Self-Assembled Supported Ionic Liquids

Separation and reuse of the catalytically active metal complexes are persistent issues in homogeneous catalysis. Supported Ionic Liquid Phase (SILP) catalysts, where the catalytic center is dissolved in a thin film of a stable ionic liquid, deposited on a solid support, present a promising alternative. However, the dissolution of the metal center in the film leaves little control over its position and its activity. We present here four novel, task-specific ionic liquids [FPhn ImH R]I (n=1, 2; R=PEG2 , C12 H25 ), designed to self-assemble on a silica surface without any covalent bonding and offering a metal binding site in a controlled distance to the support. Advanced multinuclear solid-state NMR spectroscopic techniques under Magic Angle Spinning, complemented by molecular dynamics (MD) simulations, allow us to determine their molecular conformation when deposited inside SBA-15 as a model silica support. We provide here conceptual proof for a rational design of ionic liquids self-assembling into thin films, opening an avenue for a second, improved generation of SILP catalysts.

Three Decades of REDOR in Protein Science: A Solid-State NMR Technique for Distance Measurement and Spectral Editing

Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of 1H-X dipolar couplings in recent years, the limit of measurable distances has reached ~15-20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems.

Cholesterol Modulates the Interaction between HIV-1 Viral Protein R and Membrane

Being a major metabolite for maintaining cellular homeostasis, as well as an important structural component in lipid membrane, cholesterol also plays critical roles in the life cycles of some viruses, including human immunodeficiency virus-1 (HIV-1). The involvement of cholesterol in HIV-1 infectivity, assembly and budding has made it an important research target. Viral protein R (Vpr) is an accessory protein of HIV-1, which is involved in many major events in the life cycle of HIV-1. In addition to its multi-functional roles in the HIV-1 life cycle, it is shown to interact with lipid membrane and form a cation-selective channel. In this work, we examined the effect of cholesterol on the interaction of Vpr and lipid membrane. Using calcein release assay, we found that the membrane permeability induced by the membrane binding of Vpr was significantly reduced in the presence of cholesterol in membrane. In addition, using solid-state NMR (ssNMR) spectroscopy, Vpr was shown to experience multiple chemical environments in lipid membrane, as indicated by the broad line shape of carbonyl 13C resonance of Cys-76 residue ranging from 165-178 ppm, which can be attributed to the existence of complex Vpr-membrane environments. We further showed that the presence of cholesterol in membrane will alter the distribution of Vpr in the complex membrane environments, which may explain the change of the Vpr induced membrane permeability in the presence of cholesterol.

Distance measurements to quadrupolar nuclei: Evolution of the rotational echo double resonance technique

Molecular structure determination is the basis for understanding chemical processes and the property of materials. The direct dependence of the magnetic dipolar interaction on the distance makes solid-state nuclear magnetic resonance (NMR) an excellent tool to study molecular structure when X-ray crystallography fails to provide atomic-resolution data. Although techniques to measure distances between pairs of isolated nuclear spin-1/2 pairs are routine and easy to implement using the rotational echo double resonance (REDOR) experiment (Gullion & Schaefer, 1989), the existence of a nucleus with a spin > 1/2, appearing in approximately 75% of the elements in the periodic table, poses a challenge due to difficulties stemming from the large nuclear quadrupolar coupling constant (QCC). This mini-review presents the existing solid-state magic-angle spinning NMR techniques aimed toward the efficient and accurate determination of internuclear distances between a spin-1/2 and a "quadrupolar" nucleus having a spin larger than one half. Analytical expressions are provided for the various recoupling curves stemming from different techniques, and a coherent nomenclature for these various techniques is suggested. Treatment of some special cases such as multiple spin effects and spins with close Larmor frequencies is also discussed. The most advanced methods can recouple spins with quadrupolar frequencies up to tens of megahertz and beyond, expanding the distance measurement capabilities of solid-state NMR to an increasingly growing number of applications and nuclear spin systems.

Dipolar dephasing for structure determination in a paramagnetic environment

We demonstrate the efficacy of the REDOR-type sequences in determining dipolar coupling strength in a paramagnetic environment. Utilizing paramagnetic effects of enhanced relaxation rates and rapid electronic fluctuations in Cu(II)-(DL-Ala)₂.H₂O, the dipolar coupling for the methyl C-H that is 4.20 ​Å (methyl carbon) away from the Cu²⁺ ion, was estimated to be 8.8 ​± ​0.6 ​kHz. This coupling is scaled by a factor of ~0.3 in comparison to the rigid limit value of ~32 ​kHz, in line with partial averaging of the dipolar interaction by rotational motion of the methyl group. Limited variation in the scaling factor of the dipolar coupling strength at different temperatures is observed. The C-H internuclear distance derived from the size of the dipolar coupling is similar to that observed in the crystal structure. The errors in the dipolar coupling strength observed in the REDOR-type experiments are similar to those reported for diamagnetic systems. Increase in resolution due to the Fermi contact shifts, coupled with MAS frequencies of 30-35 ​kHz allowed to estimate the hyperfine coupling strengths for protons and carbons from the temperature dependence of the chemical shift and obtain a high resolution ¹H-¹H spin diffusion spectrum. This study shows the utility of REDOR-type sequences in obtaining reliable structural and dynamical information from a paramagnetic complex. We believe that this can help in studying the active site of paramagnetic metalloproteins at high resolution.

Proton-detected solid-state NMR spectroscopy of spin-1/2 nuclei with large chemical shift anisotropy

Constant-time (CT) dipolar heteronuclear multiple quantum coherence (D-HMQC) has previously been demonstrated as a method for proton detection of high-resolution wideline NMR spectra of spin-1/2 nuclei with large chemical shift anisotropy (CSA). However, ¹H transverse relaxation and t₁-noise often reduce the sensitivity of D-HMQC experiments, preventing the theoretical gains in sensitivity provided by ¹H detection from being realized. Here we demonstrate a series of improved pulse sequences for ¹H detection of spin-1/2 nuclei under fast MAS, with ¹⁹⁵Pt SSNMR experiments on cisplatin as an example. First, a t₁-incrementation protocol for D-HMQC dubbed Arbitrary Indirect Dwell (AID) is demonstrated. AID allows the use of arbitrary, rotor asynchronous t₁-increments, but removes the constant time period from CT D-HMQC, resulting in improved sensitivity by reducing transverse relaxation losses. Next, we show that short high-power adiabatic pulses (SHAPs), which efficiently invert broad MAS sideband manifolds, can be effectively incorporated into ¹H detected symmetry-based resonance echo double resonance (S-REDOR) and t₁-noise eliminated (TONE) D-HMQC experiments. The S-REDOR experiments with SHAPs provide approximately double the dipolar dephasing, as compared to experiments with rectangular inversion pulses. We lastly show that sensitivity and resolution can be further enhanced with the use of swept excitation pulses as well as adiabatic magic angle turning (aMAT).

Selective 1H-14N Distance Measurements by 14N Overtone Solid-State NMR Spectroscopy at Fast MAS

Accurate distance measurements between proton and nitrogen can provide detailed information on the structures and dynamics of various molecules. The combination of broadband phase-modulated (PM) pulse and rotational-echo saturation-pulse double-resonance (RESPDOR) sequence at fast magic-angle spinning (MAS) has enabled the measurement of multiple 1H-14N distances with high accuracy. However, complications may arise when applying this sequence to systems with multiple inequivalent 14N nuclei, especially a single 1H sitting close to multiple 14N atoms. Due to its broadband characteristics, the PM pulse saturates all 14N atoms; hence, the single 1H simultaneously experiences the RESPDOR effect from multiple 1H-14N couplings. Consequently, no reliable H-N distances are obtained. To overcome the problem, selective 14N saturation is desired, but it is difficult because 14N is an integer quadrupolar nucleus. Alternatively, 14N overtone (OT) NMR spectroscopy can be employed owing to its narrow bandwidth for selectivity. Moreover, owing to the sole presence of two energy levels (m = ± 1), the 14N OT spin dynamics behaves similarly to that of spin-1/2. This allows the interchangeability between RESPDOR and rotational-echo double-resonance (REDOR) since their principles are the same except the degree of 14N OT population transfer; saturation for the former whereas inversion for the latter. As the ideal saturation/inversion is impractical due to the slow and orientation-dependent effective nutation of 14N OT, the working condition is usually an intermediate between REDOR and RESPDOR. The degree of 14N OT population transfer can be determined from the results of protons with short distances to 14N and then can be used to obtain long-distance determination of other protons to the same 14N site. Herein, we combine the 14N OT and REDOR/RESPDOR to explore the feasibility of selective 1H-14N distance measurements. Experimental demonstrations on simple biological compounds of L-tyrosine.HCl, N-acetyl-L-alanine, and L-alanyl-L-alanine were performed at 14.1 T and MAS frequency of 62.5 kHz. The former two consist of a single 14N site, whereas the latter consists of two 14N sites. The experimental optimizations and reliable fittings by the universal curves are described. The extracted 1H-14N distances by OT-REDOR are in good agreement with those determined by PM-RESPDOR and diffraction techniques.

Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations

HIV-1 entry into cells is mediated by the fusion protein gp41. Cholesterol plays an important role in this virus-cell fusion, but molecular structural information about cholesterol-gp41 interaction is so far absent. Here, we present experimental and computational data about cholesterol complexation with gp41 in lipid bilayers. We focus on the C-terminal region of the protein, which comprises a membrane-proximal external region (MPER) and the transmembrane domain (TMD). We measured peptide-cholesterol contacts in virus-mimetic lipid bilayers using solid-state NMR spectroscopy, and augmented these experimental data with all-atom molecular dynamics simulations. 2D 19F NMR spectra show correlation peaks between MPER residues and the cholesterol isooctyl tail, indicating that cholesterol is in molecular contact with the MPER-TMD trimer. 19F-13C distance measurements between the peptide and 13C-labeled cholesterol show that C17 on the D ring and C9 at the intersection of B and C rings are ~7.0 Å from the F673 side-chain 4-19F. At high peptide concentrations in the membrane, the 19F-13C distance data indicate three cholesterol molecules bound near F673 in each trimer. Mutation of a cholesterol recognition amino acid consensus motif did not change these distances, indicating that cholesterol binding does not require this sequence motif. Molecular dynamics simulations further identify two hotspots for cholesterol interactions. Taken together, these experimental data and simulations indicate that the helix-turn-helix conformation of the MPER-TMD is responsible for sequestering cholesterol. We propose that this gp41-cholesterol interaction mediates virus-cell fusion by recruiting gp41 to the boundary of the liquid-disordered and liquid-ordered phases to incur membrane curvature.

1H, 29Si and 119Sn double and triple resonance NMR spectroscopy of the small-pore framework sodium stannosilicate Na2SnSi3O9·2H2O

The small-pore framework sodium stannosilicate AV-10, chemical composition Na₂SnSi₃O₉·2H₂O and known crystallographic structure, was synthesized by hydrothermal crystallization. This stannosilicate is built up of a three-dimensional network of corner-shared SiO₄ tetrahedra and SnO₆ octahedra. The SnO₆ sites are linked to six SiO₄ tetrahedra (Sn(6Si)) while each of the two crystallographically different SiO₄ units are connected to two SnO₆ and SiO₄ units (Si(2Si,2Sn)). This material was used as model compound for developing a solid-state MAS NMR strategy aimed on the challenges and possibilities for structural studies, particularly considering the short and medium range order to verify the connectivity of SiO₄ and SnO₆ of such compounds despite the low natural abundances of 4.68% for ²⁹Si and 8.59% for ¹¹⁹Sn nuclei as a real challenge. ²⁹Si{¹¹⁹Sn} and ¹¹⁹Sn{²⁹Si} REDOR (Rotational-Echo Double-Resonance) NMR measurements after ¹H cross-polarization (CP) were carried out. The REDOR curves show a significant change after the "normal" quadratic short time evolution from which both (i) the shortest internuclear ²⁹Si - ¹¹⁹Sn distances (and vice versa) and (ii) the number of corner-sharing SiO₄ tetrahedra around the SnO₆ octahedra (and vice versa) can be obtained. Based on these data, optimized ²⁹Si{¹¹⁹Sn} and ¹¹⁹Sn{²⁹Si} REPT-HMQC (Recoupled Polarization Transfer-Heteronuclear Multiple-Quantum Correlation, again after ¹H CP) experiments were implemented, which directly show those heterogroup connectivity as correlation peaks in a 2D spectrum. This information was also obtained using 2D²⁹Si{¹¹⁹Sn}-J-Coupling NMR experiments. Furthermore, 2D²⁹Si INADEQUATE NMR experiments are also feasible, showing the connectivity of SiO₄ tetrahedra. The combination of REDOR, REPT-HMQC, J-Coupling and INADEQUATE experiments yielded a complete analysis of the short and medium range structure of this microporous stannosilicate, in agreement with the previously published structure obtained Ab Initio from powder X-Ray diffraction data (XRD).

On the direct relation between REDOR and DIPSHIFT experiments in solid-state NMR

Rotational-echo double resonance (REDOR) and Dipolar-coupling chemical-shift correlation (DIPSHIFT) are commonly used experiments to probe heteronuclear dipole-dipole couplings between isolated pairs of spin-12 nuclei in magic-angle-spinning (MAS) solid-state NMR. Their widespread use is due to their robustness to experimental imperfections and a straightforward interpretation of data. Both of these experiments use rotor-synchronised π pulses to recouple the heteronuclear dipole-dipole couplings, and the observed intensity of resonances is modulated by a recoupled phase factor depending on the position or duration of the recoupling pulses. Several modifications to both of these experiments have been proposed, for example, the development of DIPSHIFT which employs strategies that mimic the multi-rotor-period nature of REDOR. We show here that REDOR and DIPSHIFT are in fact alternate implementations of the same experiment. The overt similarity in the design of REDOR and DIPSHIFT is also reflected in their theoretical description. Dipolar dephasing curves in REDOR are obtained by increasing the recoupling duration whilst keeping the position of the pulses constant, which results in a dephasing factor that is a function of only the dephasing time. DIPSHIFT, on the other hand, is a constant-time version of REDOR; the dipolar dephasing is a function of the position of the pulses with respect to the rotor period. We discuss the advantages and disadvantages of each implementation and suggest domains of applicability for these sequences.

Perspectives on high-field and solid-state NMR methods of quadrupole nuclei

High magnetic field can dramatically increase the spectral resolution and sensitivity of quadrupole nuclei S > 1/2 by the reduction of the second-order quadrupole broadening. A brief overview and outlook on spectral acquisition, the importance of high magnetic field, inter-nuclei distance measurement, various 2D separation and correlation methods of quadrupole nuclei are presented. The complications and consequences of spin dynamics under rf irradiation for the (2S + 1) level system and level-crossing with the satellite transition frequencies under magic-angle spinning are discussed. There is a scaling down of (S + 1/2) to the efficiency of many experiments in comparison with a spin-1/2 due to the fact that only two central transition spin states out of the (2S + 1) levels contribute to polarization transfer and spin correlation.

Solid state NMR - An indispensable tool in organic-inorganic biocomposite characterization; refining the structure of octacalcium phosphate composites with the linear metabolic di-acids succinate and adipate

Octacalcium phosphate (OCP; Ca8(HPO4)2(PO4)4. 5H2O) is a plausible precursor phase of biological hydroxyapatite, which composites with a number of biologically relevant organic metabolites. Widely used material science physicochemical structure determination techniques successfully characterize the mineral component of these composites but leave details of the structure, and interactions with mineral, of the organic component almost completely obscure. The metabolic linear di-acids succinate (SUC) and adipate (ADI) differentially expand the hydrated (100) layer of OCP. 13C13C correlation (proton driven spin diffusion, PDSD) experiments on OCP composited with (U-13C4)-SUC, and (U13C6)-ADI, show that the two di-acids per unit cell adopt non-centrosymmetric but mutually identical structures. 13C{31P}, rotational echo double resonance (REDOR) shows that one end of each linear di-acid is displaced further from the surface of the apatitic OCP layer relative to the other end. Overall the results indicate two di-acids per unit cell disposed perpendicularly across the OCP hydrated layer with one carboxylate of each di-acid substituting a hydrated surface OCP phosphate group. This study re-affirms the unique advantages of ssNMR in elucidating structural details of organic-inorganic biocomposites, and thereby mechanisms underlying the roles of small metabolites in influencing biomineralization mechanisms and outcomes.

Surface proteins and the formation of biofilms by Staphylococcus aureus

Staphylococcus aureus biofilms pose a serious clinical threat as reservoirs for persistent infections. Despite this clinical significance, the composition and mechanism of formation of S. aureus biofilms are unknown. To address these problems, we used solid-state NMR to examine S. aureus (SA113), a strong biofilm-forming strain. We labeled whole cells and cell walls of planktonic cells, young biofilms formed for 12-24h after stationary phase, and more mature biofilms formed for up to 60h after stationary phase. All samples were labeled either by (i) [¹⁵N]glycine and l-[1-¹³C]threonine, or in separate experiments, by (ii) l-[2-¹³C,¹⁵N]leucine. We then measured ¹³C-¹⁵N direct bonds by C{N} rotational-echo double resonance (REDOR). The increase in peptidoglycan stems that have bridges connected to a surface protein was determined directly by a cell-wall double difference (biofilm REDOR difference minus planktonic REDOR difference). This procedure eliminates errors arising from differences in ¹⁵N isotopic enrichments and from the routing of ¹³C label from threonine degradation to glycine. For both planktonic cells and the mature biofilm, 20% of pentaglycyl bridges are not cross-linked and are potential surface-protein attachment sites. None of these sites has a surface protein attached in the planktonic cells, but one-fourth have a surface protein attached in the mature biofilm. Moreover, the leucine-label shows that the concentration of β-strands in leucine-rich regions doubles in the mature biofilm. Thus, a primary event in establishing a S. aureus biofilm is extensive decoration of the cell surface with surface proteins that are linked covalently to the cell wall and promote cell-cell adhesion.

Characterization of the tertiary structure of the peptidoglycan of Enterococcus faecalis

Solid-state NMR spectra of whole cells and isolated cell walls of Enterococcus faecalis grown in media containing combinations of 13C and 15N specific labels in d- and l-alanine and l-lysine (in the presence of an alanine racemase inhibitor alaphosphin) have been used to determine the composition and architecture of the cell-wall peptidoglycan. The compositional variables include the concentrations of (i) peptidoglycan stems without bridges, (ii) d-alanylated wall teichoic acid, (iii) cross-links, and (iv) uncross-linked tripeptide and tetra/pentapeptide stems. Connectivities of l-alanyl carbonyl‑carbon bridge labels to d-[3-13C]alanyl and l-[ε-15N]lysyl stem labels prove that the peptidoglycan of E. faecalis has the same hybrid short-bridge architecture (with a mix of parallel and perpendicular stems) as the FemA mutant of Staphylococcus aureus, in which the cross-linked stems are perpendicular to one another and the cross-linking is close to the ideal 50% value. This is the first determination of the cell-wall chemical and geometrical architecture of whole cells of E. faecalis, a major source of nosocomial infections worldwide.

1 H-19 F REDOR-filtered NMR spin diffusion measurements of domain size in heterogeneous polymers

Solid state NMR spectroscopy is inherently sensitive to chemical structure and composition and thus makes an ideal method to probe the heterogeneity of multicomponent polymers. Specifically, NMR spin diffusion experiments can be used to extract reliable information about spatial domain sizes on multiple length scales, provided that magnetization selection of one domain can be achieved. In this paper, we demonstrate the preferential filtering of protons in fluorinated domains during NMR spin diffusion experiments using ¹ H-¹⁹ F heteronuclear dipolar dephasing based on rotational echo double resonance (REDOR) MAS NMR techniques. Three pulse sequence variations are demonstrated based on the different nuclei detected: direct ¹ H detection, plus both ¹ H➔¹³ C cross polarization and ¹ H➔¹⁹ F cross polarization detection schemes. This ¹ H-¹⁹ F REDOR-filtered spin diffusion method was used to measure fluorinated domain sizes for a complex polymer blend. The efficacy of the REDOR-based spin filter does not rely on spin relaxation behavior or chemical shift differences and thus is applicable for performing NMR spin diffusion experiments in samples where traditional magnetization filters may prove unsuccessful. This REDOR-filtered NMR spin diffusion method can also be extended to other samples where a heteronuclear spin pair exists that is unique to the domain of interest.

The Application of REDOR NMR to Understand the Conformation of Epothilone B

The structural information of small therapeutic compounds complexed in biological matrices is important for drug developments. However, structural studies on ligands bound to such a large and dynamic system as microtubules are still challenging. This article reports an application of the solid-state NMR technique to investigating the bioactive conformation of epothilone B, a microtubule stabilizing agent, whose analog ixabepilone was approved by the U.S. Food and Drug Administration (FDA) as an anticancer drug. First, an analog of epothilone B was designed and successfully synthesized with deuterium and fluorine labels while keeping the high potency of the drug; Second, a lyophilization protocol was developed to enhance the low sensitivity of solid-state NMR; Third, molecular dynamics information of microtubule-bound epothilone B was revealed by high-resolution NMR spectra in comparison to the non-bound epothilone B; Last, information for the macrolide conformation of microtubule-bound epothilone B was obtained from rotational-echo double-resonance (REDOR) NMR data, suggesting the X-ray crystal structure of the ligand in the P450epoK complex as a possible candidate for the conformation. Our results are important as the first demonstration of using REDOR for studying epothilones.

Recoupling dipolar interactions with multiple I=1 quadrupolar nuclei: A 11B{6Li} and 31P{6Li} rotational echo double resonance study of lithium borophosphate glasses

The case of rotational echo double resonance (REDOR) experiments on the observe nuclei ¹¹B and ³¹P interacting with multiple I=1 quadrupolar nuclei is analyzed in detail by SIMPSON simulations and experimental studies. The simulations define the region within the parameter space spanned by nutation frequency, quadrupolar coupling constant and spinning frequency where the parabolic analysis of the initial REDOR curve in terms of dipolar second moments has validity. The predictions are tested by experimental studies on the crystalline model compounds lithium diborate and lithium pyrophosphate, which are subsequently extended to measure dipolar second moments M₂(¹¹B{⁶Li}) and M₂(³¹P{⁶Li}) in three borophosphate glasses. The data indicate that the lithium cations interact significantly more strongly with the phosphate than with the borate species, despite the formally anionic character of four-coordinate boron and the formally neutral character of the ultraphosphate (P⁽³⁾) units to which they are linked.

Theoretical study of a simple rotational-echo double-resonance NMR for homonuclear spin-1/2 pairs

We investigate theoretically intriguing aspects of a simple rotational-echo double-resonance (REDOR) NMR technique for homonuclear spin-1/2 pairs undergoing MAS. The simple technique sets Gaussian soft π pulses at every half MAS rotational period in the pulse sequence. The reduction in rotational echo amplitude (the REDOR echo reduction) is observed at the end of the evolution period te  = (n + 1)Tr, where Tr is a MAS rotational period. The exact average Hamiltonians for the homonuclear REDOR (hm-REDOR) technique are calculated by dividing the evolution period into four periods. We show theoretically and experimentally that the hm-REDOR technique produces the REDOR echo reductions for homonuclear spin-1/2 pairs. In addition, the theoretical results reveal that the REDOR echo reductions are independent of the chemical-shift difference, δ, under a simple condition of κ = δ/ωr  ≥ 6 and te  < 10 ⋅ (1/d'), where ωr is the sample spinning frequency and d' is the dipolar coupling constant expressed in Hz. We call this simple condition the master condition. This means that the REDOR echo reductions for a homonuclear spin-1/2 pair can be calculated under the master condition by considering only d' and ωr , which is the case for a heteronuclear spin pair. Finally, we demonstrate that four-phase cycling yields the multiple-quantum filtered hm-REDOR experiment, where the appearance of the REDOR echo reductions shows that the echo reductions are definitely attributable to the homonuclear dipolar interaction even if there is a slight unwanted effect from the recovered chemical-shift anisotropy in these reductions.

Measurement of homonuclear magnetic dipole-dipole interactions in multiple 1/2-spin systems using constant-time DQ-DRENAR NMR

A new pulse sequence entitled DQ-DRENAR (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. As described in the present manuscript, the efficiency and performance of this sequence can be significantly improved, if the measurement is done in the constant-time mode. We describe both the theoretical analysis of this method and its experimental validation of a number of crystalline model compounds, considering both symmetry-based and back-to-back (BABA) DQ-coherence excitation schemes. Based on the combination of theoretical analysis and experimental results we discuss the effect of experimental parameters such as the chemical shift anisotropy (CSA), the spinning rate, and the radio frequency field inhomogeneity upon its performance. Our results indicate that constant-time (CT-) DRENAR is a method of high efficiency and accuracy for compounds with multiple homonuclear spin systems with particular promise for the analysis of stronger-coupled and short T2 spin systems.

Frequency-selective REDOR and spin-diffusion relays in uniformly labeled whole cells

Solid-state NMR is a powerful and non-perturbative method to measure and define chemical composition and architecture in bacterial cell walls, even in the context of whole cells. Most NMR studies on whole cells have used selectively labeled samples. Here, we introduce an NMR sequence relay using frequency-selective REDOR (fsREDOR) and spin diffusion elements to probe a unique amine contribution in uniformly (13)C- and (15)N-labeled Staphylococcus aureus whole cells that we attribute to the d-alanine of teichoic acid. In addition to the primary peptidoglycan structural scaffold, cell walls can contain significant amounts of teichoic acid that contribute to cell-wall function. When incorporated into teichoic acid, d-alanine is present as an ester, connected via its carbonyl to a ribitol carbon, and thus has a free amine. Teichoic acid d-Ala is removed during cell-wall isolations and can only be detected in the context of whole cells. The sequence presented here begins with fsREDOR and a chemical shift evolution period for 2D data acquisition, followed by DARR spin diffusion and then an additional fsREDOR period. fsREDOR elements were used for (13)C observation to avoid complications from (13)C-(13)C couplings due to uniform labeling and for (15)N dephasing to achieve selectivity in the nitrogens serving as dephasers. The results show that the selected amine nitrogen of interest is near to teichoic acid ribitol carbons and also the methyl group carbon associated with alanine. In addition, its carbonyl is not significantly dephased by amide nitrogens, consistent with the expected microenvironment around teichoic acid.

An optimal double-magic flip angle for performing the distance measurement REDOR experiment on a spin S=1

Distance measurements between a half-spin and a quadrupolar S=1 spin having a small quadrupolar coupling constant can be performed using the rotational echo double resonance (REDOR) experiment. We derived an analytical expression for the probability of transitions between energy levels resulting from the application of an arbitrary pulse flip angle to the quadrupolar spin and consequently minimized the probability that populations of individual levels do not undergo a spin transition during the pulse. As a result we discovered that if the flip angle of the quadrupolar spin pulse is 109.47°, the maximal recoupling values are the largest possible and the signal reaches a maximum value of 8/9, larger than in the use of either a 90° pulse or a 180° pulse. In addition, the slope of the initial decay is higher than that of the 90° pulse. The recoupling signal can be modeled by an exact analytical formula in the ideal case and simulations show that the advantage of the 109.47° pulse is preserved when the quadrupolar coupling constant CQ has a finite value typical of (2)H and (6)Li spins (up to CQ~200kHz). Experimental results on two spin pairs, (2)H-(13)C and (6)Li-(13)C, demonstrate the validity and accuracy of this method.

Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition

The genomics and proteomics revolutions have been enormously successful in providing crucial "parts lists" for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The "sum-of-the-parts" bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by Escherichia coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in Vibrio cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture.

REDOR solid-state NMR as a probe of the membrane locations of membrane-associated peptides and proteins

Rotational-echo double-resonance (REDOR) solid-state NMR is applied to probe the membrane locations of specific residues of membrane proteins. Couplings are measured between protein (13)CO nuclei and membrane lipid or cholesterol (2)H and (31)P nuclei. Specific (13)CO labeling is used to enable unambiguous assignment and (2)H labeling covers a small region of the lipid or cholesterol molecule. The (13)CO-(31)P and (13)CO-(2)H REDOR respectively probe proximity to the membrane headgroup region and proximity to specific insertion depths within the membrane hydrocarbon core. One strength of the REDOR approach is use of chemically-native proteins and membrane components. The conventional REDOR pulse sequence with 100 kHz (2)H π pulses is robust with respect to the (2)H quadrupolar anisotropy. The (2)H T1's are comparable to the longer dephasing times (τ's) and this leads to exponential rather than sigmoidal REDOR buildups. The (13)CO-(2)H buildups are well-fitted to A×(1-e(-γτ)) where A and γ are fitting parameters that are correlated as the fraction of molecules (A) with effective (13)CO-(2)H coupling d=3γ/2. The REDOR approach is applied to probe the membrane locations of the "fusion peptide" regions of the HIV gp41 and influenza virus hemagglutinin proteins which both catalyze joining of the viral and host cell membranes during initial infection of the cell. The HIV fusion peptide forms an intermolecular antiparallel β sheet and the REDOR data support major deeply-inserted and minor shallowly-inserted molecular populations. A significant fraction of the influenza fusion peptide molecules form a tight hairpin with antiparallel N- and C-α helices and the REDOR data support a single peptide population with a deeply-inserted N-helix. The shared feature of deep insertion of the β and α fusion peptide structures may be relevant for fusion catalysis via the resultant local perturbation of the membrane bilayer. Future applications of the REDOR approach may include samples that contain cell membrane extracts and use of lower temperatures and dynamic nuclear polarization to reduce data acquisition times.

Progression of NMR studies of membrane-active peptides from lipid bilayers to live cells

Understanding the structure of membrane-active peptides faces many challenges associated with the development of appropriate model membrane systems as the peptide structure depends strongly on the lipid environment. This perspective provides a brief overview of the approach taken to study antimicrobial and amyloid peptides in phospholipid bilayers using oriented bilayers and magic angle spinning techniques. In particular, Boltzmann statistics REDOR and maximum entropy analysis of spinning side bands are used to analyse systems where multiple states of peptide or lipid molecules may co-exist. We propose that in future, rather than model membranes, structural studies in whole cells are feasible.

Peptidoglycan architecture of Gram-positive bacteria by solid-state NMR

Peptidoglycan is an essential component of cell wall in Gram-positive bacteria with unknown architecture. In this review, we summarize solid-state NMR approaches to address some of the unknowns in the Gram-positive bacteria peptidoglycan architecture: 1) peptidoglycan backbone conformation, 2) PG-lattice structure, 3) variations in the peptidoglycan architecture and composition, 4) the effects of peptidoglycan bridge-length on the peptidoglycan architecture in Fem mutants, 5) the orientation of glycan strands with respect to the membrane, and 6) the relationship between the peptidoglycan structure and the glycopeptide antibiotic mode of action. Solid-state NMR analyses of Staphylococcus aureus cell wall show that peptidoglycan chains are surprisingly ordered and densely packed. The peptidoglycan disaccharide backbone adopts 4-fold screw helical symmetry with the disaccharide unit periodicity of 40Å. Peptidoglycan lattice in the S. aureus cell wall is formed by cross-linked PG stems that have parallel orientations. The structural characterization of Fem-mutants of S. aureus with varying lengths of bridge structures suggests that the PG-bridge length is an important determining factor for the PG architecture.

Characterization of the Vibrio cholerae extracellular matrix: a top-down solid-state NMR approach

Bacterial biofilms are communities of bacterial cells surrounded by a self-secreted extracellular matrix. Biofilm formation by Vibrio cholerae, the human pathogen responsible for cholera, contributes to its environmental survival and infectivity. Important genetic and molecular requirements have been identified for V. cholerae biofilm formation, yet a compositional accounting of these parts in the intact biofilm or extracellular matrix has not been described. As insoluble and non-crystalline assemblies, determinations of biofilm composition pose a challenge to conventional biochemical and biophysical analyses. The V. cholerae extracellular matrix composition is particularly complex with several proteins, complex polysaccharides, and other biomolecules having been identified as matrix parts. We developed a new top-down solid-state NMR approach to spectroscopically assign and quantify the carbon pools of the intact V. cholerae extracellular matrix using ¹³C CPMAS and ¹³C{(¹⁵N}, ¹⁵N{³¹P}, and ¹³C{³¹P}REDOR. General sugar, lipid, and amino acid pools were first profiled and then further annotated and quantified as specific carbon types, including carbonyls, amides, glycyl carbons, and anomerics. In addition, ¹⁵N profiling revealed a large amine pool relative to amide contributions, reflecting the prevalence of molecular modifications with free amine groups. Our top-down approach could be implemented immediately to examine the extracellular matrix from mutant strains that might alter polysaccharide production or lipid release beyond the cell surface; or to monitor changes that may accompany environmental variations and stressors such as altered nutrient composition, oxidative stress or antibiotics. More generally, our analysis has demonstrated that solid-state NMR is a valuable tool to characterize complex biofilm systems.

Phase-modulated LA-REDOR: a robust, accurate and efficient solid-state NMR technique for distance measurements between a spin-1/2 and a quadrupole spin

Distances between a spin-1/2 and a spin>1/2 can be efficiently measured by a variety of magic-angle spinning solid state NMR methods such as Rotational Echo Adiabatic Passage Double Resonance (REAPDOR), Low-Alpha/Low-Amplitude REDOR (LA-REDOR) and Rotational-Echo Saturation-Pulse Double-Resonance (R/S-RESPDOR). In this manuscript we show that the incorporation of a phase modulation into a long quadrupolar recoupling pulse, lasting 10 rotor periods that are sandwiched between rotor-synchronized pairs of dipolar recoupling π pulses, extends significantly the range of the values of the quadrupole moments that can be accessed by the experiment. We show by a combination of simulations and experiments that the new method, phase-modulated LA-REDOR, is very weakly dependent on the actual value of the radio-frequency field, and is highly robust with respect to off-resonance irradiation. The experimental results can be fitted by numerical simulations or using a universal formula corresponding to an equal-transition-probability model. Phase-modulated LA-REDOR (13)C{(11)B} and (15)N{(51)V} dipolar recoupling experiments confirm the accuracy and applicability of this new method.

Fast REDOR with CPMG multiple-echo acquisition

Rotational-Echo Double Resonance (REDOR) is a widely used experiment for distance measurements in solids. The conventional REDOR experiment measures the signal dephasing from hetero-nuclear recoupling under magic-angle spinning (MAS) in a point by point manner. A modified Carr-Purcell Meiboom-Gill (CPMG) multiple-echo scheme is introduced for fast REDOR measurement. REDOR curves are measured from the CPMG echo amplitude modulation under dipolar recoupling. The real time CPMG-REDOR experiment can speed up the measurement by an order of magnitude. The effects from hetero-nuclear recoupling, the Bloch-Siegert shift and echo truncation to the signal acquisition are discussed and demonstrated.

Sum of the parts: composition and architecture of the bacterial extracellular matrix

Bacterial biofilms are complex multicellular assemblies that exhibit resistance to antibiotics and contribute to the pathogenesis of serious and chronic infectious diseases. New approaches and quantitative data are needed to define the molecular composition of bacterial biofilms. Escherichia coli biofilms are known to contain polysaccharides and functional amyloid fibers termed curli, yet accurate determinations of biofilm composition at the molecular level have been elusive. The ability to define the composition of the extracellular matrix (ECM) is crucial for the elucidation of structure-function relationships that will aid the development of chemical strategies to disrupt biofilms. We have developed an approach that integrates non-perturbative preparation of the ECM with electron microscopy, biochemistry, and solid-state NMR spectroscopy to define the chemical composition of the intact and insoluble ECM of a clinically important pathogenic bacterium--uropathogenic E. coli. Our data permitted a sum-of-all-the-parts analysis. Electron microscopy revealed supramolecular shell-like structures that encapsulated single cells and enmeshed the bacterial community. Biochemical and solid-state NMR measurements of the matrix and constitutive parts established that the matrix is composed of two major components, curli and cellulose, each in a quantifiable amount. This approach to quantifying the matrix composition is widely applicable to other organisms and to examining the influence of biofilm inhibitors. Collectively, our NMR spectra and the electron micrographs of the purified ECM inspire us to consider the biofilm matrix not as an undefined slime, but as an assembly of polymers with a defined composition and architecture.

REDOR NMR for drug discovery

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