Methyl group rotation,1H spin-lattice relaxation in an organic solid, and the analysis of nonexponential relaxation

Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR

Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.

Electron Beam Radiation as a Safe Method for the Sterilization of Aceclofenac and Diclofenac—The Usefulness of EPR and 1H-NMR Methods in Determination of Molecular Structure and Dynamics

Diclofenac (DC) [2-(2,6-Dichloroanilino)phenyl]acetic acid,) and aceclofenac (AC) 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl]oxyacetic acid in substantia were subjected to ionizing radiation in the form of a beam of high-energy electrons from an accelerator in a standard sterilization dose of 25 kGy and higher radiation doses (50–400 kGy). We characterized non-irradiated and irradiated samples of DC and AC by using the following methods: organoleptic analysis (color, form), spectroscopic (IR, NMR, EPR), chromatographic (HPLC), and others (microscopic analysis, capillary melting point measurement, differential scanning calorimetry (DSC)). It was found that a absorbed dose of 50 kGy causes a change in the color of AC and DC from white to cream-like, which deepens with increasing radiation dose. No significant changes in the FT-IR spectra were observed, while no additional peaks were observed in the chromatograms, indicating emerging radio-degradation products (25 kGy). The melting point determined by the capillary method was 153.0 °C for AC and 291.0 °C for DC. After irradiation with the dose of 25 kGy for AC, it did not change, for DC it decreased by 0.5 °C, while for the dose of 400 kGy it was 151.0 °C and 286.0 °C for AC and DC, respectively. Both NSAIDs exhibit high radiation stability for typical sterilization doses of 25–50 kGy and are likely to be sterilized with radiation at a dose of 25 kGy. The influence of irradiation on changes in molecular dynamics and structure has been observed by ¹H-NMR and EPR studies. This study aimed to determine the radiation stability of DC and AC by spectrophotometric, thermal and chromatographic methods. A standard dose of irradiation (25 kGy) was used to confirm the possibility of using this dose to obtain a sterile form of both NSAIDs. Higher doses of radiation (50–400 kGy) have been performed to explain the changes in DC and AC after sterilization.

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 Aβ_1-40 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 C^β deuterons at high temperatures and small-angle fluctuations of the C^α-C^β 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.

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state ¹ H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.

Proton Spin-Lattice Relaxation in Organic Molecular Solids: Polymorphism and the Dependence on Sample Preparation

We report solid-state nuclear magnetic resonance ¹ H spin-lattice relaxation, single-crystal X-ray diffraction, powder X-ray diffraction, field emission scanning electron microscopy, and differential scanning calorimetry in solid samples of 2-ethylanthracene (EA) and 2-ethylanthraquinone (EAQ) that have been physically purified in different ways from the same commercial starting compounds. The solid-state ¹ H spin-lattice relaxation is always non-exponential at high temperatures as expected when CH₃ rotation is responsible for the relaxation. The ¹ H spin-lattice relaxation experiments are very sensitive to the "several-molecule" (clusters) structure of these van der Waals molecular solids. In the three differently prepared samples of EAQ, the relaxation also becomes very non-exponential at low temperatures. This is very unusual and the decay of the nuclear magnetization can be fitted with both a stretched exponential and a double exponential. This unusual result correlates with the powder X-ray diffractometry results and suggests that the anomalous relaxation is due to crystallites of two (or more) different polymorphs (concomitant polymorphism).

Basic experiments in 2H static NMR for the characterization of protein side-chain dynamics

The focus of this review is the basic methodology for applications of static deuteron NMR for studies of dynamics in the side chains of proteins. We review experimental approaches for the measurements of static line shapes and relaxation rates as well as signal enhancement strategies using the multiple echo acquisition scheme. Further, we describe computational strategies for modeling jump and diffusive motions underlying experimental data. Applications are chosen from studies of amyloid fibrils comprising the amyloid-β protein.

Comparative Dynamics of Methionine Side-Chain in FMOC-Methionine and in Amyloid Fibrils

We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition.

Solid-Solid Phase Transitions and tert-Butyl and Methyl Group Rotation in an Organic Solid: X-ray Diffractometry, Differential Scanning Calorimetry, and Solid-State 1H Nuclear Spin Relaxation

Using solid-state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments, we have investigated the effects of several solid-solid phase transitions on tert-butyl and methyl group rotation in solid 1,3,5-tri-tert-butylbenzene. The goal is to relate the dynamics of the tert-butyl groups and their constituent methyl groups to properties of the solid determined using single-crystal X-ray diffraction and differential scanning calorimetry (DSC). On cooling, the DSC experiments see a first-order, solid-solid phase transition at either 268 or 155 K (but not both) depending on thermal history. The 155 K transition (on cooling) is identified by single-crystal X-ray diffraction to be one from a monoclinic phase (above 155 K), where the tert-butyl groups are disordered (that is, with a rotational 6-fold intermolecular potential dominating), to a triclinic phase (below 155 K), where the tert-butyl groups are ordered (that is, with a rotational 3-fold intermolecular potential dominating). This transition shows very different DSC scans when both a 4.7 mg polycrystalline sample and a 19 mg powder sample are used. The ¹H spin-lattice relaxation experiments with a much larger 0.7 g sample are very complicated and, depending on thermal history, can show hysteresis effects over many hours and over very large temperature ranges. In the high-temperature monoclinic phase, the tert-butyl groups rotate with NMR activation energies (closely related to rotational barriers) in the 17-23 kJ mol^-1 range, and the constituent methyl groups rotate with NMR activation energies in the 7-12 kJ mol^-1 range. In the low-temperature triclinic phase, the rotations of the tert-butyl groups and their methyl groups in the aromatic plane are quenched (on the NMR time scale). The two out-of-plane methyl groups in the tert-butyl groups are rotating with activation energies in the 5-11 kJ mol^-1 range.

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.

Static solid-state 2H NMR methods in studies of protein side-chain dynamics

In this review, we discuss the experimental static deuteron NMR techniques and computational approaches most useful for the investigation of side-chain dynamics in protein systems. Focus is placed on the interpretation of line shape and relaxation data within the framework of motional modeling. We consider both jump and diffusion models and apply them to uncover glassy behaviors, conformational exchange and dynamical transitions in proteins. Applications are chosen from globular and membrane proteins, amyloid fibrils, peptide adsorbed on surfaces and proteins specific to connective tissues.

Fast Motions of Key Methyl Groups in Amyloid-β Fibrils

Amyloid-β (Aβ) 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 Aβ 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-β 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.

Methyl and t-butyl group rotation in a molecular solid: 1H NMR spin-lattice relaxation and X-ray diffraction

We report solid state ¹H nuclear magnetic resonance spin-lattice relaxation experiments and X-ray diffractometry in 2-t-butyldimethylsilyloxy-6-bromonaphthalene.

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.

Nonexponential (1)H spin-lattice relaxation and methyl group rotation in molecular solids

We report a quantitative measure of the nonexponential (1)H spin-lattice relaxation resulting from methyl group (CH3) rotation in six polycrystalline van der Waals solids. We briefly review the subject in general to put the report in context. We then summarize several significant issues to consider when reporting (1)H or (19)F spin-lattice relaxation measurements when the relaxation is resulting from the rotation of a CH3 or CF3 group in a molecular solid.

Solid state ¹H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: the relationship between structure and methyl group and t-butyl group rotation

We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state (1)H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the (1)H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.

Electron spin-lattice relaxation mechanisms of rapidly-tumbling nitroxide radicals

Electron spin relaxation times at 295 K were measured at frequencies between 250 MHz and 34 GHz for perdeuterated 2,2,6,6-tetramethyl-4-piperidone-1-oxyl (PDT) in five solvents with viscosities that result in tumbling correlation times, τR, between 4 and 50 ps and for three (14)N/(15)N pairs of nitroxides in water with τR between 9 and 19 ps. To test the impact of structure on relaxation three additional nitroxides with τR between 10 and 26 ps were studied. In this fast tumbling regime T2(-1)~T1(-1) at frequencies up to about 9 GHz. At 34 GHz T2(-1)>T1(-1) due to increased contributions to T2(-1) from incomplete motional averaging of g-anisotropy, and T2(-1)-T1(-1) is proportional to τR. The contribution to T1(-1) from spin rotation is independent of frequency and decreases as τR increases. Spin rotation dominates T1(-1) at 34 GHz for all τR studied, and at all frequencies studied for τR=4 ps. The contribution to T1(-1) from modulation of nitrogen hyperfine anisotropy increases as frequency decreases and as τR increases; it dominates at low frequencies for τR>~15 ps. The contribution from modulation of g anisotropy is significant only at 34 GHz. Inclusion of a thermally-activated process was required to account for the observation that for most of the radicals, T1(-1) was smaller at 250 MHz than at 1-2 GHz. The significant (15)N/(14)N isotope effect, the small H/D isotope effect, and the viscosity dependence of the magnitude of the contribution from the thermally-activated process suggest that it arises from intramolecular motions of the nitroxide ring that modulate the isotropic A values.

Amphidynamic crystals of a steroidal bicyclo[2.2.2]octane rotor: a high symmetry group that rotates faster than smaller methyl and methoxy groups

The synthesis, crystallization, single crystal X-ray structure, and solid state dynamics of molecular rotor 3 provided with a high symmetry order and relatively cylindrical bicyclo[2.2.2]octane (BCO) rotator linked to mestranol fragments were investigated in this work. By use of solid state (13)C NMR, three rotating fragments were identified within the molecule: the BCO, the C19 methoxy and the C18 methyl groups. To determine the dynamics of the BCO group in crystals of 3 by variable temperature (1)H spin-lattice relaxation (VT (1)H T1), we determined the (1)H T1 contributions from the methoxy group C19 by carrying out measurements with the methoxy-deuterated isotopologue rotor 3-d6. The contributions from the quaternary methyl group C18 were estimated by considering the differences between the VT (1)H T1 of mestranol 8 and methoxy-deuterated mestranol 8-d3. From these studies it was determined that the BCO rotator in 3 has an activation energy of only 1.15 kcal mol(-1), with a barrier for site exchange that is smaller than those of methyl (E(a) = 1.35 kcal mol(-1)) and methoxy groups (E(a) = 1.92 kcal mol(-1)), despite their smaller moments of inertia and surface areas.

Origin of abrupt rise in deuteron NMR longitudinal relaxation times of protein methyl groups below 90 K

In order to examine the origin of the abrupt change in the temperature dependence of (2)H NMR longitudinal relaxation times observed previously for methyl groups of L69 in the hydrophobic core of villin headpiece protein at around 90 K (Vugmeyster et al. J. Am. Chem. Soc. 2010, 132, 4038-4039), we extended the measurements to several other methyl groups in the hydrophobic core. We show that, for all methyl groups, relaxation times experience a dramatic jump several orders of magnitude around this temperature. Theoretical modeling supports the conclusion that the origin of the apparent transition in the relaxation times is due to the existence of the distribution of conformers distinguished by their activation energy for methyl three-site hops. It is also crucial to take into account the differential contribution of individual conformers into overall signal intensity. When a particular conformer approaches the regime at which its three-site hop rate constant is on the order of the quadrupolar coupling interaction constant, the intensity of the signal due to this conformer experiences a sharp drop, thus changing the balance of the contributions of different conformers into the overall signal. As a result, the observed apparent transition in the relaxation rates can be explained without the assumption of an underlying transition in the rate constants. This work in combination with earlier results also shows that the model based on the distribution of conformers explains the relaxation behavior in the entire temperature range between 300 and 70 K.