Long-Range Distance Measurements of Protein Binding Sites by Rotational-Echo Double-Resonance NMR

Solid-State NMR 19F-1H-15N Correlation Experiments for Resonance Assignment and Distance Measurements of Multifluorinated Proteins

Several solid-state NMR techniques have been introduced recently to measure nanometer distances involving 19F, whose high gyromagnetic ratio makes it a potent nuclear spin for structural investigation. These solid-state NMR techniques either use 19F correlation with 1H or 13C to obtain qualitative interatomic contacts or use the rotational-echo double-resonance (REDOR) pulse sequence to measure quantitative distances. However, no NMR technique is yet available for disambiguating 1H-19F distances in multiply fluorinated proteins and protein-ligand complexes. Here, we introduce a three-dimensional (3D) 19F-15N-1H correlation experiment that resolves the distances of multiple fluorines to their adjacent amide protons. We show that optimal polarization transfer between 1H and 19F spins is achieved using an out-and-back 1H-19F REDOR sequence. We demonstrate this 3D correlation experiment on the model protein GB1 and apply it to the multidrug-resistance transporter, EmrE, complexed to a tetrafluorinated substrate. This technique should be useful for resolving and assigning distance constraints in multiply fluorinated proteins, leading to significant savings of time and precious samples compared to producing several singly fluorinated samples. Moreover, the method enables structural determination of protein-ligand complexes for ligands that contain multiple fluorines.

Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy

Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.

From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR

Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional ¹³C and ¹⁵N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance ¹⁹F and ¹H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on ¹⁹F- and ¹H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.

Solid-state NMR studies of nucleic acid components

Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.

Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis ( Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.

Using solid-state 31P{19F} REDOR NMR to measure distances between a trifluoromethyl group and a phosphodiester in nucleic acids

REDOR is a solid-state NMR technique frequently applied to biological structure problems. Through incorporation of phosphorothioate groups in the nucleic acid backbone and mono-fluorinated nucleotides, 31P{19F} REDOR has been used to study the binding of DNA to drugs and RNA to proteins through the detection of internuclear distances as large as 13-14 A. In this work, 31P{19F} REDOR is further refined for use in nucleic acids by the combined use of selective placement of phosphorothioate groups and the introduction of nucleotides containing trifluoromethyl (-CF3) groups. To ascertain the REDOR-detectable distance limit between an unique phosphorous spin and a trifluoromethyl group and to assess interference from intermolecular couplings, a series of model compounds and DNA dodecamers were synthesized each containing a unique phosphorous label and trifluoromethyl group or a single 19F nucleus. The dipolar coupling constants of the various 31P and 19F or -CF3 containing compounds were compared using experimental and theoretical dephasing curves involving several models for intermolecular interactions.

Recognition of an unnatural difluorophenyl nucleotide by uracil DNA glycosylase

The DNA repair enzyme uracil DNA glycosylase (UDG) utilizes base flipping to recognize and remove unwanted uracil bases from the genome but does not react with its structural congener, thymine, which differs by a single methyl group. Two factors that determine whether an enzyme flips a base from the duplex are its shape and hydrogen bonding properties. To probe the role of these factors in uracil recognition by UDG, we have synthesized a DNA duplex that contains a single difluorophenyl (F) nucleotide analogue that is an excellent isostere of uracil but possesses no hydrogen bond donor or acceptor groups. By using binding affinity measurements, solution (19)F NMR, and solid state (31)P[(19)F] rotational-echo double-resonance (REDOR) NMR measurements, we establish that UDG partially unstacks F from the duplex. However, due to the lack of hydrogen bonding groups that are required to support an open-to-closed conformational transition in UDG, F cannot stably dock in the UDG active site. We propose that F attains a metastable unstacked state that mimics a previously detected intermediate on the uracil-flipping pathway and suggest structural models of the metastable state that are consistent with the REDOR NMR measurements.

Recent developments in solid-state magic-angle spinning, nuclear magnetic resonance of fully and significantly isotopically labelled peptides and proteins

In recent years, a large number of solid-state nuclear magnetic resonance (NMR) techniques have been developed and applied to the study of fully or significantly isotopically labelled ((13)C, (15)N or (13)C/(15)N) biomolecules. In the past few years, the first structures of (13)C/(15)N-labelled peptides, Gly-Ile and Met-Leu-Phe, and a protein, Src-homology 3 domain, were solved using magic-angle spinning NMR, without recourse to any structural information obtained from other methods. This progress has been made possible by the development of NMR experiments to assign solid-state spectra and experiments to extract distance and orientational information. Another key aspect to the success of solid-state NMR is the advances made in sample preparation. These improvements will be reviewed in this contribution. Future prospects for the application of solid-state NMR to interesting biological questions will also briefly be discussed.

Characterization of the Complex of a Trifluoromethyl-Substituted Shikimate-Based Bisubstrate Inhibitor and 5-Enolpyruvylshikimate-3-phosphate Synthase by REDOR NMR

A combination of (15)N[(19)F], (31)P[(15)N], and (31)P[(19)F] rotational-echo double-resonance NMR has been used to characterize the conformation of a bound trifluoromethylketal, shikimate-based bisubstrate inhibitor of 5-enolpyruvylshikimate-3-phosphate synthase. The solid-state NMR experiments were performed on the complex formed in solution and then lyophilized at low temperatures in the presence of stabilizing lyoprotectants. The results of these experiments indicate that none of the side chains of the six arginines that surround the active site forms a compact salt bridge with the phosphate groups of the bound inhibitor.

Frozen-solution conformational analysis by REDOR spectroscopy

Frozen-solution conformational analysis (FrSCA) can be performed on organic compounds using REDOR spectroscopy. REDOR measurements on frozen aqueous solutions of 13C-methyl beta-15N-aminoglucoside indicate a bimodal distribution of conformations in a 68:32 ratio, with 13C-15N distances of 4.31 and 3.55 A, respectively. The high resolution and straightforward sample preparation make FrSCA an attractive alternative to solution-based NMR methods of conformational analysis.

Conformation of a bound inhibitor of blood coagulant factor Xa

13C[(15)N] and (13)C[(19)F] rotational-echo double-resonance NMR have been used to characterize the enzyme-bound structure of ZK-816042, an amidine-imidazoline inhibitor of human factor Xa (FXa). The NMR experiments were performed on a lyophilized FXa-inhibitor complex. The complex was formed in solution in the presence of stabilizing excipients and frozen after gradual supercooling prior to lyophilization. The results indicate that the inhibitor binds with a distribution of orientations of the imidazoline ring.

REDOR with a relative full-echo reference

REDOR and REDOR-like 13C[19F] and 2H[19F] NMR experiments have been performed on lyophilized whole cells of Staphylococcus aureus. The bacteria were grown to maturity on media containing L-[13C(3)]alanine or L-[methyl-d(3)]alanine, and then complexed with the 4-fluorobiphenyl derivative of chloroeremomycin, an analogue of the widely used antibiotic, vancomycin. The position of the 19F of the drug bound in the bacterial cell wall was determined relative to L-alanine 13C and 2H labels in the peptidoglycan peptide stem that was closest to the fluorinated biphenyl moiety of the drug. These determinations were made by dipolar recoupling methods that do not require an absolute measurement of the REDOR full echo (the signal observed without rotor-synchronized dephasing pulses) of the labels in the peptide stem.

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.

Band-selective recoupling of homonuclear double-quantum dipolar interaction with a generalized composite 0 degrees pulse: application to 13C aliphatic region-selective magnetization transfer in solids

Recoupling of homonuclear double quantum (DQ)-dipolar interactions is a useful technique for the structural analysis of molecules in solids. We have designed a series of elemental 0 degrees pulses for the recoupling sequences with the rf phase rotation about the z-axis, known as CN. The proposed 0 degrees pulses whose total flip angle >/=360 degrees provide spin rotation vectors in the xy-plane. Thus, the residual spin rotation can be canceled by rf phase rotation about the z-axis. An analysis by the coherent averaging theory showed that effective bandwidths of the recoupling sequences are limited not by the reduction in the dipolar scaling factor but by the increase in the residual spin rotation due to offset. A CN sequence with these elemental pulses provides an effective bandwidth of DQ-dipolar recoupling from ca. 0.5nu(R) to 4nu(R) for numerical simulations. Here, nu(R) is the sample spinning frequency. The 0 degrees pulses were applied to band-selective recoupling for the magnetization transfer in uniformly 13C-labeled molecules. Narrow-band recoupling enhances the magnetization transfer between spins within the effective range by decoupling the dipolar interactions between spins one of which is outside the range. The narrow band operation reduces rf field strength, which improves the CH decoupling. Increases in signal intensities by the use of the proposed 0 degrees pulses are experimentally shown for 13C-labeled amino acids.

Incorporation of 2'-deoxy-5-(trifluoromethyl)uridine and 5-cyano-2'-deoxyuridine into DNA

In an attempt to synthesize DNA containing 2'-deoxy-5-(trifluoromethyl)uridine (1) using previously published protocols, we found that the trifluoromethyl group converted into a cyano group, resulting in DNA containing 5-cyano-2'-deoxyuridine (3). We show that nucleoside 1 can be incorporated into DNA using phosphoramidite 2 in combination with acetyl-protected deoxycytidine and phenoxyacetyl-protected purine phosphoramidites. Replacing thymidine in DNA with 1 caused a slight decrease in DNA duplex stability at pH 6.9.

Measurement of interfluorine distances in solids

(19)F homonuclear dipolar recoupling methods were used to measure internuclear distances ranging from 5 to 12 A in fluorinated organic compounds in the solid state. Magic-angle-spinning-based high-resolution techniques were utilized. Trifluoromethyl and aromatic fluorine groups were separated by rigid aromatic spacers; these compounds were diluted into nonfluorinated host molecule matrices to give isolated homonuclear spin pairs with known internuclear distances. Radiofrequency-driven recoupling (RFDR) was used to elicit magnetization exchange between the spin pairs in 1D and 2D experiments. Simulation of the exchange was accomplished using a Monte Carlo-type algorithm to search the parameter space. These methods allow the determination of distances with an accuracy of 1 A at shorter distances and 2 A at longer distances, with the assumption of no prior knowledge of T(2)(ZQ).

Site-directed solid-state NMR measurement of a ligand-induced conformational change in the serine bacterial chemoreceptor

The challenging nature of studies of membrane proteins has made it difficult to determine the molecular mechanism of transmembrane signaling. For the bacterial chemoreceptor family, there are crystal structures of the internal and external domains, structural models of the transmembrane domain, and evidence for subtle ligand-induced conformational changes, but the signaling mechanism remains controversial. We have used a novel site-directed solid-state NMR distance measurement approach, using (13)C(19)F REDOR, to measure a ligand-induced change of 1.0 +/- 0.3 A in the distance between helices alpha 1 and alpha 4 of the ligand-binding domain in the intact, membrane-bound serine receptor. This distance change is shown not to be due to motion of the side chain and thus is due to motion of either the alpha 1 or the alpha 4 helix. Additional distance measurements can be used to determine the type of backbone motion and to follow it to the cytoplasm, to test and refine current proposals for the mechanism of transmembrane signaling. This is a promising general method for high-resolution measurements of local structure in intact, membrane-bound proteins.

Orientation-dependent (19)F dipolar couplings within a trifluoromethyl group are revealed by static multipulse NMR in the solid state

The homonuclear dipolar coupling between the three equivalent (19)F-spins of a trifluoromethyl group, rotating about its threefold symmetry axis, was studied by multipulse solid-state NMR. A modified CPMG sequence was used first to resolve the dipolar splitting of a powder sample, and then to follow its orientation-dependence in uniaxially aligned samples. Our aim is to employ the CF(3)-group as a highly sensitive reporter to describe the mobility and spacial alignment of (19)F-labeled molecules in biomembranes. As an example, the fluorinated anti-inflammatory drug, flufenamic acid, was embedded as a guest compound in lipid bilayers. Undistorted (19)F dipolar spectra of its CF(3)-group were obtained without (1)H-decoupling, revealing a sharp triplet lineshape. When an oriented membrane sample was tilted in the magnetic field, the change in dipolar splittings confirmed that the guest molecule is motionally averaged about the membrane normal, as expected. A different behavior of flufenamic acid, however, was observed under conditions of low bilayer hydration. From this set of orientation-dependent lineshapes we conclude that the axis of motional averaging becomes aligned perpendicular to the sample normal. It thus appears that flufenamic acid induces a hexagonal phase in the membrane at low hydration. Finally, the dipolar (19)F NMR experiments were extended to frozen samples, where no molecular diffusion occurs besides the fast rotation about the CF(3)-axis. Also under these conditions, the CPMG experiment with composite pulses could successfully resolve the dipolar coupling between the three (19)F-nuclei.

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.

Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain

Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid alpha-spectrin SH3 domain were generated in four different ways, and their (13)C CPMAS spectra were compared. The spectrum of a [u-(13)C, (15)N]-labeled sample generated by precipitation shows very narrow (13)C signals and resolved scalar carbon-carbon couplings. Linewidths of 16-19 Hz were found for the three alanine C(beta )signals of a selectively labeled [70% 3-(13)C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D (13)C-(13)C RFDR spectra of the [u-(13)C, (15)N]-labeled SH3 sample. A comparison of the (13)C chemical shifts of the found signal patterns with the (13)C assignment obtained in solution shows an intriguing match.

Lysine 22 in UDP-N-acetylglucosamine enolpyruvyl transferase from Enterobacter cloacae is crucial for enzymatic activity and the formation of covalent adducts with the substrate phosphoenolpyruvate and the antibiotic fosfomycin

UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) catalyzes the first committed step in the biosynthesis of the bacterial cell wall component peptidoglycan. The enzyme is the target of the antibiotic fosfomycin. A lysine residue (K22), strictly conserved in MurAs and the structurally and mechanistically related 5-enolpyruvylshikimate 3-phosphate synthases (EPSPS), is located near the active center of the enzyme. This residue is thought to be involved directly in the binding of the substrate phosphoenolpyruvate (PEP) and also to participate in the conformational change leading to the formation of the catalytically competent enzyme complex. Using site-directed mutagenesis, we have replaced this lysine with arginine (K22R), valine (K22V), and glutamate (K22E). These mutant proteins were expressed, purified, and characterized in comparison to wild-type MurA and a previously described inactive C115S mutant protein. It was found that all three K22 mutant proteins had less than 0.5% of the wild-type activity. Using isothermal titration calorimetry, it could be shown that the binding parameters for the UDP-sugar nucleotide substrate are not affected by the mutations, except for the K22E mutant protein. Similarly, binding of PEP was found to be unaffected in the K22 mutant proteins as demonstrated by tryptophan fluorescence quench titrations. On the other hand, the level of formation of a covalent adduct with either PEP or fosfomycin with the thiol group of cysteine 115 was diminished. The propensity to form an adduct with PEP decreased in the following order: wild type >> K22R > K22V > K22E. A comparable effect was found on the formation of the inhibitory covalent adduct of MurA and the antibiotic fosfomycin. These results are discussed in terms of an involvement of lysine 22 in a conformational change of MurA.

Substrate and inhibitor-induced conformational changes in the structurally related enzymes UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS)

UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) have both a unique three-dimensional topology and overall reaction mechanism in common. In the case of MurA, the substrate-free, unliganded protein exhibits an "open" conformation. Upon binding of substrates, the protein forms a much more tightly packed so-called "closed" form following an induced fit mechanism. In this closed form, the substrates are properly positioned for catalysis. On the basis of the structural and mechanistic similarities of MurA and EPSPS, a similar conformational change is likely to occur in EPSPS to generate a catalytically competent active site. However, there is currently little experimental evidence available to support the occurrence of such a conformational change in EPSPS. Using limited tryptic digestion of MurA,(1) it could be shown that formation of the "closed" conformation of MurA is accompanied by a marked increase of stability toward proteolytic degradation. Formation of the closed conformation was achieved by addition of either an excess of both substrates or the sugar nucleotide substrate in conjunction with the antibiotic fosfomycin. Analysis of the MurA tryptic fragments by MALDI-TOF mass spectrometry demonstrates that the protection of the protein in either case is caused by (1) a specific shielding of regions thereby becoming less accessible as a result of the conformational change, and (2) an unspecific overall protection of the whole protein due to an apparently reduced flexibility of the peptide backbone in the binary and ternary complexes. The establishment of methods to describe the effects of tryptic digestion on MurA under various conditions was then extended to EPSPS. Although EPSPS was found to be much more stable toward proteolysis than MurA, the presence of shikimate 3-phosphate (S3P) and the inhibitor glyphosate led to a pronounced suppression of proteolytic degradation. When unliganded EPSPS was treated with trypsin, three of the peptide fragments obtained could be identified by mass spectrometry. Two of these are located in a region corresponding to the "catalytic" loop in MurA which participates in the conformational change. This indicates a conformational change in EPSPS, similar to the one observed in MurA, leading to the protection mentioned above. Corroborating evidence was obtained using a conformational sensitive monoclonal antibody against EPSPS which showed a 20-fold reduced affinity toward the protein complexed with S3P and glyphosate as compared to the unliganded enzyme.

THE SHIKIMATE PATHWAY

The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven metabolic steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, the precursor of the aromatic amino acids and many aromatic secondary metabolites. All pathway intermediates can also be considered branch point compounds that may serve as substrates for other metabolic pathways. The shikimate pathway is found only in microorganisms and plants, never in animals. All enzymes of this pathway have been obtained in pure form from prokaryotic and eukaryotic sources and their respective DNAs have been characterized from several organisms. The cDNAs of higher plants encode proteins with amino terminal signal sequences for plastid import, suggesting that plastids are the exclusive locale for chorismate biosynthesis. In microorganisms, the shikimate pathway is regulated by feedback inhibition and by repression of the first enzyme. In higher plants, no physiological feedback inhibitor has been identified, suggesting that pathway regulation may occur exclusively at the genetic level. This difference between microorganisms and plants is reflected in the unusually large variation in the primary structures of the respective first enzymes. Several of the pathway enzymes occur in isoenzymic forms whose expression varies with changing environmental conditions and, within the plant, from organ to organ. The penultimate enzyme of the pathway is the sole target for the herbicide glyphosate. Glyphosate-tolerant transgenic plants are at the core of novel weed control systems for several crop plants.

Multiple-quantum relaxation in the magic-angle-spinning NMR of 13C spin pairs

We determine the decay rate constants of zero-, double- and single-quantum coherence for 13C spin pairs in magic-angle-spinning solid-state NMR. The double-quantum coherence is excited by a C7 pulse sequence and converted into zero-quantum coherence by a frequency-selective pair of pi/2 pulses. The zero-quantum coherence is reconverted into observable magnetization by a second pair of pi/2 pulses followed by a second C7 sequence. In a magnetically dilute system where the 13C-13C distance is 0.296 nm, the relaxation rate constants are consistent with a model of uncorrelated random fields at the two labeled 13C sites. In a fully-labelled system with a short 13C-13C distance of 0.153 nm, the measured rate constants are inconsistent with the uncorrelated random field model.

Structural parameters from 19F homonuclear dipolar couplings, obtained by multipulse solid-state NMR on static and oriented systems

Local macromolecular structure can be determined by solid-state NMR measurements of weak dipolar couplings between selectively labeled groups. The nonperturbing use of 2H, 13C, or 15N in biological systems, however, faces drawbacks in terms of a low sensitivity and a comparatively short distance range relative to 1H. To extend these limitations, we illustrate the use of 19F as an alternative NMR probe. The Carr-Purcell-Meiboom-Gill (CPMG) multipulse sequence was adapted here to measure homonuclear dipolar couplings between two fluorine labels in static samples at 470 MHz. Two lipids (4, 4-DMPC-F2, and a difluorinated sterol), which are arranged in liquid crystalline bilayers, serve as models to assess the scope of the technique. In these 19F-background-free biological samples, weak couplings down to 100 Hz could be resolved directly from the splitting of the pure dipolar powder lineshape, and 1H-decoupling was not required. Order parameters were determined for the anisotropic motion of the lipids, consistent with their expected behavior in the membrane. Besides measuring the distance-dependent term of the dipolar coupling in powder samples, we have also used oriented membranes to extract additional angular information from the dipolar anisotropy. The strategy presented here thus has the potential to obtain not only the internuclear distance between two labels, but also their angular orientation in the sample, provided the molecules are aligned as a membrane or a fiber.

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.

Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli

Site-directed incorporation of the amino acid analogue p-fluoro-phenylalanine (p-F-Phe) was achieved in Escherichia coli. A yeast suppressor tRNA(Phe)amber/phenylalanyl-tRNA synthetase pair was expressed in an analogue-resistant E. coli strain to direct analogue incorporation at a programmed amber stop codon in the DHFR marker protein. The programmed position was translated to 64-75% as p-F-Phe and the remainder as phenylalanine and lysine. Depending on the expression conditions, the p-F-Phe incorporation was 11-21-fold higher at the programmed position than the background incorporation at phenylalanine codons, showing high specificity of analogue incorporation. Protein expression yields of 8-12 mg/L of culture, corresponding to about two thirds of the expression level of the wild-type DHFR protein, are sufficient to provide fluorinated proteins suitable for 19F-NMR spectroscopy and other sample-intensive methods. The use of a nonessential "21st" tRNA/synthetase pair will permit incorporation of a wide range of analogues, once the synthetase specificity has been modified accordingly.

Slowed enzymatic turnover allows characterization of intermediates by solid-state NMR

EPSP (5-enolpyruvylshikimate-3-phosphate) synthase catalyzes condensation of shikimate 3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form EPSP, a precursor to the aromatic amino acids. S3P and [2-13C]POP were bound to mutant or wild type E. coli forms of the enzyme prior to lyophilization. CPMAS-echo and rotational-echo double-resonance (REDOR) NMR experiments, employing a slow catalytic EPSP synthase mutant and a long prelyophilization incubation interval, allowed our observation of the gradual formation of a strong 31P-13C coupling consistent with the well characterized tetrahedral intermediate. However, after shorter low temperature incubation intervals of substrates with mutant or wild-type enzymes, carbon CPMAS-echo NMR spectra showed the 13C label at 155 ppm, consistent with sp2 geometry of this carbon. REDOR revealed that the phosphorus of PEP was cleaved. However, phosphorus at a distance of 7.5 A was observed, due to the phosphate of a nearby bound S3P. Heating the sample allowed the reaction to progress, as shown by the diminution of the 155 ppm peak and growth of a peak at 108 ppm. The sp3 geometry implied by the 108 ppm peak strongly suggested formation of a S3P-PEP condensation product. REDOR indicated that phosphorus was still distant, but now only 6.1 (wild type) or 5.9 A (mutant) distant. We think that the early intermediates with peaks at 155 and 108 ppm are covalently bound to the enzyme. We also think that the tetrahedral intermediate that we observed was formed after product was generated.

Closed form of liganded glutamine-binding protein by rotational-echo double-resonance NMR

Rotational-echo double-resonance NMR has been used to determine internuclear distances in the complex of glutamine-binding protein and its ligand, l-glutamine. The distances between the ligand and Tyr185 are consistent with the results of molecular dynamics simulations constrained by three REDOR-determined distances to His156. This model is also consistent with six other REDOR-determined internuclear distances, most of which agree with values from the first report of an X-ray structure of the complex of glutamine-binding protein and l-glutamine.

REDOR dephasing by multiple spins in the presence of molecular motion

Closed-form, numerical algorithms are presented for calculating REDOR dephasing for three general cases: (i) collections of isolated I-S spin pairs; (ii) many S spins coupled to an I spin; and (iii) an I-S spin pair in relative motion. For the case when more than one S spin is dipolar coupled to an I spin, the calculation assumes that the S-S homonuclear interaction does not affect REDOR dephasing. Full numerical simulations show that this assumption is true if the S-spin lineshapes are inhomogeneously broadened, the S-spin chemical shifts are far from rotational resonance, and a version of REDOR is used which minimizes the number of S-spin pi pulses. For the rapidly rotating -CF3 group of poly(trifluoroethyl methacrylate), the formalisms of (ii) and (iii) are combined to calculate the dephasing. The experimentally measured dephasing matches theory when the wiggling motion of the -OCH2CF3 moiety of the polymer is taken into account.

Distance between phosphine-sulfide sidechains of a disubstituted peptide by DRAMA 31P NMR

Dipolar restoration at the magic angle (DRAMA) has been used to measure the 31P-31P internuclear distance between phosphine-sulfide substituted sidechanins on the fourth and eighth residues of a 12-residue helical peptide. The 7.4 A distance is the same for the peptide lyophilized in bulk or isolated in a cryo- and lyoprotected matrix of poly(ethylene glycol) and sucrose. However, the 31P linewidth for the undiluted peptide is an order of magnitude greater than for the matrix-isolated peptide indicating charge and hydration heterogeneity in the bulk state.

Structural constraints on the complex of elongation factor Tu with magnesium guanosine diphosphate from rotational-echo double-resonance NMR

Rotational-echo, double-resonance (REDOR) NMR measurements of 31P-15N dipolar couplings have been made on a complex of Mg guanosine diphosphate (MgGDP) with uniformly 15N-labeled elongation factor Tu. The complex was embedded in a lyophilized buffer glass. The observed 15N REDOR dephasing by 31P was accounted for quantitatively by distances from 15N of Gly23 and Lys24 to P alpha and P beta of MgGDP as determined by X-ray crystallography of MgGDP complex formed using an elongation factor Tu that is missing a 15 residue loop in the vicinity of the binding site.

High-resolution NMR of biological solids

Solid-state NMR experiments have recently provided a number of biochemical insights: motionally averaged 2H lineshapes have shown that the motion of a backbone loop protecting a protein binding site is not ligand gated; isotropic 13C chemical shifts of freeze-quenched enzyme-ligand intermediates have revealed mechanistic details of reaction pathways; multiple heteronuclear distance determinations have characterized the binding-site geometry of a 46 kDa noncrystalline enzyme complex; and homonuclear recoupling experiments have established that insoluble amyloid fibrils form a pleated beta sheet.