Distance measurements in nucleic acids using windowless dipolar recoupling solid state NMR

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.

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.

Dipolar truncation in magic-angle spinning NMR recoupling experiments

Quantitative solid-state NMR distance measurements in strongly coupled spin systems are often complicated due to the simultaneous presence of multiple noncommuting spin interactions. In the case of zeroth-order homonuclear dipolar recoupling experiments, the recoupled dipolar interaction between distant spins is attenuated by the presence of stronger couplings to nearby spins, an effect known as dipolar truncation. In this article, we quantitatively investigate the effect of dipolar truncation on the polarization-transfer efficiency of various homonuclear recoupling experiments with analytical theory, numerical simulations, and experiments. In particular, using selectively (13)C-labeled tripeptides, we compare the extent of dipolar truncation in model three-spin systems encountered in protein samples produced with uniform and alternating labeling. Our observations indicate that while the extent of dipolar truncation decreases in the absence of directly bonded nuclei, two-bond dipolar couplings can generate significant dipolar truncation of small, long-range couplings. Therefore, while alternating labeling alleviates the effects of dipolar truncation, and thus facilitates the application of recoupling experiments to large spin systems, it does not represent a complete solution to this outstanding problem.

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.

Homonuclear and Heteronuclear NMR Studies of a Statherin Fragment Bound to Hydroxyapatite Crystals

Acidic proteins found in mineralized tissues act as nature's crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), Ca10(PO4)6(OH)2, the main mineral component of bone and teeth. Key to understanding the structural basis of protein-crystal recognition and protein control of hard tissue growth is the nature of interactions between the protein side chains and the crystal surface. In an earlier work we have measured the proximity of the lysine (K6) side chain in an SN-15 peptide fragment of the salivary protein statherin adsorbed to the Phosphorus-rich surface of HAP using solid-state NMR recoupling experiments. 15N{31P} rotational echo double resonance (REDOR) NMR data on the side-chain nitrogen in K6 gave rise to three different models of protein-surface interaction to explain the experimental data acquired. In this work we extend the analysis of the REDOR data by examining the contribution of interactions between surface phosphorus atoms to the observed 15N REDOR decay. We performed 31P-31P recoupling experiments in HAP and (NH4)2HPO4 (DHP) to explore the nature of dipolar coupled 31P spin networks. These studies indicate that extensive networks of dipolar coupled 31P spins can be represented as stronger effective dipolar couplings, the existence of which must be included in the analysis of REDOR data. We carried out 15N{31P} REDOR in the case of DHP to determine how the size of the dephasing spin network influences the interpretation of the REDOR data. Although use of an extended 31P coupled spin network simulates the REDOR data well, a simplified 31P dephasing system composed of two spins with a larger dipolar coupling also simulates the REDOR data and only perturbs the heteronuclear couplings very slightly. The 31P-31P dipolar couplings between phosphorus nuclei in HAP can be replaced by an effective dipolar interaction of 600 Hz between two 31P spins. We incorporated this coupling and applied the above approach to reanalyze the 15N{31P} REDOR of the lysine side chain approaching the HAP surface and have refined the binding models proposed earlier. We obtain 15N-31P distances between 3.3 and 5 A from these models that are indicative of the possibility of a lysine-phosphate hydrogen bond.

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.

Solid-state NMR structural studies of peptides immobilized on gold nanoparticles

In this paper we describe solid-state NMR experiments that provide information on the structures of surface-immobilized peptides. The peptides are covalently bound to alkanethiolates that are self-assembled as monolayers on colloidal gold nanoparticles. The secondary structure of the immobilized peptides was characterized by quantifying the Ramachandran angles phi and psi. These angles were determined in turn from distances between backbone carbonyl 13C spins, measured with the double-quantum filtered dipolar recoupling with a windowless sequence experiment, and by determination of the mutual orientation of chemical shift anisotropy tensors of 13C carbonyl spins on adjacent peptide planes, obtained from the double-quantum cross-polarization magic-angle spinning spectrum. It was found that peptides composed of periodic sequences of leucines and lysines were bound along the length of the peptide sequence and displayed a tight alpha-helical secondary structure on the gold nanoparticles. These results are compared to similar studies of peptides immobilized on hydrophobic surfaces.

Structural studies of biomaterials using double-quantum solid-state NMR spectroscopy

Proteins directly control the nucleation and growth of biominerals, but the details of molecular recognition at the protein-biomineral interface remain poorly understood. The elucidation of recognition mechanisms at this interface may provide design principles for advanced materials development in medical and ceramic composites technologies. Here, we describe both the theory and practice of double-quantum solid-state NMR (ssNMR) structure-determination techniques, as they are used to determine the secondary structures of surface-adsorbed peptides and proteins. In particular, we have used ssNMR dipolar techniques to provide the first high-resolution structural and dynamic characterization of a hydrated biomineralization protein, salivary statherin, adsorbed to its biologically relevant hydroxyapatite (HAP) surface. Here, we also review NMR data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules using double-quantum ssNMR spectroscopy.

A study of homonuclear dipolar recoupling pulse sequences in solid-state nuclear magnetic resonance

Dipolar recoupling pulse sequences are of great importance in magic angle spinning solid-state NMR. Recoupling sequences are used for excitation of double-quantum coherence, which, in turn, is employed in experiments to estimate internuclear distances and molecular torsion angles. Much effort is spent on the design of recoupling sequences that are able to produce double-quantum coherence with high efficiency in demanding spin systems, i.e., spin systems with small dipole-dipole couplings and large chemical-shift anisotropies (CSAs). The sequence should perform robustly under a variety of experimental conditions. This paper presents experiments and computer calculations that extend the theory of double-quantum coherence preparation from the strong coupling/small CSA limit to the weak coupling limit. The performance of several popular dipole-dipole recoupling sequences-DRAWS, POST-C7, SPC-5, R1, and R2-are compared. It is found that the optimum performance for several of these sequences, in the weak coupling/large CSA limit, varies dramatically, with respect to the sample spinning speed, the magnitude and orientation of the CSAs, and the magnitude of dipole-dipole couplings. It is found that the efficiency of double-quantum coherence preparation by gamma-encoded sequences departs from the predictions of first-order theory. The discussion is supported by density-matrix calculations.

Assembly of alpha-helical peptide coatings on hydrophobic surfaces

The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules. Here we present data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. Small linear peptides composed of alternating leucine and lysine residues were synthesized, and their adsorption onto porous polystyrene surfaces was studied using a combination of solid-state NMR techniques. Using conventional solid-state NMR experiments and newly developed double-quantum techniques, their helical structure was verified. Large-amplitude dynamics on the NMR time scale were not observed, suggesting irreversible adsorption of the peptides. Their association, adsorption, and structure were examined as a function of helix length and sequence periodicity, and it was found that, at higher solution concentrations, peptides as short as seven amino acids adsorb with defined secondary structures. Two-dimensional double-quantum experiments using (13)C-enriched peptide sequences allow high-resolution determination of secondary structure in heterogeneous environments where the peptides are a minor component of the material. These results shed light on how polymeric surfaces may be surface-modified by structured peptides and demonstrate the level of molecular structural and dynamic information solid-state NMR can provide.

Estimation of carbon-carbon bond lengths and medium-range internuclear distances by solid-state nuclear magnetic resonance

We describe magic-angle-spinning NMR methods for the accurate determination of internuclear dipole-dipole couplings between homonuclear spins-(1/2) in the solid state. The new sequences use symmetry principles to treat the effect of magic-angle sample-rotation and resonant radio frequency fields. The pulse-sequence symmetries generate selection rules which reduce the interference of undesirable interactions and improve the robustness of the pulse sequences with respect to chemical shift anisotropies. We show that the pulse sequences may be used to estimate distances between 13C spins in organic solids, including bond lengths in systems with large chemical shift anisotropies, such as conjugated systems. For bond-length measurements, the precision of the method is +/-2 pm with a systematic overestimate of the internuclear distance by 3 +/- 1 pm. The method is expected to be a useful tool for investigating structural changes in macromolecules.

Modeling furanose ring dynamics in DNA

Determination of the conformational flexibility of the furanose ring is of vital importance in understanding the structure of DNA. In this work we have applied a model of furanose ring motion to the analysis of deuterium line shape data obtained from sugar rings in solid hydrated DNA. The model describes the angular trajectories of the atoms in the furanose ring in terms of pseudorotation puckering amplitude (q) and the pseudorotation puckering phase phi. Fixing q, the motion is thus treated as Brownian diffusion through an angular-dependent potential U(phi). We have simulated numerous line shapes varying the adjustable parameters, including the diffusion coefficient D, pseudorotation puckering amplitude q, and the form of the potential U(phi). We have used several forms of the potential, including equal double-well potentials, unequal double-well potentials, and a potential truncated to "second order" in the Fourier series. To date, we have obtained best simulations for both equilibrium and nonequilibrium (partially relaxed) solid-state deuterium NMR line shapes for the sample [2' '-2H]-2'-deoxycytidine at the position C3 (underlined) in the DNA sequence [d(CGCGAATTCGCG)]2, using a double-well potential with an equal barrier height of U(0) = 5.5k(B)T ( approximately 3.3 kcal/mol), a puckering amplitude of q = 0.4 A, and a diffusion coefficient characterizing the underlying stochastic jump rate D = 9.9 x 10(8) Hz. Then the rate of flux for the C-D bond over the barrier, i.e., the escape velocity or the overall rate of puckering between modes, was found to be 0.7 x 10(7) Hz.

Review: model peptides and the physicochemical approach to beta-amyloids

beta-Amyloid peptides are the main protein components of neuritic plaques and may be important in the pathogenesis of Alzheimer's Disease. The determination of the structure of beta-amyloid fibrils poses a challenge because of the limited solubility of beta-amyloid peptides and the noncrystalline nature of fibrils formed from these peptides. In this paper, we describe several physicochemical approaches which have been used to examine fibrils and the fibrillogenesis of peptide models of beta-amyloid. Recent advances in solid state NMR, such as the DRAWS pulse sequence, have made this approach a particularly attractive one for peptides such as beta-amyloid, which are not yet amenable to high-resolution solution phase NMR and crystallography. The application of solid state NMR techniques has yielded information on a model peptide comprising residues 10-35 of human beta-amyloid and indicates that in fibrils, this peptide assumes a parallel beta-strand conformation, with all residues in exact register. In addition, we discuss the use of block copolymers of Abeta peptides and polyethylene glycol as probes for the pathways of fibrillogenesis. These methods can be combined with other new methods, such as high-resolution synchrotron X-ray diffraction and small angle neutron and X-ray scattering, to yield structural data of relevance not only to disease, but to the broader question of protein folding and self-assembly.

Two-dimensional structure of beta-amyloid(10-35) fibrils

Beta-amyloid (Abeta) peptides are the main protein component of the pathognomonic plaques found in the brains of patients with Alzheimer's disease. These heterogeneous peptides adopt a highly organized fibril structure both in vivo and in vitro. Here we use solid-state NMR on stable, homogeneous fibrils of Abeta(10-35). Specific interpeptide distance constraints are determined with dipolar recoupling NMR on fibrils prepared from a series of singly labeled peptides containing (13)C-carbonyl-enriched amino acids, and skipping no more that three residues in the sequence. From these studies, we demonstrate that the peptide adopts the structure of an extended parallel beta-sheet in-register at pH 7.4. Analysis of DRAWS data indicates interstrand distances of 5.3 +/- 0.3 A (mean +/- standard deviation) throughout the entire length of the peptide, which is compatible only with a parallel beta-strand in-register. Intrastrand NMR constraints, obtained from peptides containing labels at two adjacent amino acids, confirm the secondary structural findings obtained using DRAWS. Using peptides with (13)C incorporated at the carbonyl position of adjacent amino acids, structural transitions from alpha-helix to beta-sheet were observed at residues 19 and 20, but using similar techniques, no evidence for a turn could be found in the putative turn region comprising residues 25-29. Implications of this extended parallel organization for Abeta(10-35) for overall fibril formation, stability, and morphology based upon specific amino acid contacts are discussed.

Dipolar recoupling NMR of biomolecular self-assemblies: determining inter- and intrastrand distances in fibrilized Alzheimer's beta-amyloid peptide

We demonstrate a new method for investigating the structure of self-associating biopolymers using dipolar recoupling NMR techniques. This approach was applied to the study of fibrillar beta-amyloid (Abeta) peptides (the primary component of the plaques of Alzheimer's disease) containing only a single isotopic spin label (13C), by employing the DRAWS (dipolar recoupling with a windowless sequence) technique to measure 13C-13C distances. The 'single-label' approach simplified analysis of DRAWS data, since only interstrand contacts are present, without the possibility of any intrastrand contacts. As previously reported [T.L.S. Benzinger, D.M. Gregory, T.S. Burkoth, H. Miller-Auer, D.G. Lynn, R.E. Botto, S.C. Meredith, Proc. Natl. Acad. Sci. 95 (1998) 13407.], contacts of approximately 5 A were observed at all residues studied, consistent with an extended parallel beta-sheet structure with each amino acid in exact register. Here, we propose that our strategy is completely generalizable, and provides a new approach for characterizing any iterative, self-associating biopolymer. Towards the end of generalizing and refining our approach, in this paper we evaluate several issues raised by our previous analyses. First, we consider the effects of double-quantum (DQ) transverse relaxation processes. Next, we discuss the effects of various multiple-spin geometries on modeling of DRAWS data. Several practical issues are also discussed: these include (1) the use of DQ filtering experiments, either to corroborate DRAWS data, or as a rapid screening assessment of the proper placement of isotopic spin labels; and (2) the comparison of solid samples prepared by either lyophilization or freezing. Finally, data obtained from the use of single labels is compared with that obtained in doubly 13C-labeled model compounds of known crystal structure. It is shown that such data are obtainable in far more complex peptide molecules. These data,taken together, refine the DRAWS method, and demonstrate its precision and utility in obtaining high resolution structural data in complex biomolecular aggregates such as Abeta.

Propagating structure of Alzheimer's beta-amyloid(10-35) is parallel beta-sheet with residues in exact register

The pathognomonic plaques of Alzheimer's disease are composed primarily of the 39- to 43-aa beta-amyloid (Abeta) peptide. Crosslinking of Abeta peptides by tissue transglutaminase (tTg) indicates that Gln15 of one peptide is proximate to Lys16 of another in aggregated Abeta. Here we report how the fibril structure is resolved by mapping interstrand distances in this core region of the Abeta peptide chain with solid-state NMR. Isotopic substitution provides the source points for measuring distances in aggregated Abeta. Peptides containing a single carbonyl 13C label at Gln15, Lys16, Leu17, or Val18 were synthesized and evaluated by NMR dipolar recoupling methods for the measurement of interpeptide distances to a resolution of 0.2 A. Analysis of these data establish that this central core of Abeta consists of a parallel beta-sheet structure in which identical residues on adjacent chains are aligned directly, i. e., in register. Our data, in conjunction with existing structural data, establish that the Abeta fibril is a hydrogen-bonded, parallel beta-sheet defining the long axis of the Abeta fibril propagation.

A peptide that inhibits hydroxyapatite growth is in an extended conformation on the crystal surface

Proteins play an important role in the biological mechanisms controlling hard tissue development, but the details of molecular recognition at inorganic crystal interfaces remain poorly characterized. We have applied a recently developed homonuclear dipolar recoupling solid-state NMR technique, dipolar recoupling with a windowless sequence (DRAWS), to directly probe the conformation of an acidic peptide adsorbed to hydroxyapatite (HAP) crystals. The phosphorylated hexapeptide, DpSpSEEK (N6, where pS denotes phosphorylated serine), was derived from the N terminus of the salivary protein statherin. Constant-composition kinetic characterization demonstrated that, like the native statherin, this peptide inhibits the growth of HAP seed crystals when preadsorbed to the crystal surface. The DRAWS technique was used to measure the internuclear distance between two 13C labels at the carbonyl positions of the adjacent phosphoserine residues. Dipolar dephasing measured at short mixing times yielded a mean separation distance of 3.2 +/- 0.1 A. Data obtained by using longer mixing times suggest a broad distribution of conformations about this average distance. Using a more complex model with discrete alpha-helical and extended conformations did not yield a better fit to the data and was not consistent with chemical shift analysis. These results suggest that the peptide is predominantly in an extended conformation rather than an alpha-helical state on the HAP surface. Solid-state NMR approaches can thus be used to determine directly the conformation of biologically relevant peptides on HAP surfaces. A better understanding of peptide and protein conformation on biomineral surfaces may provide design principles useful for the modification of orthopedic and dental implants with coatings and biological growth factors that are designed to enhance biocompatibility with surrounding tissue.

High resolution and high fields in biological solid state NMR

2H solid state NMR spectra of a polypeptide in an oriented membrane environment is demonstrated to have an orientational resolution of 0.3 degree. Such data results in high resolution structural constraints. Similar spectra are demonstrated at 23.2 T using a resistive magnet at the National High Magnetic Field Laboratory.