Experimental aspects of multidimensional solid-state NMR correlation spectroscopy

Mastering the magnetic susceptibility of magnetically responsive bicelles with 3β-amino-5-cholestene and complexed lanthanide ions

The magnetic susceptibility of lanthanide-chelating bicelles was selectively enhanced by introducing 3β-amino-5-cholestene (aminocholesterol, Chol-NH₂) in the bilayer. Unprecedented magnetic alignment of the bicelles was achieved without altering their size. An aminocholesterol conjugate (Chol-C₂OC₂-NH₂), in combination with different lanthanide ions, offers the possibility of fine-tuning the bicelle's magnetic susceptibility.

Bioinspired, Size-Tunable Self-Assembly of Polymer-Lipid Bilayer Nanodiscs

Polymer-based nanodiscs are valuable tools in biomedical research that can offer a detergent-free solubilization of membrane proteins maintaining their native lipid environment. Herein, we introduce a novel ca. 1.6 kDa SMA-based polymer with styrene:maleic acid moieties that can form nanodiscs containing a planar lipid bilayer which are useful to reconstitute membrane proteins for structural and functional studies. The physicochemical properties and the mechanism of formation of polymer-based nanodiscs are characterized by light scattering, NMR, FT-IR, and TEM. A remarkable feature is that nanodiscs of different sizes, from nanometer to sub-micrometer diameter, can be produced by varying the lipid-to-polymer ratio. The small-size nanodiscs (up to ca. 30 nm diameter) can be used for solution NMR spectroscopy studies whereas the magnetic-alignment of macro-nanodiscs (diameter of > ca. 40 nm) can be exploited for solid-state NMR studies on membrane proteins.

Exploring the salt-cocrystal continuum with solid-state NMR using natural-abundance samples: implications for crystal engineering

There has been significant recent interest in differentiating multicomponent solid forms, such as salts and cocrystals, and, where appropriate, in determining the position of the proton in the X-H⋯A-YX-⋯H-A+-Y continuum in these systems, owing to the direct relationship of this property to the clinical, regulatory and legal requirements for an active pharmaceutical ingredient (API). In the present study, solid forms of simple cocrystals/salts were investigated by high-field (700 MHz) solid-state NMR (ssNMR) using samples with naturally abundant 15N nuclei. Four model compounds in a series of prototypical salt/cocrystal/continuum systems exhibiting {PyN⋯H-O-}/{PyN+-H⋯O-} hydrogen bonds (Py is pyridine) were selected and prepared. The crystal structures were determined at both low and room temperature using X-ray diffraction. The H-atom positions were determined by measuring the 15N-1H distances through 15N-1H dipolar interactions using two-dimensional inversely proton-detected cross polarization with variable contact-time (invCP-VC) 1H→15N→1H experiments at ultrafast (νR ≥ 60-70 kHz) magic angle spinning (MAS) frequency. It is observed that this method is sensitive enough to determine the proton position even in a continuum where an ambiguity of terminology for the solid form often arises. This work, while carried out on simple systems, has implications in the pharmaceutical industry where the salt/cocrystal/continuum condition of APIs is considered seriously.

Diazole-based powdered cocrystal featuring a helical hydrogen-bonded network: structure determination from PXRD, solid-state NMR and computer modeling

We present the structure of a new equimolar 1:1 cocrystal formed by 3,5-dimethyl-1H-pyrazole (dmpz) and 4,5-dimethyl-1H-imidazole (dmim), determined by means of powder X-ray diffraction data combined with solid-state NMR that provided insight into topological details of hydrogen bonding connectivities and weak interactions such as CH···π contacts. The use of various 1D/2D (13)C, (15)N and (1)H high-resolution solid-state NMR techniques provided structural insight on local length scales revealing internuclear proximities and relative orientations between the dmim and dmpz molecular building blocks of the studied cocrystal. Molecular modeling and DFT calculations were also employed to generate meaningful structures. DFT refinement was able to decrease the figure of merit R(F(2)) from ~11% (PXRD only) to 5.4%. An attempt was made to rationalize the role of NH···N and CH···π contacts in stabilizing the reported cocrystal. For this purpose four imidazole derivatives with distinct placement of methyl substituents were reacted with dmpz to understand the effect of methylation in blocking or enabling certain intermolecular contacts. Only one imidazole derivative (dmim) was able to incorporate into the dmpz trimeric motif thus resulting in a cocrystal, which contains both hydrophobic (methyl groups) and hydrophilic components that self-assemble to form an atypical 1D network of helicoidal hydrogen bonded pattern, featuring structural similarities with alpha-helix arrangements in proteins. The 1:1 dmpz···dmim compound I is the first example of a cocrystal formed by two different azoles.

A proton spin diffusion based solid-state NMR approach for structural studies on aligned samples

Rapidly expanding research on nonsoluble and noncrystalline chemical and biological materials necessitates sophisticated techniques to image these materials at atomic-level resolution. Although their study poses a formidable challenge, solid-state NMR is a powerful tool that has demonstrated application to the investigation of their molecular architecture and functioning. In particular, 2D separated-local-field (SLF) spectroscopy is increasingly applied to obtain high-resolution molecular images of these materials. However, despite the common use of SLF experiments in the structural studies of a variety of aligned molecules, the lack of a resonance assignment approach has been a major disadvantage. As a result, solid-state NMR studies have mostly been limited to aligned systems that are labeled with an isotope at a single site. Here, we demonstrate an approach for resonance assignment through a controlled reintroduction of proton spin diffusion in the 2D proton-evolved-local-field (PELF) pulse sequence. Experimental results and simulations suggest that the use of spin diffusion also enables the measurement of long-range heteronuclear dipolar couplings that can be used as additional constraints in the structural and dynamical studies of aligned molecules. The new method is used to determine the de novo atomic-level resolution structure of a liquid crystalline material, N-(4-methoxybenzylidene)-4-butylaniline, and its use on magnetically aligned bicelles is also demonstrated. We expect this technique to also be valuable in the structural studies of functional molecules like columnar liquid crystals and other biomaterials.

Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR

Filamentous bacteriophages (filamentous bacterial viruses or Inovirus) are simple and well-characterised macromolecular assemblies that are widely used in molecular biology and biophysics, both as paradigms for studying basic biological questions and as practical tools in areas as diverse as immunology and solid-state physics. The strains fd, M13 and f1 are virtually identical filamentous phages that infect bacteria expressing F-pili, and are sometimes grouped as the Ff phages. For historical reasons fd has often been used for structural studies, but M13 and f1 are more often used for biological experiments. Many other strains have been identified that are genetically quite distinct from Ff and yet have a similar molecular structure and life cycle. One of these, Pf1, gives the highest resolution X-ray fibre diffraction patterns known for filamentous bacteriophage. These diffraction patterns have been used in the past to derive a molecular model for the structure of the phage. Solid-state NMR experiments have been used in separate studies to derive a significantly different model of Pf1. Here we combine previously published X-ray fibre diffraction data and solid-state NMR data to give a consensus structure model for Pf1 filamentous bacteriophage, and we discuss the implications of this model for assembly of the phage at the bacterial membrane.

Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation

Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state (31)P and (13)C NMR spectroscopy. (31)P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (T(c)) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the T(c). (13)C NMR spectra of site-specifically (13)C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers.

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

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

A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints

To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, E (z) (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.

Efficient cross-polarization using a composite 0 degrees pulse for NMR studies on static solids

In most solid-state NMR experiments, cross-polarization is an essential step to detect low-gamma nuclei such as (13)C and (15)N. In this study, we present a new cross-polarization scheme using spin-locks composed of composite 0 degrees pulses in the RF channels of high-gamma and low-gamma nuclei to establish the Hartmann-Hahn match. The composite 0 degrees pulses with no net nutation-angle{(2pi)(X)-(2pi)(-X)-(2pi)(Y)-(2pi)(-Y) -}(n) applied simultaneously to both high-gamma (I) and low-gamma (S) nuclei create an effective heteronuclear dipolar Hamiltonian H(d)((0))=d/2(2I(Z)S(Z)+I(X)S(X)+I(Y)S(Y)), which is capable of transferring the Z-component of the I spin magnetization to the Z-component of the S spin magnetization. It also retains a homonuclear dipolar coupling Hamiltonian that enables the flip-flop transfer among abundant spins. While our experimental results indicate that the new pulse sequence, called composite zero cross-polarization (COMPOZER-CP) performs well on adamantane, it is expected to be more valuable to study semi-solids like liquid crystalline materials and model lipid membranes. Theoretical analysis of COMPOZER-CP is presented along with experimental results. Our experimental results demonstrate that COMPOZER-CP overcomes the RF field inhomogeneity and Hartmann-Hahn mismatch for static solids. Experimental results comparing the performance of COMPOZER-CP with that of the traditional constant-amplitude CP and rampCP sequences are also presented in this paper.

Practical aspects of Lee-Goldburg based CRAMPS techniques for high-resolution 1H NMR spectroscopy in solids: implementation and applications

Elucidating the local environment of the hydrogen atoms is an important problem in materials science. Because (1)H spectra in solid-state nuclear magnetic resonance (NMR) suffer from low resolution due to homogeneous broadening, even under magic-angle spinning (MAS), information of chemical interest may only be obtained using certain high-resolution (1)H MAS techniques. (1)H Lee-Goldburg (LG) CRAMPS (Combined Rotation And Multiple-Pulse Spectroscopy) methods are particularly well suited for studying inorganic-organic hybrid materials, rich in (1)H nuclei. However, setting up CRAMPS experiments is time-consuming and not entirely trivial, facts that have discouraged their widespread use by materials scientists. To change this status quo, here we describe and discuss some important aspects of the experimental implementation of CRAMPS techniques based on LG decoupling schemes, such as FSLG (Frequency Switched), and windowed and windowless PMLG (Phase Modulated). In particular, we discuss the influence on the quality of the (1)H NMR spectra of the different parameters at play, for example LG (Lee-Goldburg) pulses, radio-frequency (rf) phase, frequency switching, and pulse imperfections, using glycine and adamantane as model compounds. The efficiency and robustness of the different LG-decoupling schemes is then illustrated on the following materials: organo-phosphorus ligand, N-(phosphonomethyl)iminodiacetic acid [H(4)pmida] [I], and inorganic-organic hybrid materials (C(4)H(12)N(2))[Ge(2)(pmida)(2)OH(2)] x 4H(2)O [II] and (C(2)H(5)NH(3))[Ti(H(1.5)PO(4))(PO(4))](2) x H(2)O [III].

Multidimensional solid state NMR of anisotropic interactions in peptides and proteins

Accurate determinations of chemical shift anisotropy (CSA) tensors are valuable for NMR of biological systems. In this review we describe recent developments in CSA measurement techniques and applications, particularly in the context of peptides and proteins. These techniques include goniometeric measurements of single crystals, slow magic-angle spinning studies of powder samples, and CSA recoupling under moderate to fast MAS. Experimental CSA data can be analyzed by comparison with ab initio calculations for structure determination and refinement. This approach has particularly high potential for aliphatic (13)C analysis, especially Calpha tensors which are directly related to structure. Carbonyl and (15)N CSA tensors demonstrate a more complex dependence upon hydrogen bonding and electrostatics, in addition to conformational dependence. The improved understanding of these tensors and the ability to measure them quantitatively provide additional opportunities for structure determination, as well as insights into dynamics.

Environmentally friendly flame retardants. A detailed solid-state NMR study of melamine orthophosphate

We used solid-state NMR spectroscopy to gain detailed information about the proton positions, proximities and the hydrogen-bonding network in the environmentally friendly flame retardant melamine orthophosphate (MP). High-resolution proton one- and two-dimensional solid-state NMR spectra were obtained at high external magnetic field in combination with fast magic angle spinning of the sample. Furthermore, we recorded homo- and heteronuclear correlation spectra of types (15)N–(15)N, (1)H–(13)C, (1)H–(15)N and (1)H–(31)P. In addition, we determined the geometry of the NH and NH(2) groups in MP by (15)N–(1)H heteronuclear recoupling experiments.We were able to completely assign the different isotropic chemical shifts in MP. Furthermore, we could identify the protonation of the melamine and orthophosphate moieties. The experimental results are discussed in connection with the structural model obtained by powder X-ray diffraction together with a combined molecular modeling-Rietveld refinement approach (De Ridder et al. Helv. Chim. Acta 2004; 87: 1894). We show that the geometry of the NH2 groups can only be successfully estimated by solid-state NMR.

NMR structural studies of the antibiotic lipopeptide daptomycin in DHPC micelles

Daptomycin is a cyclic anionic lipopeptide that exerts its rapid bactericidal effect by perturbing the bacterial cell membrane, a mode of action different from most other currently commercially available antibiotics (except e.g. polymyxin and gramicidin). Recent work has shown that daptomycin requires calcium in the form of Ca2+ to form a micellar structure in solution and to bind to bacterial model membranes. This evidence sheds light on the initial steps in the mechanism of action of this novel antibiotic. To understand how daptomycin goes on to perturb bacterial membranes, its three-dimensional structure has been determined in the presence of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micelles. NMR spectra of daptomycin in DHPC were obtained under two conditions, namely in the presence of Ca2+ as used by Jung et al. [D. Jung, A. Rozek, M. Okon, R.E.W. Hancock, Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin, Chem. Biol. 11 (2004) 949-57] to solve the calcium-conjugated structure of daptomycin in solution and in a phosphate buffer as used by Rotondi and Gierasch [K.S. Rotondi, L.M. Gierasch, A well-defined amphipathic conformation for the calcium-free cyclic lipopeptide antibiotic, daptomycin, in aqueous solution, Biopolymers 80 (2005) 374-85] to solve the structure of apo-daptomycin. The structures were calculated using molecular dynamics time-averaged refinement. The different sample conditions used to obtain the NMR spectra are discussed in light of fluorescence data, lipid flip-flop and calcein release assays in PC liposomes, in the presence and absence of Ca2+ [D. Jung, A. Rozek, M. Okon, R.E.W. Hancock, Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin, Chem. Biol. 11 (2004) 949-57]. The implications of these results for the membrane perturbation mechanism of daptomycin are discussed.

NMR studies on fully hydrated membrane proteins, with emphasis on bacteriorhodopsin as a typical and prototype membrane protein

The 3D structures or dynamic feature of fully hydrated membrane proteins are very important at ambient temperature, in relation to understanding their biological activities, although their data, especially from the flexible portions such as surface regions, are unavailable from X-ray diffraction or cryoelectron microscope at low temperature. In contrast, high-resolution solid-state NMR spectroscopy has proved to be a very convenient alternative means to be able to reveal their dynamic structures. To clarify this problem, we describe here how we are able to reveal such structures and dynamic features, based on intrinsic probes from high-resolution solid-state NMR studies on bacteriorhodopsin (bR) as a typical membrane protein in 2D crystal, regenerated preparation in lipid bilayer and detergents. It turned out that their dynamic features are substantially altered upon their environments where bR is present. We further review NMR applications to study structure and dynamics of a variety of membrane proteins, including sensory rhodopsin, rhodopsin, photoreaction centers, diacylglycerol kinases, etc.

The truncated driven NOE and (13)C NMR sensitivity enhancement in magnetically-aligned bicelles

The truncated driven nuclear Overhauser effect (NOE) sequence is examined as a means of sensitivity enhancement in (13)C NMR spectroscopy of magnetically-aligned bicelles consisting of 4.5:1 mixtures of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) plus DHPC (1,2-dihexanoyl-sn-glycero-3-phosphocholine), with 1 mole% DMPE-PEG 2000 (1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-methoxy(polyethylene glycol)-2000). Steady-state NOE enhancements were observed at all carbon segments except the lipid carbonyls, but full NOE enhancements were obtained only for the most mobile carbon segments, specifically the choline quaternary methyls and terminal acyl chain methyls of both DMPC and DHPC, as well as the ethylene oxide segments of the PEG head group of DMPE-PEG 2000. Other carbon segments exhibited NOE enhancements that scaled with mobility as determined by transient NOE measurements combined with spin-lattice relaxation measurements. We conclude that the truncated driven NOE provides sensitivity enhancement complimentary to that yielded by cross-polarization techniques and for mobile membrane-associated species may be preferred for its robustness and ease of setup.

Cross- and axial-peak intensities in 2D-SLF experiments based on cross-polarization--the role of the initial density matrix

Simulations and experiments on simple oriented systems have been used to estimate the relative ratio of cross-peak to axial-peak intensities in 2D-SLF experiments based on dipolar oscillations during cross-polarization (CP). The density matrix prior to dipolar evolution is considered and for an isolated spin pair, it is shown that direct calculations of the ratios match well with simulations and experimental results. Along with the standard CP pulse sequence, two other pulse sequences namely CP with polarization inversion (PI-CP) and another novel variation of the standard CP experiment (EXE-CP) reported recently have been considered. Inclusion of homonuclear dipolar coupling has been observed to increase the axial-peak intensities. In combination with Lee-Goldburg (LG) decoupling, experiments on an oriented liquid crystalline sample have been carried out and the performance of the pulse schemes have been compared. The applicability of the new pulse sequence for different samples and different nuclei is discussed. Such studies are expected to lead to a better understanding of the experiments and to the design of useful pulse sequences.

Selective averaging for high-resolution solid-state NMR spectroscopy of aligned samples

Solid-state NMR experiments benefit from being performed at high fields, and this is essential in order to obtain spectra with the resolution and sensitivity required for applications to protein structure determination in aligned samples. Since the amount of rf power that can be applied is limited, especially for aqueous protein samples, the most important pulse sequences suffer from bandwidth limitations resulting from the same spread in chemical shift frequencies that aids resolution. SAMPI4 is a pulse sequence that addresses these limitations. It yields separated local field spectra with narrower and more uniform linewidths over the entire spectrum than the currently used PISEMA and SAMMY experiments. In addition, it is much easier to set up on commercial spectrometers and can be incorporated as a building block into other multidimensional pulse sequences. This is illustrated with a two-dimensional HETCOR experiment, where it is crucial to transfer polarization from the amide protons to their directly bonded nitrogens over a wide range of chemical shift frequencies. A quantum-mechanical treatment of the spin Hamiltonians under high-power rf pulses is presented which gives the scaling factor for SAMPI4 as well as the durations of the rf pulses to achieve optimal decoupling.

2D separated-local-field spectra from projections of 1D experiments

A novel procedure for reconstruction of 2D separated-local-field (SLF) NMR spectra from projections of 1D NMR data is presented. The technique, dubbed SLF projection reconstruction from one-dimensional spectra (SLF-PRODI), is particularly useful for uniaxially oriented membrane protein samples and represents a fast and robust alternative to the popular PISEMA experiment which correlates (1)H-(15)N dipole-dipole couplings with (15)N chemical shifts. The different 1D projections in the SLF-PRODI experiment are obtained from 1D spectra recorded under influence of homonuclear decoupling sequences with different scaling factors for the heteronuclear dipolar couplings. We demonstrate experimentally and numerically that as few as 2-4 1D projections will normally be sufficient to reconstruct a 2D SLF-PRODI spectrum with a quality resembling typical PISEMA spectra, leading to significant reduction of the acquisition time.

Sensitivity and resolution enhancement in solid-state NMR spectroscopy of bicelles

Magnetically aligned bicelles are becoming attractive model membranes to investigate the structure, dynamics, geometry, and interaction of membrane-associated peptides and proteins using solution- and solid-state NMR experiments. Recent studies have shown that bicelles are more suitable than mechanically aligned bilayers for multidimensional solid-state NMR experiments. In this work, we describe experimental aspects of the natural abundance (13)C and (14)N NMR spectroscopy of DMPC/DHPC bicelles. In particular, approaches to enhance the sensitivity and resolution and to quantify radio-frequency heating effects are presented. Sensitivity of (13)C detection using single pulse excitation, conventional cross-polarization (CP), ramp-CP, and NOE techniques are compared. Our results suggest that the proton decoupling efficiency of the FLOPSY pulse sequence is better than that of continuous wave decoupling, TPPM, SPINAL, and WALTZ sequences. A simple method of monitoring the water proton chemical shift is demonstrated for the measurement of sample temperature and calibration of the radio-frequency-induced heating in the sample. The possibility of using (14)N experiments on bicelles is also discussed.

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, topology, and tilt of cell-signaling peptides containing nuclear localization sequences in membrane bilayers determined by solid-state NMR and molecular dynamics simulation studies

Cell-signaling peptides have been extensively used to transport functional molecules across the plasma membrane into living cells. These peptides consist of a hydrophobic sequence and a cationic nuclear localization sequence (NLS). It has been assumed that the hydrophobic region penetrates the hydrophobic lipid bilayer and delivers the NLS inside the cell. To better understand the transport mechanism of these peptides, in this study, we investigated the structure, orientation, tilt of the peptide relative to the bilayer normal, and the membrane interaction of two cell-signaling peptides, SA and SKP. Results from CD and solid-state NMR experiments combined with molecular dynamics simulations suggest that the hydrophobic region is helical and has a transmembrane orientation with the helical axis tilted away from the bilayer normal. The influence of the hydrophobic mismatch, between the hydrophobic length of the peptide and the hydrophobic thickness of the bilayer, on the tilt angle of the peptides was investigated using thicker POPC and thinner DMPC bilayers. NMR experiments showed that the hydrophobic domain of each peptide has a tilt angle of 15 +/- 3 degrees in POPC, whereas in DMPC, 25 +/- 3 degree and 30 +/- 3 degree tilts were observed for SA and SKP peptides, respectively. These results are in good agreement with molecular dynamics simulations, which predict a tilt angle of 13.3 degrees (SA in POPC), 16.4 degrees (SKP in POPC), 22.3 degrees (SA in DMPC), and 31.7 degrees (SKP in DMPC). These results and simulations on the hydrophobic fragment of SA or SKP suggest that the tilt of helices increases with a decrease in bilayer thickness without changing the phase, order, and structure of the lipid bilayers.

Fast proton spin-lattice relaxation time in the rotating frame during the application of time averaged precession frequency

A relatively rapid phase alternation of the effective field in the time averaged precession frequency (TAPF) sequence results in averaging of the proton RF spin-lock field. The spin-locking of the proton magnetization becomes less efficient and thus shortens T(1rho)(H), the proton spin-lattice relaxation time in the rotating frame. The relaxation time also depends on the ratio of tau(1) and tau(2) intervals i.e. tau(1)/tau(2) and not only on the number of tau(c)=tau(1)+tau(2) blocks, i.e. the number of the phase transients. Experiments are performed on solid samples of ferrocene and glycine and for some time intervals, T(1rho)(H) is shortened by factors of 9-100 compared to the relaxation times obtained in the standard experiment.

Multi-dimensional 1H-13C HETCOR and FSLG-HETCOR NMR study of sphingomyelin bilayers containing cholesterol in the gel and liquid crystalline states

(13)C cross polarization magic angle spinning (CP-MAS) and (1)H MAS NMR spectra were collected on egg sphingomyelin (SM) bilayers containing cholesterol above and below the liquid crystalline phase transition temperature (T(m)). Two-dimensional (2D) dipolar heteronuclear correlation (HETCOR) spectra were obtained on SM bilayers in the liquid crystalline (L(alpha)) state for the first time and display improved resolution and chemical shift dispersion compared to the individual (1)H and (13)C spectra and significantly aid in spectral assignment. In the gel (L(beta)) state, the (1)H dimension suffers from line broadening due to the (1)H-(1)H homonuclear dipolar coupling that is not completely averaged by the combination of lipid mobility and MAS. This line broadening is significantly suppressed by implementing frequency switched Lee-Goldburg (FSLG) homonuclear (1)H decoupling during the evolution period. In the liquid crystalline (L(alpha)) phase, no improvement in line width is observed when FSLG is employed. All of the observed resonances are assignable to cholesterol and SM environments. This study demonstrates the ability to obtain 2D heteronuclear correlation experiments in the gel state for biomembranes, expands on previous SM assignments, and presents a comprehensive (1)H/(13)C NMR assignment of SM bilayers containing cholesterol. Comparisons are made to a previous report on cholesterol chemical shifts in dimyristoylphosphatidylcholine (DMPC) bilayers. A number of similarities and some differences are observed and discussed.

Current Applications of Bicelles in NMR Studies of Membrane-Associated Amphiphiles and Proteins,

This review covers current trends in studies of membrane amphiphiles and membrane proteins using both fast tumbling bicelles and magnetically aligned bicelle media for both solution state and solid state NMR. The fast tumbling bicelles provide a versatile biologically mimetic membrane model, which in many cases is preferable to micelles, both because of the range of lipids and amphiphiles that may be combined and because radius of curvature effects and strain effects common with micelles may be avoided. Drug and small molecule binding and partitioning studies should benefit from their application in fast tumbling bicelles, tailored to mimic specific membranes. A wide range of topology and immersion depth studies have been shown to be effective in fast tumbling bicelles, while residual dipolar couplings add another dimension to structure refinement possibilities, particularly for situations in which the peptide is uniformly labeled with 15N and 13C. Solid state NMR studies of polytopic transmembrane proteins demonstrate that it is possible to express, purify, and reconstitute membrane proteins, ranging in size from single transmembrane domains to seven-transmembrane GPCRs, into bicelles. The line widths and quality of the resulting 15NH dipole-15N chemical shift spectra demonstrate that there are no insurmountable obstacles to the study of large membrane proteins in magnetically aligned media.

Determinations of 15N Chemical Shift Anisotropy Magnitudes in a Uniformly 15N,13C-Labeled Microcrystalline Protein by Three-Dimensional Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy

Amide 15N chemical shift anisotropy (CSA) tensors provide quantitative insight into protein structure and dynamics. Experimental determinations of 15N CSA tensors in biologically relevant molecules have typically been performed by NMR relaxation studies in solution, goniometric analysis of single-crystal spectra, or slow magic-angle spinning (MAS) NMR experiments of microcrystalline samples. Here we present measurements of 15N CSA tensor magnitudes in a protein of known structure by three-dimensional MAS solid-state NMR. Isotropic 15N, 13C alpha, and 13C' chemical shifts in two dimensions resolve site-specific backbone amide recoupled CSA line shapes in the third dimension. Application of the experiments to the 56-residue beta1 immunoglobulin binding domain of protein G (GB1) enabled 91 independent determinations of 15N tensors at 51 of the 55 backbone amide sites, for which 15N-13C alpha and/or 15N-13C' cross-peaks were resolved in the two-dimensional experiment. For 37 15N signals, both intra- and interresidue correlations were resolved, enabling direct comparison of two experimental data sets to enhance measurement precision. Systematic variations between beta-sheet and alpha-helix residues are observed; the average value for the anisotropy parameter, delta (delta = delta(zz) - delta(iso)), for alpha-helical residues is 6 ppm greater than that for the beta-sheet residues. The results show a variation in delta of 15N amide backbone sites between -77 and -115 ppm, with an average value of -103.5 ppm. Some sites (e.g., G41) display smaller anisotropy due to backbone dynamics. In contrast, we observe an unusually large 15N tensor for K50, a residue that has an atypical, positive value for the backbone phi torsion angle. To our knowledge, this is the most complete experimental analysis of 15N CSA magnitude to date in a solid protein. The availability of previous high-resolution crystal and solution NMR structures, as well as detailed solid-state NMR studies, will enhance the value of these measurements as a benchmark for the development of ab initio calculations of amide 15N shielding tensor magnitudes.

Solid-state NMR investigation of the membrane-disrupting mechanism of antimicrobial peptides MSI-78 and MSI-594 derived from magainin 2 and melittin

The mechanism of membrane interaction of two amphipathic antimicrobial peptides, MSI-78 and MSI-594, derived from magainin-2 and melittin, is presented. Both the peptides show excellent antimicrobial activity. The 8-anilinonaphthalene-1-sulfonic acid uptake experiment using Escherichia coli cells suggests that the outer membrane permeabilization is mainly due to electrostatic interactions. The interaction of MSI-78 and MSI-594 with lipid membranes was studied using 31P and 2H solid-state NMR, circular dichroism, and differential scanning calorimetry techniques. The binding of MSI-78 and MSI-594 to the lipid membrane is associated with a random coil to alpha-helix structural transition. MSI-78 and MSI-594 also induce the release of entrapped dye from POPC/POPG (3:1) vesicles. Measurement of the phase-transition temperature of peptide-DiPoPE dispersions shows that both MSI-78 and MSI-594 repress the lamellar-to-inverted hexagonal phase transition by inducing positive curvature strain. 15N NMR data suggest that both the peptides are oriented nearly perpendicular to the bilayer normal, which infers that the peptides most likely do not function via a barrel-stave mechanism of membrane-disruption. Data obtained from 31P NMR measurements using peptide-incorporated POPC and POPG oriented lamellar bilayers show a disorder in the orientation of lipids up to a peptide/lipid ratio of 1:20, and the formation of nonbilayer structures at peptide/lipid ratio>1:8. 2H-NMR experiments with selectively deuterated lipids reveal peptide-induced disorder in the methylene units of the lipid acyl chains. These results are discussed in light of lipid-peptide interactions leading to the disruption of membrane via either a carpet or a toroidal-type mechanism.

Order parameters based on (13)C(1)H, (13)C(1)H(2) and (13)C(1)H(3) heteronuclear dipolar powder patterns: a comparison of MAS-based solid-state NMR sequences

Order parameters describing conformational exchange processes on the nanosecond to microsecond timescale can be obtained from powder patterns in solid-state NMR (SSNMR) experiments. Extensions of these experiments to magic-angle spinning (MAS) based high-resolution experiments have been demonstrated, which show a great promise for site-specific probes of biopolymers. In this study, we present a detailed comparison of two pulse sequences, transverse Manfield-Rhim-Elleman-Vaughn (T-MREV) and Lee-Goldburg cross-polarization (LGCP), using experimental and simulation tools to explore their utility in the study of order parameters. We discuss systematic errors due to passively coupled (13)C or (1)H nuclei, as well as due to B(1) inhomogeneity. Both pulse sequences can provide quantitative measurements of the order parameter, but the LGCP experiment is capable of greater accuracy provided that the B(1) field is highly homogeneous. The T-MREV experiment is far better compensated for B(1) inhomogeneity, and it also performs better in situations with limited signal.

Structural Analysis of a Melaminium Polyphosphate from X-ray Powder Diffraction and Solid-State NMR Data

The crystal structure of the environmentally friendly flame retardant melaminium polyphosphate (MPoly) (2,4,6-triamino-1,3,5-triazinium x PO(3))(n)was determined by a direct-space global optimization technique from X-ray powder diffraction data. Solid-state NMR was used to corroborate the proposed hydrogen-bonding model and to determine the average degree of polymerization (n > 100). An analysis of the crystal structure of MPoly reveals aspects of molecular geometry and packing that are characteristic for melamine-containing compounds and polyphosphate salts. A comparison of MPoly with the crystal structures of its precursors melaminium orthophosphate (MP) and melaminium dihydrogenpyrophosphate (MPy) provides insight in the mechanism of the endothermic dehydration processes that takes place in the reaction path MP --> MPy --> MPoly. Solid-state NMR characterization of various samples of the same batch showed inhomogeneities in the MPoly composition. Various quantities of orthophosphates were found, which cannot be assigned to be MP.

PITANSEMA-MAS, a solid-state NMR method to measure heteronuclear dipolar couplings under MAS

A 2D NMR method is presented for the measurement of the dipole-dipole interaction between a proton and a low-frequency nuclear spin species in the solid state under the magic angle spinning. It employs the time averaged nutation concept to dramatically reduce the required radio frequency (rf) power on the low γ nuclear channel and spin exchange at the magic angle is used to suppress (1)H-(1)H dipolar interactions and chemical shifts. The flexibility in choosing the spinning speed, rf power and the scaling factor of the pulse sequence are of considerable importance for the structural studies of biological solids. The performance of the pulse sequence has been numerically and experimentally demonstrated on several solids.

Can PISEMA experiments be used to extract structural parameters for mobile beta-barrels?

The effect of mobility on 15N chemical shift/15N-(1)H dipolar coupling (PISEMA) solid state NMR experiments applied to macroscopically oriented beta-barrels is assessed using molecular dynamics simulation data of the NalP autotransporter domain embedded in a DMPC bilayer. In agreement with previous findings for alpha-helices, the fast librational motion of the peptide planes is found to have a considerable effect on the calculated PISEMA spectra. In addition, the dependence of the chemical shift anisotropy (CSA) and dipolar coupling parameters on the calculated spectra is evaluated specifically for the beta-barrel case. It is found that the precise choice of the value of the CSA parameters sigma11, sigma22 and sigma33 has only a minor effect, whereas the choice of the CSA parameter theta shifts the position of the peaks by up to 20 ppm and changes the overall shape of the spectrum significantly. As was found for alpha-helices, the choice of the NH bond distance has a large effect on the dipolar coupling constant used for the calculations. Overall, it is found that the alternating beta-strands in the barrel occupy distinct regions of the PISEMA spectra, forming patterns which may prove useful in peak assignment.

Studies of Organically Functionalized Mesoporous Silicas Using Heteronuclear Solid-State Correlation NMR Spectroscopy under Fast Magic Angle Spinning

Highly resolved solid-state HETCOR NMR spectra between protons and low gamma nuclei ((13)C and (29)Si) can be suitably obtained on surfaces using a "brute force" (1)H-(1)H decoupling by MAS at rates > or =40 kHz. Despite a small rotor volume (<10 microL), a (1)H-(13)C HETCOR spectrum of allyl groups (AL, -CH(2)-CH=CH(2)) covalently anchored to the surface of MCM-41 silica was acquired without using isotope enrichment. The advantages of using fast MAS in such studies include easy setup, robustness, and the opportunity of using low RF power for decoupling. In the case of the (1)H-(29)Si HETCOR experiment, the sensitivity can be dramatically increased, in some samples by more than 1 order of magnitude, through implementing into the pulse sequence a Carr-Purcell-Meiboom-Gill train of pi pulses at the (29)Si spin frequency. The use of low-power heteronuclear decoupling is essential in the (1)H-(29)Si CPMG-HETCOR experiment, due to unusually long acquisition periods. These methods provided detailed structural characterization of the surface of AL-MCM mesoporous silica.

A 2D Solid-State NMR Experiment To Resolve Overlapping Aromatic Resonances of Thiophene-Based Nematogens

In this study, we demonstrate the feasibility of resolving overlapping 13C chemical shift spectral lines of aromatic rings in a thiophene-based nematogen in the mesophase using a 2D PITANSEMA solid-state NMR method. This technique provided the information about chemical shift values as well as dipolar couplings that are used for determining the orientational order parameter. Large C-H dipolar coupling values measured for thiophene in contrast to phenyl rings suggest that the heterocyclic ring is not part of the molecular axis. Using the order parameter, we determined the orientation of C-H vectors of the thiophene ring. We believe that the 2D solid-state NMR can be extended to other types of liquid crystalline materials such as the banana-based mesogens for determining the orientational order and bent angle.

15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores

This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

Structural basis of the temperature transition of Pf1 bacteriophage

The filamentous bacteriophage Pf1 undergoes a reversible temperature-dependent transition that is also influenced by salt concentrations. This structural responsiveness may be a manifestation of the important biological property of flexibility, which is necessary for long, thin filamentous assemblies as a protection against shear forces. To investigate structural changes in the major coat protein, one- and two-dimensional solid-state NMR spectra of concentrated solutions of Pf1 bacteriophage were acquired, and the structure of the coat protein determined at 0 degrees C was compared with the structure previously determined at 30 degrees C. Despite dramatic differences in the NMR spectra, the overall change in the coat protein structure is small. Changes in the orientation of the C-terminal helical segment and the conformation of the first five residues at the N-terminus are apparent. These results are consistent with prior studies by X-ray fiber diffraction and other biophysical methods.

NMR experiments on aligned samples of membrane proteins

NMR methods can be used to determine the structures of membrane proteins. Lipids can be chosen so that protein-containing micelles, bicelles, or bilayers are available as samples. All three types of samples can be aligned weakly or strongly, depending on their rotational correlation time. Solution NMR methods can be used with weakly aligned micelle and small bicelle samples. Solid-state NMR methods can be used with mechanically aligned bilayer and magnetically aligned bicelle samples.

Structural and orientational constraints of bacteriorhodopsin in purple membranes determined by oriented-sample solid-state NMR spectroscopy

We report for the first time, oriented-sample solid-state NMR experiments, specifically polarization inversion spin exchange at the magic angle (PISEMA) and 1H-15N heteronuclear chemical shift correlation (HETCOR), applied to an integral seven-transmembrane protein, bacteriorhodopsin (bR), in natural membranes. The spectra of [15N]Met-bR revealed clearly distinguishable signals from the helical and loop regions. By deconvolution of the helix resonances, it was possible to establish constraints for some helix tilt angles. It was estimated that the extracellular section of helix B has a tilt of less than 5 degrees from the membrane normal, while the tilt of helix A was estimated to be 18-22 degrees , both of which are in agreement with most crystal structures. Comparison of the experimental PISEMA spectrum with simulated spectra based on crystal structures showed that PISEMA and HETCOR experiments are extremely sensitive to the polytopic protein structure, and the solid-state NMR spectra for membrane-embedded bR matched most favorably with the recent 1FBB electron crystallography structure. These results suggest that this approach has the potential to yield structural and orientational constraints for large integral polytopic proteins whilst intercalated and functionally competent in a natural membrane.