The interaction of helical polypeptides with biological model membranes

Proton-decoupled solid-state ¹⁵N NMR spectroscopy was used to investigate helical peptides reconstituted into oriented phospholipid bilayers. Hydrophobic channel peptides such as the N-terminal region of Vpu of human immunodeficiency virus (HIV-1) adopt transmembrane orientations, whereas amphipathic peptide antibiotics are oriented parallel to the bilayer surface. The alignment of helical peptides in lipid membranes was analysed in some detail using model peptides. In particular, peptides with pH-dependent topology and a series of peptides that allow one to study the contributions of specific interactions were designed. The energies of transfer of several amino acids from the in-plane to transmembrane localisation were determined. In addition, the alignment of peptides and phospholipids under conditions of hydrophobic mismatch have been investigated in considerable detail.     

Pore structure, thinning effect, and lateral diffusive dynamics of oriented lipid membranes interacting with antimicrobial peptide protegrin-1: 31P and 2H solid-state NMR study

Membrane pores that are induced in oriented membranes by an antimicrobial peptide (AMP), protegrin-1 (PG-1), are investigated by (31)P and (2)H solid state NMR spectroscopy. We incorporated a well-studied peptide, protegrin-1 (PG-1), a beta-sheet AMP, to investigate AMP-induced dynamic supramolecular lipid assemblies at different peptide concentrations and membrane compositions. Anisotropic NMR line shapes specifying toroidal pores and thinned membranes, which are formed in membrane bilayers by the binding of AMPs, have been analyzed for the first time. Theoretical NMR line shapes of lipids distributed on the surface of toroidal pores and thinned membranes reproduce reasonably well the line shape characteristics of our experimentally measured (31)P and (2)H solid-state NMR spectra of oriented lipids binding with PG-1. The lateral diffusions of lipids are also analyzed from the motionally averaged one- and two-dimensional (31)P and (2)H solid-state NMR spectra of oriented lipids that are binding with AMPs.     

Resolution enhancement in solid-state NMR of oriented membrane proteins by anisotropic differential linebroadening

We demonstrate that a significant improvement in the spectral resolution may be achieved in solid-state NMR experiments of proteins in inhomogeneously disordered oriented lipid bilayers. Using 1H homonuclear decoupling instead of standard 1H heteronuclear decoupling, the 15N line widths may be reduced by up to seven times for such samples. For large oriented membrane proteins, such resolution enhancements may be crucial for assignment and structural interpretation.     

Structure determination of a membrane protein in proteoliposomes

An NMR method for determining the three-dimensional structures of membrane proteins in proteoliposomes is demonstrated by determining the structure of MerFt, the 60-residue helix-loop-helix integral membrane core of the 81-residue mercury transporter MerF. The method merges elements of oriented sample (OS) solid-state NMR and magic angle spinning (MAS) solid-state NMR techniques to measure orientation restraints relative to a single external axis (the bilayer normal) from individual residues in a uniformly (13)C/(15)N labeled protein in unoriented liquid crystalline phospholipid bilayers. The method relies on the fast (>10(5) Hz) rotational diffusion of membrane proteins in bilayers to average the static chemical shift anisotropy and heteronuclear dipole-dipole coupling powder patterns to axially symmetric powder patterns with reduced frequency spans. The frequency associated with the parallel edge of such motionally averaged powder patterns is exactly the same as that measured from the single line resonance in the spectrum of a stationary sample that is macroscopically aligned parallel to the direction of the applied magnetic field. All data are collected on unoriented samples undergoing MAS. Averaging of the homonuclear (13)C/(13)C dipolar couplings, by MAS of the sample, enables the use of uniformly (13)C/(15)N labeled proteins, which provides enhanced sensitivity through direct (13)C detection as well as the use of multidimensional MAS solid-state NMR methods for resolving and assigning resonances. The unique feature of this method is the measurement of orientation restraints that enable the protein structure and orientation to be determined in unoriented proteoliposomes.     

Peptide-related alterations of membrane-associated water: deuterium solid-state NMR investigations of phosphatidylcholine membranes at different hydration levels

Deuterated water associated with oriented POPC bilayers was investigated before and after the addition of 2 mol% peptide. Membranes in the presences of antimicrobial-(LAH4), pore-forming- (the segments M2 of influenza A and S4 of the domain I of rat brain sodium channels) or lysine-containing model peptides (LAK1 and LAK3) were investigated by (2)H and proton-decoupled (31)P solid-state NMR. The NMR spectra were recorded as a function of hydration in the range between 15 and 93% relative humidity and of sample composition. In the presence of peptides an increased association of water is observed. A quantitative analysis suggests that the peptide-induced changes in the lipid bilayer packing have a significant effect on membrane-water association. The quadrupolar splittings of (2)H(2)O at a given degree of hydration indicate that the changes of the water deuterium order parameter are specific for the peptide sequence and the lipid composition.     

Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle

Membrane protein orientation has traditionally been determined by NMR using mechanically or magnetically aligned samples. Here we show a new NMR approach that abolishes the need for preparing macroscopically aligned membranes. When the protein undergoes fast uniaxial rotation around the bilayer normal, the 0 degrees -frequency of the motionally averaged powder spectrum is identical to the frequency of the aligned protein whose alignment axis is along the magnetic field. Thus, one can use unoriented membranes to determine the orientation of the protein relative to the bilayer normal. We demonstrate this approach on the M2 transmembrane peptide (M2TMP) of influenza A virus, which is known to assemble into a proton-conducting tetrameric helical bundle. The fast uniaxial rotational diffusion of the M2TMP helical bundle around the membrane normal is characterized via 2H quadrupolar couplings, C-H and N-H dipolar couplings, 13C chemical shift anisotropies, and 1H T1rho relaxation times. We then show that 15N chemical shift anisotropy and N-H dipolar coupling measured on these powder samples can be analyzed to yield precise tilt angles and rotation angles of the helices. The data show that the tilt angle of the M2TMP helices depends on the membrane thickness to reduce the hydrophobic mismatch. Moreover, the orientation of a longer M2 peptide containing both the transmembrane domain and cytoplasmic residues is similar to the orientation of the transmembrane domain alone, suggesting that the transmembrane domain regulates the orientation of this protein and that structural information obtained from M2TMP may be extrapolated to the longer peptide. This powder-NMR approach for orientation determination is generally applicable and can be extended to larger membrane proteins.     

Intermolecular packing and alignment in an ordered beta-hairpin antimicrobial peptide aggregate from 2D solid-state NMR

The aggregation and packing of a membrane-disruptive beta-hairpin antimicrobial peptide, protegrin-1 (PG-1), in the solid state are investigated to understand its oligomerization and hydrogen-bonding propensity. Incubation of PG-1 in phosphate buffer saline produced well-ordered nanometer-scale aggregates, as indicated by 13C and 15N NMR line widths, chemical shifts, and electron microscopy. Two-dimensional 13C and 1H spin diffusion experiments using C-terminus strand and N-terminus strand labeled peptides indicate that the beta-hairpin molecules in these ordered aggregates are oriented parallel to each other with like strands lining the intermolecular interface. In comparison, disordered and lyophilized peptide samples are randomly packed with both parallel and antiparallel alignments. The PG-1 aggregates show significant immobilization of the Phe ring near the beta-turn, further supporting the structural ordering. The intermolecular packing of PG-1 found in the solid state is consistent with its oligomerization in lipid bilayers. This solid-state aggregation approach may be useful for determining the quaternary structure of peptides in general and for gaining insights into the oligomerization of antimicrobial peptides in lipid bilayers in particular.     

Characterization of (1)H-(1)H distances in a uniformly (2)H,(15)N-labeled SH3 domain by MAS solid-state NMR spectroscopy (section sign)

In this communication, we demonstrate the feasibility of obtaining long-range (1)H-(1)H distance information by MAS solid-state NMR for a microcrystalline, uniformly (2)H,(15)N-labeled sample of a SH3 domain of chicken alpha-spectrin. The experiments yield NOESY-type spectra and rely on the favorable dispersion of the (15)N chemical shifts of the protein backbone. Perdeuteration of nonexchangeable sites is employed to simplify proton spin systems and to obtain multiple structural information. Two mixing schemes, (1)H-(1)H double quantum filtered Post-C7 and (1)H spin diffusion, are implemented to obtain quantitative (1)H-(1)H distance information. Post-C7 and spin diffusion cross-peak buildup rates are discussed for initial-rate fitting and in the framework of n = 0 rotational resonance (rotor driven spin diffusion), respectively. Different deuteration schemes were tested to find conditions where short-range (1)H-(1)H interactions are truncated (e.g., between H(N) and H(alpha)), but long-range interactions are retained (e.g., between H(N) and H(N)).     

Headgroup motion in a lyotropic lamellar phase by deuterium and nitrogen-14 relaxation studies

Deuterium (2H) and nitrogen-14 (14N) NMR spectroscopy were used to investigate the molecular dynamics of a lyotropic liquid crystal. Deuterium spectral densities of motion for the C1 deuterated site on the chain of the molecule decylammonium chloride (DACl) at the Larmor frequency 61.4 MHz and those for the (14)N at the headgroup (NH(3)(+)) at 28.9 MHz are analyzed quantitatively in the lamellar phase of the DACl-d(11)/water binary system to shed light on the headgroup dynamics. The motional model used is the small step rotational diffusion for reorientations plus internal rotations of the methylene group in the strong collision limit. The tumbling motion of the long axis of the DACl molecule in the aggregates seems to be as rigorous as the molecular spinning motion, likely due to the proposed motional model. The similarity of deuterium spectral densities from the C1 and C2/C3 sites may indicate a relatively rigid unit of C1-C2-C3 in the backbone.     

Effect of SiO2 on the dynamics of proton conducting [Nafion/(SiO2)X] composite membranes: a solid-state 19F NMR study

Composite membranes, consisting of Nafion and inorganic oxide additives, are frequently discussed alternative materials to overcome the known low conductivity of pure Nafion at temperatures above 100 °C and at low relative humidity. It has been reported that under dry conditions, these membranes show enhanced water uptake and diffusion as compared to filler-free Nafion. This work focuses on the polymer mobility in Nafion/SiO(2) composites and on the impact of the silica particles on the polymer dynamics. [Nafion/(SiO(2))(X)] composite membranes (with X ranging from 0 to 15 wt%) in the dry and wet states were investigated by variable temperature solid-state (19)F NMR spectroscopy. (19)F T(1) and T(1ρ) relaxation times, and NMR lineshapes (linewidths and spinning sideband intensities) were analyzed to get information about the polymer mobility. It is found that Nafion composite membranes, in general, possess a higher mobility as compared to recast Nafion which is in agreement with previous results from conductivity studies. These findings are attributed to the ability of the SiO(2) particles to keep more water inside the composite membranes which also leads to a higher mobility of the polymer component. The results are further supported by the experimental (19)F{(1)H} CP/MAS NMR spectra. It is also shown that the structure of the composite membranes is more stable after dehydration, and possible condensation reactions are diminished in these membranes. In addition, the decrease in ionic exchange capacity after dehydration is less pronounced for the composite membranes as compared to filler-free Nafion.     

NMR study of the adsorption-desorption kinetics of dissolved tetraalanine in MCM-41 mesoporous material

In this study we show how deuterium magic-angle spinning NMR spectroscopy can be used to investigate the adsorption-desorption kinetics of molecules in solution at surface-liquid interfaces. An aqueous solution of deuterium-labeled tetraalanine is inserted in the pores of MCM-41 mesoporous material, and its 2H MAS NMR spectrum is measured as a function of temperature and fraction of filling of the pores. Prior to this study, the different types of water in MCM-41 are characterized as a function of water loading of the pores. Analysis of 2H MAS sideband line shapes enabled the determination of the adsorption and desorption rates and the activation energies of desorption.     

Characterization of reactive sites in supported catalysts by 51V/15N rotational echo double resonance NMR spectroscopy: formation of phenylimido groups at surface-bound oxovanadium sites

Silica-supported oxovanadium groups were reacted in a gas-solid reaction with aniline at 175 degrees C. The reaction was clean as monitored in situ by UV-vis spectroscopy and resulted in the elimination of water as the principal product of the reaction and the disappearance of the terminal V=O stretch in the Raman spectrum. 15N MAS solid-state NMR spectroscopy showed only a single nitrogen-containing species on the surface. Proton-dephased 15N NMR showed only weak attenuation of its intensity, indicating that there are no protons directly bonded to the nitrogen. The formation of a vanadium-imido covalent bond was characterized by 51V/15N rotational echo double resonance NMR spectroscopy where the quadrupolar 51V nucleus was monitored and the spin-1/2 15N nucleus was dephased.     

Modeling furanose ring dynamics in DNA

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

Orientational order and dynamics of molecules in the nematic phase 4-trans-(4-trans-n-propylcyclohexyl)cyclohexanenitrile

A sample of 4-trans-(4-trans-n-propylcyclohexyl)cyclohexanenitrile (CCH3) has been synthesized containing six deuterons randomly distributed between axial and equatorial positions in the cyanylated ring. The local orientational order parameters for axes fixed in this ring have been measured by obtaining the deuterium N.M.R. spectrum. The results show that the lack of symmetry and flexibility of the molecule affect the order matrix. The biaxiality in the local order matrix is small and could be close to zero, depending on the location, as yet unknown, of the principal axes. The spectral densities J₁(ω) and J₂(ω) have been measured for a sample oriented with the director orthogonal to B₀. It is shown that these spectral densities cannot be explained by the mechanism of relaxation being caused solely by director fluctuations. It is also not possible to explain the spectral densities by invoking only small-step rotational diffusion. A combination of these two relaxation mechanisms does fit the data.     

2H NMR characterization of phenylene ring flip motion in poly(p-phenylene vinylene) films

Solid-state ²H quadrupole echo nuclear magnetic resonance (NMR) spectra and measurements of ²H spin lattice relaxation times have been obtained for films of poly(p-phenylene vinylene) deuterated in phenylene ring positions (PPV-d₄). NMR line shapes show that all the phenylene rings of PPV undergo 180° rotational jumps about the 1,4 ring axis (“ring flips”) at 225°C. The temperature dependence of the ²H line shapes show that the jump motion is thermally activated, with a median activation energy, E_a = 15 kcal/mol, and a distribution of activation energies of less than ±2 kcal/mol. The jump rate was also determined from the magnitude of the anisotropic T₂ relaxation associated with ²H line shapes and from the curvature of inversion recovery intensity data. The experimental activation energy for jumps is comparable to the intramolecular potential barrier for rotation about phenylene vinylene bonds. ²H NMR provides a method for determining the phenylene-vinylene rotational barrier in pristine PPV, and may potentially be used to study conjugation in conducting films.     

Dependence of the size of a protein-SDS complex on detergent and Na+ concentrations

Sodium dodecyl sulfate (SDS) micelles provide ideal mimetic media for high-resolution NMR studies of membrane proteins and proteins or peptides interacting with micellar aggregates. (15)N NMR relaxation of the backbone amides of a protein-SDS complex has been measured under different experimental conditions. The rotational diffusion time of this complex has been found highly sensitive to detergent and NaCl concentrations. A comparison with calculated rotational diffusion times of protein-free SDS micelles under the same conditions suggests that the size of both aggregates must follow a similar functional dependence on detergent/NaCl concentration.     

Plant cell-wall cross-links by REDOR NMR spectroscopy

We present a new method that integrates selective biosynthetic labeling and solid-state NMR detection to identify in situ important protein cross-links in plant cell walls. We have labeled soybean cells by growth in media containing l-[ring-d(4)]tyrosine and l-[ring-4-(13)C]tyrosine, compared whole-cell and cell-wall (13)C CPMAS spectra, and examined intact cell walls using (13)C{(2)H} rotational echo double-resonance (REDOR) solid-state NMR. The proximity of (13)C and (2)H labels shows that 25% of the tyrosines in soybean cell walls are part of isodityrosine cross-links between protein chains. We also used (15)N{(13)C} REDOR of intact cell walls labeled by l-[ε-(15)N,6-(13)C]lysine and depleted in natural-abundance (15)N to establish that the side chains of lysine are not significantly involved in covalent cross-links to proteins or sugars.     

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.     

Furanose dynamics in the HhaI methyltransferase target DNA studied by solution and solid-state NMR relaxation

Both solid-state and solution NMR relaxation measurements are routinely used to quantify the internal dynamics of biomolecules, but in very few cases have these two techniques been applied to the same system, and even fewer attempts have been made so far to describe the results obtained through these two methods through a common theoretical framework. We have previously collected both solution 13C and solid-state 2H relaxation measurements for multiple nuclei within the furanose rings of several nucleotides of the DNA sequence recognized by HhaI methyltransferase. The data demonstrated that the furanose rings within the GCGC recognition sequence are very flexible, with the furanose rings of the cytidine, which is the methylation target, experiencing the most extensive motions. To interpret these experimental results quantitatively, we have developed a dynamic model of furanose rings based on the analysis of solid-state 2H line shapes. The motions are modeled by treating bond reorientations as Brownian excursions within a restoring potential. By applying this model, we are able to reproduce the rates of 2H spin-lattice relaxation in the solid and 13C spin-lattice relaxation in solution using comparable restoring force constants and internal diffusion coefficients. As expected, the 13C relaxation rates in solution are less sensitive to motions that are slower than overall molecular tumbling than to the details of global molecular reorientation, but are somewhat more sensitive to motions in the immediate region of the Larmor frequency. Thus, we conclude that the local internal motions of this DNA oligomer in solution and in the hydrated solid state are virtually the same, and we validate an approach to the conjoint analysis of solution and solid-state NMR relaxation and line shapes data, with wide applicability to many biophysical problems.     

Mobility of solid tert-butyl alcohol studied by deuterium NMR

The molecular mobility of solid deuterated tert-butyl alcohol (TBA) has been studied over a broad temperature range (103–283 K) by means of solid-state 2H NMR spectroscopy, including both line shape and anisotropy of spin–lattice relaxation analyses. It has been found that, while the hydroxyl group of the TBA molecule is immobile on the 2H NMR time scale (τC > 10(–5) s), its butyl group is highly mobile. The mobility is represented by the rotation of the methyl [CD3] groups about their 3-fold axes (C3 rotational axis) and the rotation of the entire butyl [(CD3)3-C] fragment about its 3-fold axis (C3′ rotational axis). Numerical simulations of spectra line shapes reveal that the methyl groups and the butyl fragment exhibit three-site jump rotations about their symmetry axes C3 and C3′ in the temperature range of 103–133 K, with the activation energies and preexponential factors E1 = 21 ± 2 kJ/mol, k(01) = (2.6 ± 0.5) × 10(12) s(–1) and E2 = 16 ± 2 kJ/mol, k(02) = (1 ± 0.2) × 10(12) s(–1), respectively. Analysis of the anisotropy of spin–lattice relaxation has demonstrated that the reorientation mechanism of the butyl fragment changes to a free diffusion rotational mechanism above 173 K, while the rotational mechanism of the methyl groups remains the same. The values of the activation barriers for both rotations at T > 173 K have the values, which are similar to those at 103–133 K. This indicates that the interaction potential defining these motions remains unchanged. The obtained data demonstrate that the detailed analysis of both line shape and anisotropy of spin–lattice relaxation represents a powerful tool to follow the evolution of the molecular reorientation mechanisms in organic solids.