High-resolution NMR spectroscopy of a GPCR in aligned bicelles

Solid-state NMR spectra with single-site resolution of CXCR1, a G protein-coupled receptor (GPCR), were obtained in magnetically aligned phospholipid bicelles. These results demonstrate that GPCRs in phospholipid bilayers are suitable samples for structure determination by solid-state NMR. The spectra also enable studies of drug-receptor interactions.     

High-resolution 2D NMR spectroscopy of bicelles to measure the membrane interaction of ligands

Magnetically aligned bicelles are increasingly being used as model membranes in solution- and solid-state NMR studies of the structure, dynamics, topology, and interaction of membrane-associated peptides and proteins. These studies commonly utilize the PISEMA pulse sequence to measure dipolar coupling and chemical shift, the two key parameters used in subsequent structural analysis. In the present study, we demonstrate that the PISEMA and other rotating-frame pulse sequences are not suitable for the measurement of long-range heteronuclear dipolar couplings, and that they provide inaccurate values when multiple protons are coupled to a 13C nucleus. Furthermore, we demonstrate that a laboratory-frame separated-local-field experiment is capable of overcoming these difficulties in magnetically aligned bicelles. An extension of this approach to accurately measure 13C-31P and 1H-31P couplings from phospholipids, which are useful to understand the interaction of molecules with the membrane, is also described. In these 2D experiments, natural abundance 13C was observed from bicelles containing DMPC and DHPC lipid molecules. As a first application, these solid-state NMR approaches were utilized to probe the membrane interaction of an antidepressant molecule, desipramine, and its location in the membrane.     

Structure determination of aligned samples of membrane proteins by NMR spectroscopy

The paper briefly reviews the process of determining the structures of membrane proteins by NMR spectroscopy of aligned samples, describes the integration of recent developments in the interpretation of spectra of aligned proteins and illustrates the application of these methods to the trans-membrane helical domain of a protein. The emerging methods of interpreting the spectral parameters from aligned samples of isotopically labeled proteins provide opportunities for simultaneously assigning the spectra and determining the structures of the proteins, and also for comparing the results from solid-state NMR experiments on completely aligned samples with those of solution NMR experiments on weakly aligned samples.     

Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy

The structure of the membrane protein MerFt was determined in magnetically aligned phospholipid bicelles by solid-state NMR spectroscopy. With two trans-membrane helices and a 10-residue inter-helical loop, this truncated construct of the mercury transport membrane protein MerF has sufficient structural complexity to demonstrate the feasibility of determining the structures of polytopic membrane proteins in their native phospholipid bilayer environment under physiological conditions. PISEMA, SAMMY, and other double-resonance experiments were applied to uniformly and selectively (15)N-labeled samples to resolve and assign the backbone amide resonances and to measure the associated (15)N chemical shift and (1)H-(15)N heteronuclear dipolar coupling frequencies as orientation constraints for structure calculations. (1)H/(13)C/(15)N triple-resonance experiments were applied to selectively (13)C'- and (15)N-labeled samples to complete the resonance assignments, especially for residues in the nonhelical regions of the protein. A single resonance is observed for each labeled site in one- and two-dimensional spectra. Therefore, each residue has a unique conformation, and all protein molecules in the sample have the same three-dimensional structure and are oriented identically in planar phospholipid bilayers. Combined with the absence of significant intensity near the isotropic resonance frequency, this demonstrates that the entire protein, including the loop and terminal regions, has a well-defined, stable structure in phospholipid bilayers.     

Residual dipolar coupling measurements of transmembrane proteins using aligned low-q bicelles and high-resolution magic angle spinning NMR spectroscopy

Bicelles are a major medium form to produce weak alignment of soluble proteins for residual dipolar coupling (RDC) measurements. The obstacle to using the same type of bicelles for transmembrane proteins with solution-state NMR spectroscopy is the loss of signals due to the adhesion or penetration of the proteins into large bicelles, resulting in slow protein tumbling. In this study, weak alignment of the second and third transmembrane domains (TM23) of the human glycine receptor (GlyR) was achieved in low-q bicelles (q = DMPC/DHPC). Although protein-free bicelles with such low q would likely show isotropic properties, the insertion of TM23 induced weakly preferred orientations so that the RDC of the embedded protein can be measured. The extent of the alignment increased but the TM23 signal intensity decreased when q was varied from 0.19 to 0.60. A q of 0.50 was found to be an optimal compromise between alignment and the signal-to-noise ratio. In each pair of NMR experiments for RDC measurements, the same sample and pulse sequence were used, with one being performed at high-resolution magic-angle spinning to obtain pure J-couplings without RDC. A meaningful structure refinement in bicelles was possible by iteratively fitting the experimental RDCs to the back-calculated RDCs using the high-resolution NMR structure of GlyR TM23 in trifluoroethanol as the starting template. Combination of this method with the conventional high-resolution NMR in membrane mimicking mixtures of water and organic solvents offers an attractive way to derive structural information for membrane proteins in their native environment.     

Bilayer in small bicelles revealed by lipid-protein interactions using NMR spectroscopy

Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and small bicelles of dihexanoyl phosphatidylcholine (DHPC) and dimyristoyl phosphatidylcholine (DMPC) give insights into protein-lipid interactions. Intermolecular NOEs between hydrophobic tails of lipid and protein in the bicelles cover the surface area of OmpX forming a continuous cylindric jacket of approximately 2.7 nm in height. These NOEs originate only from DMPC molecules, and no NOEs from DHPC are observed. Further, these NOEs are mainly from methylene groups of the hydrophobic tails of DMPC, and only a handful of NOEs arise from methyl groups of the hydrophobic tails. The observed contacts indicate that the hydrophobic tails of DMPC are oriented parallel to the surface of OmpX and thus DMPC molecules form a bilayer in the vicinity of the protein. Thus, a bilayer exists in the small bicelles not only in the absence of but also in the presence of a membrane protein. In addition, the number of NOEs between the polar head groups of lipid molecules and protein is increased in the bicelles compared with those in micelles. This observation may be due to the closely packed head groups of the bilayer. Moreover, irregularity of hydrophobic interactions in the middle of the bilayer environment was observed. This observation together with the interactions between polar head groups and proteins gives a possible rationale for structural and functional differences of membrane proteins solubilized in micelles and in bilayer systems and hints at structural differences between protein-free and protein-loaded bilayers.     

High-resolution NMR spectroscopy under the fume hood

This work reports the possibility to acquire high-resolution (1)H NMR spectra with a fist-sized NMR magnet directly installed under the fume hood. The small NMR sensor based on permanent magnets was used to monitor the trimerization of propionaldehyde catalyzed by indium trichloride in real time by continuously circulating the reaction mixture through the magnet bore in a closed loop with the help of a peristaltic pump. Thanks to the chemical selectivity of NMR spectroscopy the progress of the reaction can be monitored on-line by determining the concentrations of both reactant and product from the area under their respective lines in the NMR spectra as a function of time. This in situ measurement demonstrates that NMR probes can be used in chemistry laboratories, e.g. for reaction optimization, or installed at specific points of interest along industrial process lines. Therefore, it will open the door for the implementation of feedback control based on spectroscopic NMR data.     

High-resolution 39K NMR spectroscopy of bio-organic solids

We report the first implementation of the multiple-quantum magic-angle-spinning method to obtain high-resolution (39)K NMR spectra for bio-organic solids. The observed spectral resolution in the isotropic dimension is nearly at the sub-ppm level, which approaches the intrinsic resolution limit determined primarily by quadrupole relaxation. We show that high-resolution solid-state (39)K NMR spectroscopy can be used as a new means of probing K(+) ions in biomolecular systems.     

High-resolution NMR studies of encapsulated proteins in liquid ethane

Many of the difficulties presented by large, aggregation-prone, and membrane proteins to modern solution NMR spectroscopy can be alleviated by actively seeking to increase the effective rate of molecular reorientation. An emerging approach involves encapsulating the protein of interest within the protective shell of a reverse micelle and dissolving the resulting particle in a low viscosity fluid, such as the short chain alkanes. Here we present the encapsulation of proteins with high structural fidelity within reverse micelles dissolved in liquid ethane. The addition of appropriate cosurfactants can significantly reduce the pressure required for successful encapsulation. At these reduced pressures, the viscosity of the ethane solution is low enough to provide sufficiently rapid molecular reorientation to significantly lengthen the spin-spin NMR relaxation times of the encapsulated protein.     

Solid-state NMR spectroscopy of aligned lipid bilayers at low temperatures

This study, for the first time, demonstrates that it is possible to mechanically align lipid bilayers at a very low temperature (as low as the gel-to-liquid crystalline phase transition temperature). Performing NMR experiments on mechanically aligned lipid bilayers at a low temperature increases the signal-to-noise ratio, the resolution, and the span of NMR parameters. The increased lifetime of the alignment and the nature of the bilayer sample would enhance the application of solid-state NMR techniques to study membrane proteins.     

Diffusion of PEG confined between lamellae of negatively magnetically aligned bicelles: pulsed field gradient 1H NMR measurements

The diffusion of various molecular weight poly(ethyleneglycol)s (PEG) confined between the lamellae of magnetically aligned bicelles has been measured using stimulated echo (STE) pulsed field gradient (PFG) 1H nuclear magnetic resonance (NMR) spectroscopy. Bicelles were formulated to contain dimyristoylphosphatidylcholine (DMPC), dimyristoylphosphatidylglycerol (DMPG), and dihexanoylphosphatidylcholine (DHPC) in the proportion DMPG/DMPC = 0.05 and q = (DMPC + DMPG)/DHPC = 4.5. PEG diffusion within the interlamellar spaces between such bicelles was found to be unrestricted over diffusion distances of tens of microns. Two confinement regimes could be differentiated according to the dependence of the reduced PEG diffusivity D/D0, where D0 is the unconfined PEG diffusion coefficient, on the relative confinement Rh/H, where Rh is the unperturbed hydration radius of the particular PEG and H approximately 60 A is the separation between apposing lamellae of the magnetically aligned bicelles. In the regime Rh/H < 0.4, the reduced PEG diffusivity was altered only in proportion to the viscosity increase associated with the bicelle dispersion relative to bulk solution. In the regime Rh/H > 0.4, the reduced PEG diffusivity scaled as (Rh/H)-2/3, in agreement with scaling theories for confined polymers.     

Selective interface detection: mapping binding site contacts in membrane proteins by NMR spectroscopy

Intermolecular contact surfaces are important regions where specific interactions mediate biological function. We introduce a new magic angle spinning solid state NMR technique, dubbed "selective interface detection spectroscopy" (SIDY). In this technique, 13C-attached protons (1Hlig) are dephased by 1H-13C REDOR. A spin diffusion period is then used to enhance long distance 1H-1H correlations, and the results are detected by a short period of cross polarization to the 13C isotope labels. This SIDY approach allows selective observation of the interface between 13C-labeled and unlabeled moieties. We have used SIDY to probe the ligand-protein binding surface between a uniformly isotopically labeled ligand cofactor, U-13C20-11-cis-retinal, and its binding site in rhodopsin (Rho), an unlabeled, membrane-embedded G-protein coupled receptor (GPCR). The observed 1HGPCR-13Clig correlations indicate multiple close contacts between the protein and the ionone ring of the ligand, in agreement with binding studies. The polyene tail of the ligand displays fewer strong correlations in the SIDY spectrum. Some correlations can be assigned to the protein side chains lining the ligand binding site, in agreement with the crystal structure.     

Lipid-ethanol interaction studied by NMR on bicelles

The interaction of ethanol with phospholipids was studied in bicelles at a physiologically relevant ethanol concentration of 20 mM and a lipid content of 14 wt % by high-resolution NMR. Transient association of ethanol with magnetically aligned bicelles imparts a small degree of anisotropy to the solute. This anisotropy allows detection of residual (1)H-(1)H and (1)H-(13)C dipolar couplings, which are superimposed on scalar couplings. Residual (2)H NMR quadrupole splittings of isotope-labeled ethanol were measured as well. The analysis of residual tensorial interactions yielded information on the orientation and motions of ethanol in the membrane-bound state. The fraction of phosphatidylcholine-bound ethanol was determined independently by gas chromatography and NMR. About 4% of ethanol is bound to phosphatidylcholine at a bicelle concentration of 14 wt % at 40 degrees C. Free and bound ethanol are in rapid exchange. The lifetime of ethanol association with phosphatidylcholine membranes is of the order of a few nanoseconds.     

High-resolution solid-state 2H NMR spectroscopy of polymorphs of glycine

High-resolution solid-state (2)H MAS NMR studies of the α and γ polymorphs of fully deuterated glycine (glycine-d(5)) are reported. Analysis of spinning sideband patterns is used to determine the (2)H quadrupole interaction parameters, and is shown to yield good agreement with the corresponding parameters determined from single-crystal (2)H NMR measurements (the maximum deviation in quadrupole coupling constants determined from these two approaches is only 1%). From analysis of simulated (2)H MAS NMR sideband patterns as a function of reorientational jump frequency (κ) for the -N(+)D(3) group in glycine-d(5), the experimentally observed differences in the (2)H MAS NMR spectrum for the -N(+)D(3) deutrons in the α and γ polymorphs is attributed to differences in the rate of reorientation of the -N(+)D(3) group. These simulations show severe broadening of the (2)H MAS NMR signal in the intermediate motion regime, suggesting that deuterons undergoing reorientational motions at rates in the range κ ≈ 10(4)-10(6) s(-1) are likely to be undetectable in (2)H MAS NMR measurements for materials with natural isotopic abundances. The (1)H NMR chemical shifts for the α and γ polymorphs of glycine have been determined from the (2)H MAS NMR results, taking into account the known second-order shift. Further quantum mechanical calculations of (2)H quadrupole interaction parameters and (1)H chemical shifts reveal the structural dependence of these parameters in the two polymorphs and suggest that the existence of two short intermolecular C-H···O contacts for one of the H atoms of the >CH(2) group in the α polymorph have a significant influence on the (2)H quadrupole coupling and (1)H chemical shift for this site.     

Nitrogen-14 solid-state NMR spectroscopy of aligned phospholipid bilayers to probe peptide-lipid interaction and oligomerization of membrane associated peptides

Characterization of the oligomerization of membrane-associated peptides is important to understand the folding and function of biomolecules like antimicrobial peptides, fusion peptides, amyloid peptides, toxins, and ion channels. However, this has been considered to be very difficult, because the amphipathic properties of the constituents of the cell membrane pose tremendous challenges to most commonly used biophysical techniques. In this study, we present the application of a simple (14)N solid-state NMR spectroscopy of aligned model membranes containing a phosphatidyl choline lipid to investigate the oligomerization of membrane-associated peptides. Since the near-symmetric nature of the choline headgroup of a phosphocholine lipid considerably reduces the (14)N quadrupole coupling, there are significant practical advantages in using (14)N solid-state NMR experiments to probe the interaction of peptide or protein with the surface of model membranes. Experimental results for several membrane-associated peptides are presented in this paper. Our results suggest that the experimentally measured (14)N quadrupole splitting of the lipid depends on the peptide-induced changes in the electrostatic potential of the lipid bilayer surface and therefore on the nature of the peptide, peptide-membrane interaction, and peptide-peptide interaction. It is inferred that the membrane orientation and oligomerization of the membrane-associated peptides can be measured using (14)N solid-state NMR spectroscopy.     

High-resolution NMR spectroscopy in unstable and inhomogeneous fields via stroboscopic acquisition

In this paper, we demonstrated that despite the insensitivity of intermolecular zero-quantum coherences (iZQCs) to B(0) variations, the influence of unstable fields on the observable single-quantum coherence signals causes strong t(1) noises in the high-resolution iZQC projection spectra. Stroboscopic acquisition was then proposed for noise suppression. The feasibility of the modified sequences with the proposed acquisition scheme was verified by computer simulations and experiments in different unstable fields generated by the Z0 and Z1 coil current oscillations, which mimic the unstable fields of NMR using externally powered magnets and MRS in the presence of physiological motions, respectively.     

High-resolution structure and conformational dynamics of rigid, cofacially aligned porphyrin-bridge-quinone systems as determined by NMR spectroscopy and ab initio simulated annealing calculations

The high-resolution solution structure and dynamics of a cofacially aligned porphyrin--phenylene--quinone compound have been determined using (1)H NMR spectroscopy and simulated annealing calculations. Members of this class of pi-stacked assemblies feature a 1,8-naphthyl pillaring motif that enforces sub van der Waals interplanar separations between juxtaposed porphyryl, aromatic bridge, and quinonyl components of the donor--spacer--acceptor compound; this structural motif gives rise to a comprehensive set of structurally significant NOE signatures that can be used as constraints in quantitative structural calculations. Examination of such data using ab initio simulated annealing analytical methods shows that 5-[8'-(4' '-[8' "-(2' " ',5' "-benzoquinonyl)-1' "-naphthyl]-1' '-phenyl)-1'-naphthyl]-10,20-diphenylporphyrin displays an unusual degree of conformational homogeneity in the condensed phase, and represents a rare example where such an analysis determines unequivocally a single unique structure in solution.