. However, the experimentally determined tensor components agree with the previously determined average CSA principal components [Cornilescu and Bax (2000) J. Am. Chem. Soc. 122, 10143-10154]. Significant deviations from the averages coincide with residues in beta-strand or extended regions, while alpha-helical residue tensor components cluster close to the average values.

13C, 15N resonance assignment of parts of the HET-s prion protein in its amyloid form

The partial 15N and 13C solid-state NMR resonance assignment of the HET-s prion protein fragment 218-289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20-40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional 13C-13C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional 15N-13C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues.

SPINAL modulated decoupling in high field double- and triple-resonance solid-state NMR experiments on stationary samples

Continuous wave irradiation has limited bandwidth for heteronuclear 1H decoupling at high fields and for 13C decoupling in 1H/13C/15N triple-resonance experiments. SPINAL-16 modulation is shown to improve the efficiency of 1H and 13C heteronuclear decoupling on single crystals of peptides and on magnetically aligned samples of membrane proteins in bicelles, which is of particular importance because aqueous samples of biomolecules are lossy at high fields, which limits the strengths of the RF fields that can be applied.

Peptides and the development of double- and triple-resonance solid-state NMR of aligned samples

Peptides have been instrumental in the development of solid-state nuclear magnetic resonance (NMR) spectroscopy, and their roles in the development of solid-state NMR of aligned samples is reviewed. In particular, the roles of synthetic peptides in the development of triple-resonance methods are described. Recent developments of pulse sequences and NMR probes for triple-resonance NMR of aligned samples are presented.

The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy

Solid-state NMR spectroscopy is being developed at a fast pace for the structural investigation of immobilized and non-crystalline biomolecules. These include proteins and peptides associated with phospholipid bilayers. In contrast to solution NMR spectroscopy, where complete or almost complete averaging leads to isotropic values, the anisotropic character of nuclear interactions is apparent in solid-state NMR spectra. In static samples the orientation dependence of chemical shift, dipolar or quadrupolar interactions, therefore, provides angular constraints when the polypeptides have been reconstituted into oriented membranes. Furthermore, solid-state NMR spectroscopy of aligned samples offers distinct advantages in allowing access to dynamic processes such as topological equilibria or rotational diffusion in membrane environments. Alternatively, magic angle sample spinning (MAS) results in highly resolved NMR spectra, provided that the sample is sufficiently homogenous. MAS spinning solid-state NMR spectra allow to measure distances and dihedral angles with high accuracy. The technique has recently been developed to selectively establish through-space and through-bond correlations between nuclei, similar to the approaches well-established in solution-NMR spectroscopy.

Solid-state nuclear magnetic resonance spectroscopy--pharmaceutical applications

Solid-state nuclear magnetic resonance (NMR) spectroscopy has become an integral technique in the field of pharmaceutical sciences. This review focuses on the use of solid-state NMR techniques for the characterization of pharmaceutical solids (drug substance and dosage form). These techniques include methods for (1) studying structure and conformation, (2) analyzing molecular motions (relaxation and exchange spectroscopy), (3) assigning resonances (spectral editing and two-dimensional correlation spectroscopy), and (4) measuring internuclear distances.

Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils

Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.

Solid-state NMR as a probe of amyloid fibril structure

Amyloid fibrils are intrinsically noncrystalline, insoluble, high-molecular-weight aggregates of peptides and proteins, with considerable biomedical and biophysical significance. Solid-state NMR techniques are uniquely capable of providing high-resolution, site-specific structural constraints for amyloid fibrils, at the level of specific interatomic distances and torsion angles. So far, a relatively small number of solid-state NMR studies of amyloid fibrils have been reported. These have addressed issues about the supramolecular organization of beta-sheets in the fibrils and the peptide conformation in the fibrils, and have concentrated on the beta-amyloid peptide of Alzheimer's disease. Many additional applications of solid-state NMR to amyloid fibrils from a variety of sources are anticipated in the near future, as these systems are ideally suited for the technique and are of widespread current interest.