Flexibility and Solvation of Amyloid-ß Hydrophobic Core.

Amyloid fibril deposits found in Alzheimer disease patients are composed of amyloid-ß (Aß) protein forming a number of hydrophobic interfaces that are believed to be mostly rigid. We have investigated the µs-ms time-scale dynamics of the intra-strand hydrophobic core and interfaces of the fibrils composed of Aß1-40 protein. Using solid-state (2)H NMR line shape experiments performed on selectively deuterated methyl groups, we probed the 3-fold symmetric and 2-fold symmetric polymorphs of native Aß as well as the protofibrils of D23N Iowa mutant, associated with an early onset of Alzheimer disease. The dynamics of the hydrophobic regions probed at Leu-17, Leu-34, Val-36, and Met-35 side chains were found to be very pronounced at all sites and in all polymorphs of Aß, with methyl axis motions persisting down to 230-200 K for most of the sites. The dominant mode of motions is the rotameric side chain jumps, with the Met-35 displaying the most complex multi-modal behavior. There are distinct differences in the dynamics among the three protein variants, with the Val-36 site displaying the most variability. Solvation of the fibrils does not affect methyl group motions within the hydrophobic core of individual cross-ß subunits but has a clear effect on the motions at the hydrophobic interface between the cross-ß subunits, which is defined by Met-35 contacts. In particular, hydration activates transitions between additional rotameric states that are not sampled in the dry protein. Thus, these results support the existence of water-accessible cavity recently predicted by molecular dynamics simulations and suggested by cryo-EM studies.

Fast Motions of Key Methyl Groups in Amyloid-ß Fibrils.

Amyloid-ß (Aß) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state 2H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aß as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-ß subunits, which has been previously found to be water-accessible. Relaxation measurements performed over 310-140 K and two magnetic field strengths provide insights into conformational variability within and between polymorphs. Core packing variations within a single polymorph are similar to what is observed for globular proteins for the core residues, whereas M35 exhibits a larger degree of variability. M35 site is also shown to undergo a solvent-dependent dynamical transition in which slower amplitude motions of methyl axes are activated at high temperature. The motions, modeled as a diffusion of methyl axis, have activation energy by a factor of 2.7 larger in the twofold compared with the threefold polymorph, whereas D23N protofibrils display a value similar to the threefold polymorph. This suggests enhanced flexibility of the hydrophobic interface in the threefold polymorph. This difference is only observed in the hydrated state and is absent in the dry fibrils, highlighting the role of solvent at the cavity. In contrast, the dynamic behavior of the core is hydration-independent.

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.

Probing the dynamics of a protein hydrophobic core by deuteron solid-state nuclear magnetic resonance spectroscopy.

With the goal of investigating dynamical features of hydrophobic cores of proteins over a wide range of temperatures, the chicken villin headpiece subdomain protein (HP36) was labeled at a "single" site corresponding to any one of the two C(delta)D(3) groups of leucine-69, which is located in a key position of the core. The main techniques employed are deuteron NMR quadrupolar echo line shape analysis, and T(1Z) (Zeeman) and T(1Q) (quadrupolar order) relaxation experiments performed at 11.7 and 17.6 T over the temperature range of 112 to 298 K. The experimental data are compared with computer simulations. The deuteron line shapes give an excellent fit to a three-mode motional model that consists of (a) fast three-site rotational jumps about the pseudo C(3) methyl spinning axis, (b) slower reorientation of the spinning axis, described by diffusion along a restricted arc, and (c) large angle jumps between traces of rotameric conformers. Relaxation behavior is described by a phenomenological distribution of activation energies for three-site hops at high temperatures that collapses to a single, distinctly smaller value for lower temperatures.

Amine Dynamics in Diamine-Appended Mg2(dobpdc) Metal-Organic Frameworks.

Variable-temperature 15N solid-state NMR spectroscopy is used to uncover the dynamics of three diamines appended to the metal-organic framework Mg2(dobpdc) (dobpdc4- = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an important family of CO2 capture materials. The results imply both bound and free amine nitrogen environments exist when diamines are coordinated to the framework open Mg2+ sites. There are rapid exchanges between two nitrogen environments for all three diamines, the rates and energetics of which are quantified by 15N solid-state NMR data and corroborated by density functional theory calculations and molecular dynamics simulations. The activation energy for the exchange provides a measure of the metal-amine bond strength. The unexpected negative correlation between the metal-amine bond strength and CO2 adsorption step pressure reveals that metal-amine bond strength is not the only important factor in determining the CO2 adsorption properties of diamine-appended Mg2(dobpdc) metal-organic frameworks.

Solvent-Driven Dynamical Crossover in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by 2H NMR Relaxation.

Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state 2H NMR relaxation to demonstrate the presence of a solvent-driven dynamical crossover between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by π-flips of the aromatic ring at high temperatures. The crossover temperature is more than 43 degrees lower for the hydrated state of the fibrils compared to the dry state, indicating that interactions with water facilitate π-flips. Further, crossover temperatures are shown to be very sensitive to polymorphic states of the fibrils, such as the 2-fold and 3-fold symmetric morphologies of the wild-type protein as well as D23N mutant protofibrils. We speculate that these differences can be attributed, at least partially, to enhanced interactions with water in the 3-fold polymorph, which has been shown to have a water-accessible cavity. Combined with previous studies of methyl group dynamics, the results highlight the presence of multiple dynamics modes in the core of the fibrils, which was originally believed to be quite rigid.

Molecular recognition in cyclodextrin complexes of amino acid derivatives: the effects of kinetic energy on the molecular recognition of a pseudopeptide in a nonconstraining host environment as revealed by a temperature-dependent crystallographic study.

The crystal structure of a triclinic 2:2 inclusion complex of beta-cyclodextrin with N-acetyl-L-phenylalanine methyl ester has been determined at several temperatures between 298 and 20 K to further study molecular recognition using solid-state supramolecular beta-cyclodextrin complexes. The study reveals kinetic energy dependent changes in guest molecule conformations, orientations, and positions in the binding pocket presented by the crystal lattice. Accompanying these changes are observable differences in guest-guest interactions and hydrogen-bonding interactions in the binding pocket that involve guest molecules, water of hydration molecules, and beta-cyclodextrin molecules. On the basis of the differences observed in the crystal structures, we present a solid-state example of a system that displays the properties of both classical and quantum chemical models. At higher temperatures, the structure conforms to a classical mechanical model with dynamic disorder. At lower temperatures, the observations conform to examples in which there is static disorder representative of models in which quantum states differing in conformation, position, and orientation of components in the crystal structure are occupied. Ab initio theoretical calculations on the different guest molecule conformations have been carried out. Superpositions of theoretical electrostatic surface potential diagrams on the observed molecular positions in the complexes provide confidence that the deconvolution of the guest molecule disorder is acceptable. Temperature-dependent solid-state magic angle spinning deuteron NMR measurements provide evidence for large-amplitude, diffusive motion on a microsecond time scale in the complex.

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.

Local structure in perovskite relaxor ferroelectrics: high-resolution 93Nb 3QMAS NMR.

Solid solutions of (1'-x)Pb(Mg(1/3)Nb(2/3))O3xPb(Sc(1/2)Nb(1/2))O3 (PMN/PSN) have been investigated using high-resolution 93Nb 3-quantum magic-angle spinning nuclear magnetic resonance experiments (3QMAS NMR). In previous MAS NMR investigations, the local B-cation ordering in these relaxor ferroelectric solid solutions was quantitatively determined. However, in conventional one-dimensional MAS spectra the effects of chemical shifts and quadrupole interaction are convoluted; this, in addition to the insufficient resolution, precludes reliable extraction of the values of isotropic chemical shift and quadrupole coupling product. In the current 3QMAS investigation, 93Nb spectra are presented for concentrations x=0, 0.1, 0.2, 0.6, 0.7, and 0.9 at high magnetic field (19.6 T) and fast sample spinning speed (35.7 kHz). Seven narrow peaks and two broad components are observed. The unique high-resolution of the two-dimensional 3QMAS spectra enables unambiguous and consistent assignments of spectral intensities to the specific 28 nearest B-site neighbor (nBn) configurations, (NMg, NSc, NNb) where each number ranges from 0 to 6 and their sum is 6. It is now possible to isolate the isotropic chemical shift and quadrupole coupling product and separately determine their values for most of the 28 nBn configurations. The isotropic chemical shift depends linearly on the number of Mg2+ cations in the configuration; delta iso CS=(13.7 +/- 0.1)NMg-970 +/- 0.4 ppm, regardless of the ratio NSc/NNb. For the seven Nb5+-deficient configurations (NMg, 6-NMg, 0) and the pure niobium configuration (0, 0, 6), the quadrupole coupling products (and hence the electric field gradients) are small (PQ approximately 6-12 MHz) and for the remaining configurations containing small, ferroelectric active Nb5+ ions, the quadrupole coupling products are significantly larger (PQ approximately 40 MHz), indicating larger electric field gradients.

Glassy dynamics of protein methyl groups revealed by deuteron NMR.

We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K using deuteron solid-state NMR longitudinal relaxation measurements. The relaxation of the longitudinal magnetization is weakly nonexponential (glassy) at high temperatures and exhibits a stronger degree of nonexponentiality below about 175 K. In addition, the characteristic relaxation times deviate from the simple Arrhenius law. We interpret this behavior via the existence of distribution of activation energy barriers for the three-site methyl jumps, which originates from somewhat different methyl environments within the local energy landscape. The width of the distribution of the activation barriers for methyl jumps is rather significant, about 1.4 kJ/mol. Our experimental results and modeling allow for the description of the apparent change at about 175 K without invoking a specific transition temperature. For most residues in the core, the relaxation behavior at high temperatures points to the existence of conformational exchange between the substates of the landscape, and our model takes into account the kinetics of this process. The observed dynamics are the same for dry and hydrated protein. We also looked at the effect of F58L mutation inside the hydrophobic core on the dynamics of one of the residues and observed a significant increase in its conformational exchange rate constant at high temperatures.

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.

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.

Q-shear transformation for MQMAS and STMAS NMR spectra.

The multiple-quantum magic-angle spinning (MQMAS) and satellite-transition magic-angle spinning (STMAS) experiments refocus second-order quadrupolar broadening of half-integer quadrupolar spins in the form of two-dimensional experiments. Isotropic shearing is usually applied along the indirect dimension of the 2D spectra such that an isotropic projection free of anisotropic quadrupolar broadening can be obtained. An alternative shear transformation by a factor equal to the coherence level (quantum number) selected during the evolution period is proposed. Such a transformation eliminates chemical shift along the indirect dimension leaving only the second-order quadrupolar-induced shift and anisotropic broadening, and is expected to be particularly useful for disordered systems. This transformation, dubbed Q-shearing, can help avoid aliasing problems due to large chemical shift ranges and spinning sidebands. It can also be used as an intermediate step to the isotropic representation for expanding the spectral window of rotor-synchronized experiments.

High field 207Pb spin-lattice relaxation in solid lead nitrate and lead molybdate.

Spin-lattice relaxation rates of lead have been measured at 17.6 T (156.9 MHz) as a function of temperature in polycrystalline lead nitrate and lead molybdate. Comparing the results with relaxation rates measured at lower fields, it is found that at high fields and low temperature, chemical shift anisotropy (CSA) makes small but observable contributions to lead relaxation in both materials. At 17.6 T and 200 K, CSA accounts for about 15% of the observed relaxation rate. Above 300 K, the dominant relaxation mechanism even at 17.6 T is an indirect Raman process involving modulation of the (207)Pb spin-rotation tensor, as first proposed by Grutzner et al. [J. Am. Chem. Soc. 123, 7094 (2001)] and later treated theoretically in more detail by Vega et al. [Phys. Rev. B 74, 214420 (2006)]. The improved signal to noise ratio at high fields makes it possible to quantify relaxation time anisotropy by analyzing saturation-recovery functions for individual frequencies on the powder pattern line shape. No orientation dependence is found for the spin-lattice relaxation rate of either material. It is argued from examination of the appropriate theoretical expressions, derived here for the first time, that the lack of observable relaxation time anisotropy is probably a general feature of this indirect Raman mechanism.

Investigation of multiaxis molecular motion by off-magic angle spinning deuteron NMR.

The relatively new deuteron NMR method of off-axis-magic angle spinning (OMAS) has been extended and used to investigate multiaxis rotational jump motion. Floquet theory is developed for simulating deuteron OMAS spectra with multisite jumps at different rates about noncoincident axes, and efficient procedures are presented for computing the sideband line shapes. It is demonstrated experimentally that reproducible adjustment of the angle between the rotor axis and the static magnetic field is feasible with precision approaching +/- 0.01 degrees. This leads to the reintroduction of a scaled, first-order quadrupole coupling that defines a new kinetic window and makes deuteron OMAS much more sensitive than ordinary magic angle spinning to motion on the kilohertz time scale. Temperature-dependent deuteron OMAS line shapes of octanoic acid/urea-d4 inclusion compound have been recorded and fitted, using least-squares procedures, to provide rates of rotation about both CN and CO bonds. The Arrhenius activation parameters for rotation about CN bonds, Ea = 60.4+/-2.4 kJ/mol and ln(A) = 24.9+/-0.3, agree well with previous values determined by selective inversion experiments. However, OMAS yields Ea = 26.3+/-0.4 kJ/mole and ln(A) = 24.9+/-0.3 for whole-body rotation about the CO bond axis in contrast to previous analysis of static quadrupole echo (QE) line shapes which gave Ea = 22.3+/-0.3 kJ/mole and ln(A) = 24.8+/-0.6 for the same sample. The underlying homogeneous linewidths of OMAS spectra are much smaller than those of QE spectra, and this provides higher precision and less systematic error in the determination of rates.

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.