Nuclear Magnetic Relaxation Data Research Articles

Influence of Pluronic F127 microenvironments on the photochemical nitric oxide release from S-nitrosoglutathione

Poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) (F127) hydrogels have been used to deliver nitric oxide (NO) topically in biomedical applications. Here, the effect of F127 microenvironments on the photochemical NO release from S-nitrosoglutathione (GSNO) was investigated in F127 solutions 7.6 wt% 15 wt% and 22.5 wt% at 15 °C and 37 °C. Small-angle X-ray Scattering (SAXS) and Differential Scanning Calorimetry (DSC) measurements, along with proton Nuclear Magnetic Resonance (1H NMR) spectral shifts and T2 relaxation data at six different concentration-temperature conditions, allowed identifying F127 microphases characterized by: a sol phase of unimers; micelles in non-defined periodic order, and a gel phase of cubic packed micelles. Kinetic measurements showed that GSNO photodecompositon proceeds faster in micellized F127 where GSNO is segregated to the intermicellar microenvironment. Real time kinetic monitoring of NO release and T2 relaxation profiles showed that NO is preferentially partitioned into the hydrophobic PPO cores of the F127 micelles, with the consequent decrease in its rate of release to the gas phase. These results show that F127 microphases affect both the kinetics of GSNO photodecomposition and the rate of NO escape and can be used to modulate the photochemical NO delivery from F127/GSNO solutions.

Nuclear relaxation rates in the herbertsmithite kagome antiferromagnets ZnCu3(OH)6Cl2

Local spectral functions and Nuclear Magnetic Relaxation (NMR) rates, 1/T1, for the spin-half Heisenberg antiferromagnet on the Kagome Lattice are calculated using Moriyas Gaussian approximation, as well as through an extrapolation of multiple frequency moments. The temperature dependence of the calculated rates is compared with the oxygen 1/T1 NMR data in Herbertsmithite. We find that the Gaussian approximation for 1/T1 shows behavior qualitatively similar to experiments with a sharp drop in rates at low temperatures, consistent with a spin-gapped behavior. However, this approximation significantly underestimates the magnitude of 1/T1 even at room temperature. Rates obtained from extrapolation of multiple frequency moments give very good agreement with the room temperature NMR data with J = 195 +/- 20 K and hyperfine couplings determined independently from other measurements. The use of multiple frequency moments also leads to additional low frequency weight in the local structure factors. The convergence of our calculations with higher frequency moments breaks down at low temperatures suggesting the existence of longer range dynamic correlations in the system despite the very short-range static correlations.

The Nedd4-1 WW Domain Recognizes the PY Motif Peptide through Coupled Folding and Binding Equilibria.

The four WW domains of human Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) interact with the PPxY (PY) motifs of the human epithelial Na(+) channel (hENaC) subunits, with the third WW domain (WW3*) showing the highest affinity. We have shown previously that the α-hENaC PY motif binding interface of WW3* undergoes conformational exchange on the millisecond time scale, indicating that conformational sampling plays a role in peptide recognition. To further understand this role, the structure and dynamics of hNedd4-1 WW3* were investigated. The nuclear Overhauser effect-derived structure of apo-WW3* resembles the domain in complex with the α-hENaC peptide, although particular side chain conformations change upon peptide binding, which was further investigated by molecular dynamics simulations. Model-free analysis of the (15)N nuclear magnetic resonance spin relaxation data showed that the apo and peptide-bound states of WW3* have similar backbone picosecond to nanosecond time scale dynamics. However, apo-WW3* exhibits pronounced chemical exchange on the millisecond time scale that is quenched upon peptide binding. (1)HN and (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments at various temperatures revealed that apo-WW3* exists in an equilibrium between the natively folded peptide binding-competent state and a random coil-like denatured state. The thermodynamics of the folding equilibrium was determined by fitting a thermal denaturation profile monitored by circular dichroism spectroscopy in combination with the CPMG data, leading to the conclusion that the unfolded state is populated to ∼ 20% at 37 °C. These results show that the binding of the hNedd4-1 WW3* domain to α-hENaC is coupled to the folding equilibrium.

Hydrate shell models of acetate ions according to nuclear magnetic relaxation data and quantum-chemical calculations

Different ion-water clusters for the CH3COO− ion that simulate the structure of its hydrate shells in solution are considered on the basis of the quantum mechanical approach. The possible coordination of water molecules around the ion is studied and the calculation results are compared with the experimental data obtained by nuclear magnetic relaxation.

Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition

By simplifying the interpretation of nuclear magnetic resonance spin relaxation and residual dipolar couplings data, recent developments involving the elongation of RNA helices are providing new atomic insights into the dynamical properties that allow RNA structures to change functionally and adaptively. Domain elongation, in concert with spin relaxation measurements, has allowed the detailed characterization of a hierarchical network of local and collective motional modes occurring at nanosecond timescale that mirror the structural rearrangements that take place following adaptive recognition. The combination of domain elongation with residual dipolar coupling measurements has allowed the experimental three-dimensional visualization of very large amplitude rigid-body helix motions in HIV-1 transactivation response element (TAR) that trace out a highly choreographed trajectory in which the helices twist and bend in a correlated manner. The dynamic trajectory allows unbound TAR to sample many of its ligand bound conformations, indicating that adaptive recognition occurs by "conformational selection" rather than "induced fit." These studies suggest that intrinsic flexibility plays essential roles directing RNA conformational changes along specific pathways.

Structural and Motional Changes Induced in apo-S100A1 Protein by the Disulfide Formation between Its Cys 85 Residue and β-Mercaptoethanol,

Recently, we have shown (Goch, G., Vdovenko, S., Kozłowska, H., and Bierzyński, A. (2005) FEBS J. 272, 2557-2565) that the chemical modification of Cys 85 residue of S100A1 protein by disulfide bond formation with small thiols such as glutathione, cysteine, or beta-mercaptoethanol (betaME) leads to a dramatic increase of the protein affinity for calcium. Therefore, the biological function of S100A1 as a calcium signal transmitter is probably regulated by the redox potential within the cell. Systematic, structural studies of various mixed disulfides of S100A1 in the apo and holo states are necessary to elucidate the mechanism of this phenomenon. Using NMR methods we have determined the structure of apo-S100A1-betaME and, on the basis of 15N nuclear magnetic relaxation data, we have characterized the structural dynamics of both: modified and unmodified molecules of apo-S100A1. The following effects of betaME modification have been observed: (1) Helices IV and IV' of two protein subunits are elongated by five residues (85-89). (2) Conformation of the calcium binding N-terminal loops is dramatically changed, and structural flexibility of the N-loops as well as C-loops markedly increases. (3) The angle between helices I and IV increases by approximately 20 degrees and between helices IV and IV' decreases by approximately 35 degrees . All these observations lead to the conclusion that betaME modification of apo-S100A1 makes its structure more similar to that of holo-S100A1, so that it becomes much better adjusted for calcium coordination.

Amplitudes and directions of internal protein motions from a JAM analysis of15N relaxation data

A method has been developed for characterizing dynamic structures of proteins in solution by using nuclear magnetic resonance (NMR) restraints and 15N relaxation data. This method is based on the concept of the jumping-among-minima (JAM) model. In this model we assume that protein dynamics can be described on the basis of conformational substates, and involves intra- and inter-substate motion. A set of substates is created by picking energy-minimized conformations from the conformational space consistent with the geometric NMR restraints. Intra-substate motions, which occur on the timescale of approximately 10 ps, are simulated with molecular dynamics (MD) calculations with force-field energy terms. Statistical weights of the conformational substates are determined to reproduce the NMR relaxation parameters. The refinement procedure consists of four stages: (i) determination of the ensemble of structures that satisfy NMR restraints, (ii) determination of intra-substate fluctuation, (iii) determination of statistical weights of conformational substates to reproduce model-free relaxation parameters, and (iv) analysis of the resulting dynamic structure to determine amplitudes and directions of internal protein motions. This method was employed to investigate structure and dynamics of the adhesion domain of human CD2 (hCD2) in solution. Two major collective modes, whose contributions to atomic mean-square fluctuations are 77.1% in total, are identified by the refinement. The first mode is interpreted as a rigid-body motion of a protein segment consisting of a part of the B--C loop, a part of the F strand, and the F--G loop. Another type of smaller-amplitude mode is indicated for the C'--C'' loop. The motions affect primarily the curvature of the slightly concave counterreceptor-binding site and represent transitions between a concave (closed) and flat (open) binding face. By comparing the ensemble of structures in solution to the complex structure with counterreceptor CD58, we found that these two types of motions resemble the change upon counterreceptor binding.

Spin-charge gauge approach to the pseudogap phase of high-Tccuprates: Theory versus experiments

We consider as a clue to the understanding of the pseudogap phase in high-T-c superconductors the metal-insulator crossover in underdoped, nonsuperconducting cuprates as temperature decreases and a similar crossover in superconducting cuprates when a strong magnetic field suppresses superconductivity. A spin [SU(2)] and charge [U(1)] Chern-Simons gauge field theory, applied to the t-J model, is developed to describe this striking phenomenon. Two length scales have been derived from the theory: the antiferromagnetic correlation length xiapproximate to(deltaparallel toln deltaparallel to)(-1/2), where delta is the doping concentration, and the thermal de Broglie wavelength of the dissipative charge carriers lambda(T)approximate to(Tdelta/t)(-1/2), where T is the temperature, t the hopping integral. At low temperatures xiless than or equal tolambda(T), the antiferromagnetic short-range order dominates, and the charge carriers become localized, showing insulating behavior. On the contrary, at high temperatures xigreater than or similar tolambda(T), the dissipative motion of charge carriers prevails, exhibiting metallic conductivity. Furthermore, the gauge interaction induces binding of spinons (spin excitation) and holons (charge carrier) into electron resonance. This process introduces a new energy scale, the inverse recombination time, which turns out to be essential in the interpretation of the out-of-plane resistivity. The major steps in the theoretical derivation of these results, particularly the calculation of the current-current correlation function and the Green's function for the physical electron, are presented with some detail. The obtained theoretical results are systematically compared with the in-plane and out-of-plane resistivity data and the magnetoresistance data, as well as the nuclear magnetic relaxation data in the pseudogap regime. Very good agreement is obtained.

Molecular reorientational dynamics of the neat ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate by measurement of 13C nuclear magnetic relaxation data.

The reorientational dynamics of the ionic liquid 1-butyl-3-methylimidzolium hexafluorophosphate ([BMIM]PF6) were studied over a wide range of temperatures by measurement of 13C spin-lattice relaxation rates and NOE factors. The reorientational dynamics were evaluated by performing fits to the experimental relaxation data. Thus, the overall reorientational motion was described by a Cole-Davidson spectral density with a Vogel-Fulcher-Tammann temperature dependence of the correlation times. The reorientational motion of the butyl chain was modelled by a combination of the latter model for the overall motion with a Bloembergen-Pur-cell-Pound spectral density and an Arrhenius temperature dependence for the internal motion. Except for C2 in the aromatic ring, an additional reduction of the spectral density by the Lipari-Szabo model had to be employed. This reduction is a consequence of fast molecular motions before the rotational diffusion process becomes effective. The C2 atom did not exhibit this reduction, because the librational motion of the corresponding C2-H vector is severely hindered due to hydrogen bonding with the hexafluorophosphate anion. The observed dynamic features of the [BMIM]+ cation confirm quantum-chemical structures obtained in a former study.

Reorientational Dynamics of the Model Compound 1,2,3,4-Tetrahydro-5,6-dimethyl- 1,4-methanonaphthalene in Neat Liquid from Temperature-Dependent 13C Nuclear Magnetic Relaxation Data: Spectral Densities and Correlation Functions

The reorientational motion of the hydrocarbon 1,2,3,4-tetrahydro-5,6-dimethyl-1,4-methanonaphthalene (5,6-Me2THMN) was studied over a wide range of temperature by the evaluation of 13C spin−lattice relaxation rates and NOE factors. The data from measurements at 22.63, 75.47, and 100.62 MHz were fitted to spectral densities introduced by Bloembergen, Purcell and Pound (1948), Davidson and Cole (1951), and for the first time, by a new spectral density derived from a Tricomi correlation function recently introduced by Zeidler (1991). For the temperature dependence of the correlation times, a Vogel−Fulcher−Tammann equation was applied. To obtain a reasonable fit with either Bloembergen−Purcell−Pound or Cole−Davidson spectral densities, it was necessary to apply the generalized order parameter from the approach by Lipari and Szabo (1982). The same quality of fit was achieved by the use of the Tricomi spectral density, although in this case it was not necessary to employ the Lipari−Szabo approach.

Cross terms and Kirkwood factors in dielectric relaxation of pure liquids

Dielectric relaxation reflects fluctuations of the total electric dipole moment of a liquid sample. If summed over molecular dipole moments, one obtains cross terms between molecular dipole moments of different particles which reflect collective contributions to dielectric relaxation. In the static case these collective effects are characterized by the well-known Kirkwood correlation factor g K . By comparing the dielectric relaxation times τ d of pure liquids with the single particle relaxation times τ s estimated from nuclear magnetic relaxation data, we show that collective effects affect the dynamical dielectric behavior. There is evidence for a relation of the simple form τ d = g K τ s .

Algorithm for preliminary evaluation of the correlation time of local dynamics in some polymeric materials

A method for preliminary evaluation of the correlation time of local dynamics of the polymeric chains, using the experimental nuclear magnetic resonance spin-lattice relaxation data, is proposed. The algorithm is based on the model of the passage of a particle over a potential energy barrier. This method was utilized for some molten polymers and concentrated polymeric solutions.

A 500 ps molecular dynamics simulation study of interleukin-1β in water: Correlation with nuclear magnetic resonance spectroscopy and crystallography

We report the results of a 500 ps molecular dynamics simulation of the cytokine interleukin-1β, a protein of 153 amino acids, immersed in a sphere of 3783 bulk water molecules with a radius of 33 Å. The simulation reproduces the amplitudes of the fast librational motions of the backbone NH bonds determined from 15N nuclear magnetic relaxation data, as well as the crystallographic B-factors. Moreover, this study suggests a molecular picture of the nature of the slow internal motions that have been inferred from nuclear magnetic resonance relaxation experiments. These experiments indicated that, in addition to fast motions common to all residues, 32 surface residues exhibit slow motions on the 400 ps to 5 ns time-scale. While the present simulation is not sufficiently long to provide a quantitative description of events on this time-scale, it is long enough to observe several large amplitude transitions that are likely candidates for these slow motions. Specifically, in many of these 32 residues, the NH groups are hydrogen bonded and infrequent dihedral transitions cause the NH vectors to jump between states with well-defined orientations. It is shown that the time course of the angular reorientational correlation functions of these residues calculated from the trajectory is a reflection of the random times at which these infrequent jumps happen to have occurred. Thus, while the rate of these transitions cannot be quantified, the simulated decay of these correlation functions is completely consistent with the physical picture in which the NH vectors, in addition to fast librational motion, undergo large amplitude jumps between conformations stabilized by hydrogen bonds.

1H and 13C nuclear magnetic relaxation and molecular motion in solid poly(L‐alanine)

Nuclear magnetic relaxation data both for proton and for carbon-13 nuclei in solid-powder poly(L-alanine) are analyzed together, in order to obtain information on the molecular motions in polypeptides. For this analysis the “model-free” approach is used. Three types of internal motions are determined in the α-helix conformation of the investigated polymer. An inhomogeneous distribution of correlation times is shown to be inherent in each type of motion. The first type is the methyl group rotation around the symmetry axis with correlation times of about one hundred picoseconds at room temperature. The second type are the small-amplitude (≈10°) individual oscillations of backbone groups as well as of the axis of the methyl group, with correlation times from ten to one hundred nanoseconds at room temperature. The last type is the α-helix backbone motion with correlation times of a few microseconds at room temperature and with amplitudes of 20° or more, which possibly represents the cooperative motion of several neighbouring groups in the main chain.

Two-dimensional plasmon-phonon interaction in layered HTSC compounds

The unit cell of high temperature superconductor YBa 2 Cu 3 O 7 is presented as two thin highly conducting CuO 2 layers separated by Y and Ba insulator layers. Neglecting electron hopping between conducting layers the dielectric function ϵ(q, ω) for arbitrary wave vector q and frequency ω is calculated in the random phase approximation. Interaction between collective electron excitations and lattice vibrations is taken into account and mixed polar phonon-plasmon modes dispersion relations are deduced. In the framework of developed model the anomalous infrared, the inelastic neutron scattering and Cu nuclear magnetic relaxation data are discussed.

Platinum-195 NMR study of platinum/titania and platinum/silica catalysts: strong metal-support interaction

We show that in Pt catalysts 195 Pt NMR provides a probe to study the interaction of metal surface atoms with adsorbates or species that have migrated from the support onto the platinum during thermal treatment. The so-called «strong metal-support interaction» (SMSI) of Pt on TiO 2 is studied as a function of the size of the Pt particles and compared to the results obtained on SiO 2 , a nonreducible oxide. Nuclear magnetic relaxation data of the surface Pt nuclei, clean or in the SMSI state, show a metallic type of relaxation via the conduction electrons. The local density of states at the Fermi energy obtained from spectral data and spin-lattice relaxation time measurements is lower on the clean surface atoms than in the bulk but does not change much when going over to the SMSI state

Application of the dynamic rotational isomeric states model to poly(ethylene oxide) and comparison with nuclear magnetic relaxation data

The dynamic rotational isomeric states (RIS) model recently developed for investigating local chain dynamics is further improved and applied to poly(ethy1ene oxide) (PEO). In general, a set of eigenvalues AI, j = 1 to Y *, characterizes the dynamic behavior of a given segment of N motional bonds, with v isomeric states available to each bond. The eigenvalues may be identified as the frequencies of the individual modes contributing to local chain relaxation. To calculate orientational autocorrelations, time correlations, and/or power spectra, Ais are combined with the weighting factors k, which are determined by the equilibrium statistics of the chain and the specific property investigated. The rates of transitions between isomeric states are assumed to be inversely proportional to solvent viscosity, leading to a linear dependence between viscosity and correlation times. Predictions of the theory are in satisfactory agreement with the isotropic correlation times and spin-lattice relaxation times from *3C and 'H NMR experiments for PEO in a variety of solvents. An activation energy of about one barrier height is theoretically calculated, in agreement with previous experimental studies.

Nuclear spin relaxation of oxygen‐17, silicon‐29 and carbon‐13 in octamethylcyclotetrasiloxane

Abstract17O, 13C and 29Si nuclear magnetic relaxation data are reported for neat liquid octamethylcyclotetrasiloxane in the temperature range 298–373 K. The electric field gradient at the site of the oxygen nucleus is estimated by ab initio calculations and the 17O relaxation data are interpreted in terms of isotropic rotational diffusion. The 13C dipole‐dipole relaxation rates are interpreted in terms of the Woessner model for internal methyl rotation superimposed on the isotropic overall tumbling. The 29Si spin‐lattice relaxation is composed of dipole‐dipole and spin‐rotation contributions, which are interpreted in a semi‐quantitative fashion.

Deuterium nuclear magnetic resonances of exchange-labeled gramicidin in an oriented lyotropic nematic phase

Lyotropic nematic liquid-crystalline phases, such as that formed by potassium laurate/decanol/KCl/water, are found to accept readily large amphiphilic solute molecules. Since these phases spontaneously orient in high magnetic fields, it becomes possible to obtain NMR spectra of biologically interesting solutes in an oriented axially symmetric environment. The amide hydrogens of the peptide backbone of gramicidin D (Dubos) were exchanged for deuterium, and the gramicidin was incorporated into a lyotropic nematic phase made with deuteriated buffer in place of water. 2H NMR spectra of oriented, exchange-labeled gramicidin were then obtained. The strong water signal from the deuteriated buffer was eliminated by using selective excitation and a polynomial subtraction procedure. The 2H NMR spectra at high temperature consist of twelve major quadrupolar doublets. The splittings observed are largely independent of temperature, suggesting a highly rigid backbone structure. Two of the doublets, which are chemically shifted relative to the others, show stronger temperature dependence. These two probably arise from the exchangeable amino hydrogens on the tryptophan indole moieties of the peptide. While we cannot yet assign all of the doublets, the spectra and nuclear magnetic relaxation data are consistent with a rigid slightly distorted beta LD6.3 helix undergoing axially symmetric reorientation about the director of the liquid-crystalline phase. The correlation time for the axially symmetric reorientation is determined by relaxation measurements to be about 10(-7) s.

New modification of model-free approach to analysis of nuclear magnetic relaxation data in proteins.

A formal approach to the analysis of 13C magnetic relaxation data in proteins has been developed. It is based on the concepts of one of the authors on the internal motions in solid polymers (Fedotov, V.D., Pulse NMR in bulk polymers, Doctoral dissertation, Kazan, USSR, 1981). According to this approach the intermolecular motions in proteins are considered as anisotropic ones and described in terms of a spectrum of correlation times. To characterize the motions a set of formal microdynamic parameters has been introduced. They are: the anisotropy parameter (a measure of spatial restriction of motion), the most probable correlation time, the parameter of the correlation time distribution width. The analysis of protonated carbon relaxation in globular proteins (bovine pancreatic trypsin inhibitor and ribonuclease S) and polymers has been carried out by the model-free approach. Microdynamic parameters of CH3-, CH2-, aromatic CH-groups have been considered within the framework of the diffusional rotation-oscillation models. To explain the backbone CH-group relaxation the model of the defect diffusion has been applied. The distinctive feature of the results obtained is the broad correlation time distribution for all groups of any type. The causes of nonexponential correlation function of local motion have been discussed. To elucidate the nature of the correlation time the carbon magnetization decays in the wide range of microdynamic parameter values imitating various experimental conditions have been calculated.