Solid-state Deuteron Research Articles

Dynamics of Serine-8 Side-Chain in Amyloid-β Fibrils and Fluorenylmethyloxycarbonyl Serine Amino Acid, Investigated by Solid-State Deuteron NMR.

Serine side-chains are strategic sites of post-translational modifications, and it is important to establish benchmarks of their internal dynamics. In this work, we compare the dynamics of serine side-chains in several biologically important systems: serine-8 in the disordered domain of Aβ1-40 fibrils in the hydrated and dry states and fluorenylmethyloxycarbonyl (Fmoc) serine with the bulky group that mimics the hydrophobicity of the fibril contacts yet lacks the complexity of the protein system. Using deuterium solid-state NMR static line shape and longitudinal relaxation techniques in the 310 to 180 K temperature range, we compare the main features of the dynamics in these systems. The main motional modes in the fibrils are large-scale fluctuations in the hydrated state of the fibrils as well as local motions such as 3-site jumps of the Cβ deuterons at high temperatures and small-angle fluctuations of the Cα-Cβ axis at low temperatures. In the hydrated fibrils, two distinct states are present with vastly different extents of large-scale diffusive motions and 3-site-jump rate constants. The hydrated state at the physiological conditions is dominated by the "free" state undergoing large-scale diffusive motions and very fast local 3-site jumps, while in the "bound" state, these large-scale motions are quenched due to transient inter- and intramolecular interactions. Additionally, in the bound state, the 3-site-jump motions are orders of magnitude slower. Details of the dynamics in the serine side-chain are dependent on fine structural features and hydration levels of the systems.

Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR.

We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298-80 K temperature range. Our main tools were static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is nonexponential at all temperatures with the extent of nonexponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al. J. Phys. Chem. B 2013, 117, 6129-6137), suggests that the hydrophobic core undergoes slow concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The crossover temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in softening the core and highlights aromatic residues as markers of the protein dynamical transitions.

Effect of subdomain interactions on methyl group dynamics in the hydrophobic core of villin headpiece protein

Thermostable villin headpiece protein (HP67) consists of the N-terminal subdomain (residues 10-41) and the autonomously folding C-terminal subdomain (residues 42-76) which pack against each other to form a structure with a unified hydrophobic core. The X-ray structures of the isolated C-terminal subdomain (HP36) and its counterpart in HP67 are very similar for the hydrophobic core residues. However, fine rearrangements of the free energy landscape are expected to occur because of the interactions between the two subdomains. We detect and characterize these changes by comparing the µs-ms time scale dynamics of the methyl-bearing side chains in isolated HP36 and in HP67. Specifically, we probe three hydrophobic side chains at the interface of the two subdomains (L42, V50, and L75) as well as at two residues far from the interface (L61 and L69). Solid-state deuteron NMR techniques are combined with computational modeling for the detailed characterization of motional modes in terms of their kinetic and thermodynamic parameters. The effect of interdomain interactions on side chain dynamics is seen for all residues but L75. Thus, changes in dynamics because of subdomain interactions are not confined to the site of perturbation. One of the main results is a two- to threefold increase in the value of the activation energies for the rotameric mode of motions in HP67 compared with HP36. Detailed analysis of configurational entropies and heat capacities complement the kinetic view of the degree of the disorder in the folded state.

Characterization of water dynamics in frozen soils by solid-state deuteron NMR

The presence of unfrozen water in soils at sub-freezing temperatures is important for biogeochemical processes as well as for the genesis of landscapes and survival of life. While several mechanisms can lead to the existence of liquid water at sub-freezing temperatures, this work focuses on the dynamical (entropic) contribution stemming from motions of water molecules at water–soil or water–ice interfaces. We demonstrate the utility of solid-state 2H NMR methods for characterization of water dynamics in soils on various time scales. Using a sample from McMurdo Dry Valleys, Antarctica, we show the existence of dynamics spanning a milliseconds to picoseconds time scale range. Computational modeling allows for a quantitative description of the dynamics, which involves models such as an exchange between bound and free water, and changes in effective viscosity of water in the soil matrix.

Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements.

We have investigated microsecond to millisecond time scale dynamics in several key hydrophobic core methyl groups of chicken villin headpiece subdomain protein (HP36) using a combination of single-site labeling, deuteron solid-state NMR line shape analysis, and computational modeling. Deuteron line shapes of hydrated powder samples are dominated by rotameric jumps and show a large variability of rate constants, activation energies, and rotameric populations. Site-specific activation energies vary from 6 to 38 kJ/mol. An additional mode of diffusion on a restricted arc is significant for some sites. In dry samples, the dynamics is quenched. Parameters of the motional models allow for calculations of configurational entropy and heat capacity, which, together with the rate constants, allow for observation of interplay between thermodynamic and kinetic picture of the landscape. Mutations at key phenylalanine residues at both distal (F47L&F51L) and proximal (F58L) locations to a relatively rigid side chain of L69 have a pronounced effect on alleviating the rigidity of this side chain at room temperature and demonstrate the sensitivity of the hydrophobic core environment to such perturbations.

Comparative Dynamics of Leucine Methyl Groups in FMOC-Leucine and in a Protein Hydrophobic Core Probed by Solid-State Deuteron Nuclear Magnetic Resonance over 7−324 K Temperature Range

Quantitative dynamics of methyl groups in 9-fluorenylmethyloxycarbonyl-leucine (FMOC-leu) have been analyzed and compared with earlier studies of methyl dynamics in chicken villin headpiece subdomain protein (HP36) labeled at L69, a key hydrophobic core position. A combination of deuteron solid-state nuclear magnetic resonance experiments over the temperature range of 7-324 K and computational modeling indicated that while the two compounds show the same modes of motions, there are marked differences in the best-fit parameters of these motions. One of the main results is that the crossover observed in the dynamics of the methyl groups in the HP36 sample at 170 K is absent in FMOC-leu. A second crossover at around 95-88 K is present in both samples. The differences in the behavior of the two compounds suggest that some of the features of methyl dynamics reflect the complexity of the protein hydrophobic core and are not determined solely by local interactions.

NMR and dielectric studies of hydrated collagen and elastin: Evidence for a delocalized secondary relaxation

Using a combination of dielectric spectroscopy and solid-state deuteron NMR, the hydration water dynamics of connective tissue proteins is studied at sub-ambient temperatures. In this range, the water dynamics follows an Arrhenius law. A scaling analysis of dielectric losses, ‘two-phase’ NMR spectra, and spin-lattice relaxation times consistently yield evidence for a Gaussian distribution of energy barriers. With the dielectric data as input, random-walk simulations of a large-angle, water reorientation provide an approximate description of stimulated-echo data on hydrated elastin. This secondary process is quasi-isotropic and delocalized. The delocalization is inferred from previous NMR diffusometry experiments. It is emphasized that the phenomenology of this process is shared by many non-aqueous binary glasses in which the constituent components exhibit a sufficient dynamical contrast.

Effects of jump dynamics on solid state nuclear magnetic resonance line shapes and spin relaxation times

This paper describes EXPRESS ( EXchange Program for RElaxing Spin Systems), a computer program that simulates the effects of Markovian jump dynamics for a wide variety of solid state nuclear magnetic resonance experiments. A graphical interface is described that facilitates the definition of rotational jumps around non-commuting axes that may occur at arbitrary, different rates. Solid state deuteron NMR is widely used to investigate such processes, and EXPRESS allows simulations of deuteron quadrupole echo and magic angle spinning line (MAS) shapes, as well as partially relaxed line shapes for measurements of anisotropic relaxation of Zeeman and quadrupolar order. Facilities are included for chemical shift tensors (at user-defined orientations relative to the quadrupole coupling tensors), so that EXPRESS is potentially useful for studies of paramagnetic systems where these interactions are of comparable magnitude. Many of the same techniques used for deuterons can be extended to half-integer quadrupolar nuclei. The same interface that specifies rotational “sites” for deuteron NMR studies is usable in EXPRESS to simulate static line shapes, MAS line shapes, and multiple pulse Carr–Purcell–Meiboom–Gill (CPMG) line shapes for the central transition of high spin quadrupoles with second order quadrupole coupling and chemical shift anisotropy. Representative simulations are displayed that show effects of slow libration on deuteron quadrupole echo line shapes and relaxation time anisotropies. EXPRESS is also used to investigate fundamental differences in the mechanism of echo formation in deuteron MAS and quadrupole CPMG experiments, and to illustrate significant differences between these techniques in the context of high spin quadrupolar nuclei. The program is modular and platform-independent, with facilities for users to add routines for experiments not yet envisioned.

Solid state deuteron relaxation time anisotropy measured with multiple echo acquisition

The signal to noise ratio of solid state deuteron NMR line shapes can be significantly improved by recording multiple echoes, generated either by a quadrupole Carr-Purcell-Meiboom-Gill pulse train (QCPMG) or by magic angle spinning (MAS). It is shown in this article, theoretically and experimentally, that when these techniques are used to record partially relaxed spectra, the relaxation times of Zeeman order, T(1Z), and quadrupole order, T(1Q), measured for individual side bands in QCPMG experiments preserve relaxation time anisotropy, while rotational side bands in MAS spectra do not. The relaxation times of individual QCPMG sidebands are not identical to those measured at the same frequencies on partially relaxed quadrupole echo powder patterns, and must be computed by explicit simulation.

Observation of a deuteron nuclear magnetic resonance Knight shift in conductive polyaniline

Solid state deuteron magic angle spinning nuclear magnetic resonance spectra of conductive ring-deuterated polyaniline consist of two peaks, one at the same chemical shift as the insulating form of the polymer and the second shifted by 5.8+/-1 ppm. The magnitude of the shift is field and temperature independent and is identified as a Knight shift. The deuterons undergoing a Knight shift originate from both the crystalline and amorphous regions of the sample, implying that conduction is mediated by delocalized polarons in both these regions. Spin count experiments demonstrate that in highly conductive samples, signal is lost not only by dephasing due to the proximity of localized unpaired electrons but also to high rf reflectance.

Deuteron NMR Study of Polyaniline and Polyaniline/Clay Nanocomposite

Different forms of solid polyaniline (Pani) and polyaniline intercalated into montmorillonite clay layers have been characterized by solid-state deuteron quadrupole echo and magic angle spinning NM...

Dynamics of an Inclusion Complex of Dichloromethane and Cryptophane-E

The dynamic properties of the guest−host complex between cryptophane-E and dichloromethane have been studied in tetrachloroethane solution, using proton and carbon-13 NMR, and in the solid state by means of deuteron NMR. The exchange of dichloromethane guest between the free state in the bulk solution and the bound state within the host cavity is slow, on the time scale of seconds, similarly to the earlier studied complex between cryptophane-E and chloroform. The reorientational dynamics of complexed dichloromethane is very fast and is only weakly affected by the reorientation of the guest−host complex as a whole. This result is very different from the case of chloroform inside of the cryptophane cavity. These different pictures of the reorientation of the two chloromethane guests are also nicely reflected in the solid-state deuteron NMR spectra of deuterated guest molecules.

Shaped Pulses for Selective Inversion in Solid-State Deuteron NMR Spectroscopy

Double sideband modulation and pulse shaping can be combined to improve the performance of selective pulses in solid-state deuteron NMR. Efficient off-resonance selective inversion of deuterons requires simultaneous irradiation of both spin-1 transitions, i.e., at symmetric offsets from the Larmor frequency (ν0± Δ). This is best accomplished with double-sideband-modulated pulses. Frequency-selective profiles can be improved by shaping the RF pulses. A variety of commonly used selective pulse shapes are evaluated for their applicability to solid-state deuteron powder patterns. A new pulse shape is introduced; the squared isosceles triangle. Generally, pulses with low bandwidth–duration product, such as the Gaussian envelope, are found to be the most effective for selective inversion in solid-state2H NMR. This is a consequence of the large inhomogeneous quadrupolar interaction and fast, anisotropic spin–spin relaxation.

Dynamic study of poly(styrene-vinyl-d3) in a glassy blend by two-dimensional solid-state deuteron NMR

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDynamic study of poly(styrene-vinyl-d3) in a glassy blend by two-dimensional solid-state deuteron NMRY. H. Chin, P. T. Inglefield, and A. A. JonesCite this: Macromolecules 1993, 26, 20, 5372–5378Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://doi.org/10.1021/ma00072a013RIGHTS & PERMISSIONSArticle Views50Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-Alerts Get e-Alerts

Saturation in Deuteron Hadamard NMR Spectroscopy of Solids

Hadamard NMR was investigated for wide-line solid-state deuteron spectroscopy by numerical simulations and experiments on hexamethylbenzene. Similar signal-to-noise ratios were obtained at large filter bandwidths (500 kHz) by both the quadrupolar echo and the Hadamard methods, although the excitation power differs by up to four orders in magnitude. Increasing the excitation power leads to systematic, noise-like features in Hadamard spectra. In contrast to phase modulation, simulations indicate that for amplitude modulation of the pseudorandom excitation, the pulse sequence burns a saturation hole into the lineshape at the carrier frequency. Violation of the cyclicity requirement by introduction of a recycle delay between successive Hadamard scans results in a high-frequency noise contribution. Finite pulse widths are shown not to cause significant spectral distortions.

Solid-state deuteron and proton NMR of guest and host motions in the Hofmann-type and related benzene clathrates

The motional behavior of the guest benzene molecule in the Hofmann-type benzene clathrate Cd(NH 3 ) 2 Ni(CN) 4 •2C 6 D 6 and related benzene clathrates Cd(en)Ni(CN) 4 •2C 6 D 6 (en=ethylenediamine) and Cd(dma) 2 Ni(CN) 4 •(1/2)C 6 D 6 (dma=dimethylamine) were investigated by 2 H NMR line shape and spin-lattice relaxation time studies

Deuteron double-quantum NMR imaging of molecular order and mobility in solid polymers

A novel solid-state deuteron NMR method for spectroscopic imaging is presented. It employs information about molecular orientation and dynamics obtained from broad 2H-NMR lineshapes governed by the anisotropic quadrupole interaction without sacrificing spatial resolution. To this end, double-quantum coherence is created, which is independent of the strength of the quadrupole coupling. In a Fourier-imaging scheme magnetic-field gradients are applied for spatial encoding during the evolution of double-quantum coherence. In the detection period single-quantum coherence is recorded, providing a spectroscopic dimension with a wide-line spectrum. Its lineshape contains spatially resolved information about molecular orientation and dynamics. Experimental results are presented for orientation imaging of drawn polyethylene and molecular-dynamics imaging in a composite sample of glassy polystyrene and glassy polycarbonate, where the two species can be discriminated based on both the NMR lineshape and the spin-latti...

Elucidation of slow motions in glycoglycerolipid bilayers by two-dimensional solid-state deuteron NMR

Two-dimensional solid-state deuteron NMR spectroscopy has been used to demonstrate the presence of a slow whole molecule motion in the gel phase of hydrated multibilayers of the glycolipid 1,2-di-O-tetradecyl-3-O-(β-D-glucopyranosyl)- sn-glycerol (β-DTGL) at 35°C. The correlation time for the motion was determined to be of the order of milliseconds. Comparison of the experimental and simulated ridge patterns suggest that a large angle jump about the long molecular axis can best account for the 2D exchange spectra of β-DTGL in the gel phase in comparison to small step Brownian diffusion.

Solid-state NMR study of protein/polypeptide backbone fluctuations interpreted by multiple trapping diffusion of dilating defects

Diverse proteins and polypeptides have been studied by proton field-cycling relaxation spectroscopy and-after deuterium exchange-by solid-state deuteron NMR. These techniques cover very different and partially complementary time scales of molecular motions spread over many orders of magnitude. On the other hand, deuteron NMR is predominantly sensitive to rotational fluctuations, while proton NMR can be affected by translational displacements in addition. The latter type of motion is considered to be connected with the multiple trapping diffusion mechanism of dilating defects in the protein structure. In particular the mean-square displacement of the diffusing defects is expected to obey a nonlinear time dependence (“anomalous diffusion”). This concept enables us to explain simultaneously (a) the small amplitudes of rotational backbone fluctuations as far as can be judged by the diverse deuteron experiments, (b) the existence of translational backbone fluctuations concluded from the proton TI dispersion measurements, and (c) the peculiar v3I4 frequency dependence evident for the proton spin-lattice relaxation time in the vicinity of room temperature. In the limit far below room temperature, indications of a crossover to a fractal time process appear.

Electro-optical DC kerr effects and solid state deuteron NMR studies of stable gel-derived glass-organic polymer composites

Novel gel-derived silica glass-organic polymer composites containing 2-methyl-4-nitroaniline (MNA) have been prepared and fabricated in bulk forms for optical sampling. Such inorganic-organic composites exhibit improved mechanical and environmental stability over purely organic materials. Electro-optical DC Kerr measurements on these composites have been carried out. Complementary solid state deuteron NMR studies also provide further insight into the chemical and physical characteristics of these unique materials.