Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR

Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using ¹⁵N rotating frame (R_1ρ) relaxation dispersion solid-state nuclear magnetic resonance spectroscopy over a wide range of spin-lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two-state exchange process with a common exchange rate of 1000 s⁻¹, corresponding to protein backbone motion on the timescale of 1 ms, and an excited-state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited-state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.     

Deuteron Solid-State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N-Terminal Domain of Amyloid-β Fibrils

We employed deuterium solid-state NMR techniques under static conditions to discern the details of the μs–ms timescale motions in the flexible N-terminal subdomain of Aβ_1–40 amyloid fibrils, which spans residues 1–16. In particular, we utilized a rotating frame (R_1ρ) and the newly developed time domain quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation measurements at the selectively deuterated side chains of A2, H6, and G9. The two experiments are complementary in terms of probing somewhat different timescales of motions, governed by the tensor parameters and the sampling window of the magnetization decay curves. The results indicated two mobile “free” states of the N-terminal domain undergoing global diffusive motions, with isotropic diffusion coefficients of 0.7−1 ⋅ 10⁸ and 0.3−3 ⋅ 10⁶ad² s⁻¹. The free states are also involved in the conformational exchange with a single bound state, in which the diffusive motions are quenched, likely due to transient interactions with the structured hydrophobic core. The conformational exchange rate constants are 2−3 ⋅ 10⁵ s⁻¹ and 2−3 ⋅ 10⁴ s⁻¹ for the fast and slow diffusion free states, respectively.     

Solid‐State NMR Study on Relationships between Miscibility and Chain Mobility in Poly(4‐Methylstyrene)/Poly(Cyclohexyl Methacrylate) Blend

The phase behavior and motional mobility in binary blends of poly(4‐methylstyrene) (P4MS) and poly(cyclohexyl methacrylate) (PCHMA) have been examined by ¹³C solid state NMR techniques. The blend miscibility was studied by measuring the ¹H spin‐relaxation times in the laboratory frame (T₁^H) and in the rotating frame (T_1ρ^H), respectively. Although intermolecular spin diffusion contributes to the proton relaxations in accordance with homogeneity, T_1ρ^H data shows signs of in complete averaging. The T_1ρ^H relaxation behavior indicates the existence of heterogeneous do mains with shortest dimensions in the nanometer range, which is also sup ported by the intermolecular cross polarization experiments with variable contact times. In addition, according to the resuits of carbon T_1ρ relaxation time measurements, it is concluded that mixing is intimate some what enough to cause a reduction in local chain mobility for P4MS and vice versa for PCHMA.     

Study on crystallographically inequivalent protons in RbH2AsO4 using static NMR and MAS NMR

Two inequivalent protons from ¹H NMR spectra of RbH₂AsO₄ in the paraelectric phase were distinguished using static NMR and MAS NMR. From the ¹H spin–lattice relaxation times in the laboratory frame, T₁, and rotating frame, T_1ρ, of the two crystallographically inequivalent hydrogen sites, i.e., H(1) and H(2), the temperature dependences of T₁ and T_1ρ for H(1) were related to the reorientational motion. The shorter H(1) bonds give rise to stronger H-bonds, and protons involved in stronger H-bonds have long relaxation times. Consequently, the RbH₂AsO₄ structure has two crystallographically inequivalent sites with two different hydrogen-bond lengths.     

Concentration-Dependent Influence of Silver Nanoparticles on Amyloid Fibrillation Kinetics of Hen Egg-White Lysozyme

Understanding the influence of nanoparticles on the formation of protein amyloid fibrillation is crucial to extend their application in related biological diagnosis and nanomedicines. In this work, Raman spectroscopy was used to probe the amyloid fibrillation of hen egg-white lysozyme in the presence of silver nanoparticles (AgNPs) at different concentrations, combined with atomic force microscopy and thioflavin T (ThT) fluorescence assays. Four representative Raman indicators were utilized to monitor transformation of the protein tertiary and secondary structures at the molecular level: the Trp doublet bands at 1340 and 1360 cm^-1, the disulfide stretching vibrational peak at 507 cm^-1, the N-C$\alpha$-C stretching vibration at 933 cm^-1, and the amide Ⅰ band. All experimental results confirmed the concentration-dependent influence of AgNPs on the hen egg-white lysozyme amyloid fibrillation kinetics. In the presence of AgNPs at low concentration (17 μg/mL), electrostatic interaction of the nanoparticles stabilizes disulfide bonds, and protects the Trp residues from exposure to hydrophilic environment, thus leading to formation of amorphous aggregates rather than fibrils. However, with the action of AgNPs at high concentration (1700 μg/mL), the native disulfide bonds of hen egg-white lysozyme are broken to form Ag-S bonds owing to the competition of electrostatic interaction from a great deal of nanoparticles. As for providing functional surfaces for protein to interact with, AgNPs play a bridge role in direct transformation from $\alpha$-helices to organized $\beta$-sheets. The present investigation sheds light on the controversial effects of AgNPs on the kinetics of hen egg-white lysozyme amyloid fibrillation.     

Micropore size analysis in hydrated cement paste by NMR

We present a time evolution of ¹H spin-lattice relaxation rates in the laboratory (1/T₁) and in the rotating (1/T_1ρ) frame of a synthetic cement paste. The typical results found for both rates allow us to follow the main hydration stages of the cement paste and the refinement of its microporosity. In particular the texturation of the porosity and the structuration of the surface of the material are evidenced on two model cement pastes. An interpretation in terms of fractal size distribution is considered as well as the effect of the curing temperature.     

Interactions of thioflavin T with serum albumins: Spectroscopic analyses

The interaction of thioflavin T (ThT) with serum albumins from four different mammalian species i.e. human, bovine, porcine and rabbit, has been investigated by circular dichroism (CD), fluorescence spectroscopy and ITC. The binding constant (K) for HSA was found to be 9.9 × 10⁴ M⁻¹, 4.3 × 10⁴ M⁻¹ for RSA, 1.07 × 10⁴ M⁻¹ for PSA and 0.3 × 10⁴ M⁻¹ for BSA and the number of binding sites (n) were 1.14, 1.06, 0.94 and 0.8, respectively, which is very significant. By using unfolding pathway of HSA in the presence of urea, domain II of HSA has been assigned to possess binding site of ThT. Its binding constant is comparable to many drugs that bind at domain II of HSA, like salicylate, warfarin, digitoxin, etc. Acting force between HSA and ThT is showing that both hydrophobic and electrostatic forces have contributed for the interaction. ΔG_binding, ΔH and ΔS were calculated to be −28.46 kJ mol⁻¹, −3.50 kJ mol⁻¹ and 81.04 J K⁻¹ mol⁻¹, respectively. The data described here will help to increase our understanding about the interaction of ThT with native proteins. The results also indicate that care must be taken while using ThT as a probe for detecting amyloid fibrils.     

Brazilin Inhibits Prostatic Acidic Phosphatase Fibrillogenesis and Decreases its Cytotoxicity

A 39‐amino acid peptide fragment that is derived from prostatic acidic phosphatase (PAP), PAP_248–286, is secreted in large amounts in human semen and forms amyloid fibrils. These fibrils can capture HIV virions and increase the attachment of virions to target cells; as such, they are called a “semen‐derived enhancer of virus infection” (SEVI). Therefore, the inhibition of the formation of PAP_248–286 amyloid fibrils is of great significance. Herein, we demonstrate that brazilin effectively inhibits PAP_248–286 aggregation. The inhibitory effect increases with increasing brazilin concentration. Thioflavin T fluorescence assays and TEM observations confirmed that a few fibrils formed when brazilin was present with PAP_248–286 in an equimolar concentration. Circular dichroism spectroscopy indicated that brazilin inhibited the secondary structural transitions from α‐helices and random coils into β‐sheets. Cytotoxicity assays showed that brazilin significantly decreased the cytotoxicity of the fibrils at 0.01 mmol L⁻¹. Isothermal titration calorimetry revealed that hydrophobic interactions were the main driving force for the binding of brazilin to the PAP_248–286 monomer (dissociation constant, 4.03 μmol L⁻¹), and that the binding affinity of brazilin for the fibrils was at least three orders of magnitude lower than that for the monomer. These results indicate that brazilin holds great potential as a small‐molecule agent against SEVIs.     

NMR measurement of the surface dynamics of poly(dimethylsiloxane) adsorbed on silica gel

CPMAS-DD ¹³C NMR spectroscopy was used to examine the mobility of poly(dimethylsiloxane) adsorbed on silica gel (PDMS/SiO₂) at submonolayer coverages. The spin-lattice relaxation time in the rotating frame (T_1ρH) decreased linearly with increasing loading. This is consistent with a decrease in the mobility of the polymer segments as the loading is increased. The decrease in mobility results from interpolymer interference. We propose a model that explains these results in terms of a surface intrinsic viscosity that incorporates the polymer-polymer interactions on the surface.     

Investigating the two inequivalent NH2(CH3)2 ions in [NH2(CH3)2]2CuCl4 using magic angle spinning nuclear magnetic resonance

The structural change near the phase transition temperatures of [NH₂(CH₃)₂]₂CuCl₄ is discussed in terms of the chemical shifts and the spin-lattice relaxation times T_1ρ in the rotating frame for ¹H MAS NMR and ¹³C CP/MAS NMR. The ¹H T_1ρ undergoes molecular motion near the phase-transition temperature (T_C2 = 253 K). In addition, the two inequivalent [NH₂(CH₃)₂] (1) and [NH₂(CH₃)₂] (2) sites were distinguishable by the ¹³C chemical shift. And, the most significant change was observed at T_C2 for the ¹³C CP/MAS NMR spectrum; this temperature corresponds to a ferroelastic phase transition with different orientations.     

Benzothiazole‐Based Neutral Ratiometric Fluorescence Sensor for Amyloid Fibrils

Early detection of amyloid fibrils is very important for the timely diagnosis of several neurological diseases. Thioflavin‐T (ThT) is a gold standard fluorescent probe for amyloid fibrils and has been used for the last few decades. However, due to its positive charge, ThT is incapable of crossing the blood–brain barrier and cannot be used for in vivo imaging of fibrils. In the present work, we synthesized a neutral ThT derivative, 2‐[2’‐Me,4’‐(dimethylamino)phenyl]benzothiazole (2Me‐DABT), which showed a strong affinity towards the amyloid fibrils. On association with the amyloid fibrils, 2Me‐DABT not only showed a large increase in its emission intensity, but also, unlike ThT, a large blueshift in its emission spectrum was observed. Thus, unlike ThT, 2Me‐DABT is a potential candidate for the ratiometric sensor of the amyloid fibrils. Detailed photophysical properties of 2Me‐DABT in amyloid fibrils and different solvent media were studied to understand its sensory activity. Fluorescence resonance energy transfer (FRET) studies suggested that the sites of localization for ThT and 2Me‐DABT in amyloid fibrils are not same and their average distance of separation in amyloid fibrils was determined. The experimental data was nicely supported by molecular docking studies, which confirmed the binding of 2Me‐DABT in the inner core of the amyloid fibrils.     

Thioflavin T: Electronic Circular Dichroism and Circularly Polarized Luminescence Induced by Amyloid Fibrils

The circularly polarized luminescence (CPL) spectrum of thioflavin T (ThT) bound to insulin amyloid fibrils has been measured for the first time. It has been found that the samples exhibiting induced circular dichroism (CD) retain the optical activity in the CPL spectra, with the same sign of the rotatory strength. The fluorescence dissymmetry factor is substantial (of the order of magnitude 10^?2). Unlike in the corresponding CD and absorption spectra, there is no shift of the CPL band with respect to the fluorescence band. It has been verified that the measured CPL spectra are free from artifacts from circularly polarized scattering of emitted light by conducting additional measurements in a medium with a refractive index similar to insulin (methylsalicylate). The CD and CPL spectra have been interpreted by means of density functional calculations carried out for ThT in its ground and first excited states in different dielectric environments and for ThT interacting with an aromatic ring. It has been found that the presence of an aromatic ring close to the ThT molecule induces Cotton effects of the same order of magnitude as the stabilization of one enantiomeric conformer. Thus, it is expected that both mechanisms contribute to the induced CD and CPL effect to a similar degree.     

Solid-state NMR study of biodegradable starch/polycaprolactone blends

Abundant literature exists on starch or modified starch blended with biodegradable polyesters to achieve good performance with cheap compost plastics. The level of miscibility in these blends is one of the most relevant parameters. In the present study, solid-state ¹H and ¹³C NMR spectra, as well as carbon spin-lattice relaxation times T₁(C) and proton spin-lattice relaxation times T₁(H) and proton spin-lattice relaxation times in the rotating frame T_1ρ(H) of biodegradable starch (or starch formate)/polycaprolactone (PCL) (or polyester (PE) oligomers) blends and samples of the neat components were measured. From the T_1ρ(H) and T₁(H) relaxation times it follows that blends starch/PCL, starch/PE-oligomers and starch formate/PE-oligomers are phase separated even on the scale of 20-110 nm. On the contrary starch formate/PCL blend is phase separated on the scale 2.5-12 nm but homogeneously mixed on the scale 20-90 nm. Moreover, shorter T₁(C) and especially T_1ρ(H) values found for the starch or starch formate component in all these blends in comparison with neat samples show that molecular mobility of starch and starch formate segments is affected by blending. This indicates some miscibility also in phase separated blends which can happen in amorphous channels of starch.     

Negative thermal expansibility change for dissociation of lysozyme variant amyloid protofibril

A disulfide‐deficient variant of hen lysozyme, 0SS, is known to form an amyloid protofibril spontaneously, and to dissociate into monomers at high hydrostatic pressure. We carried out native PAGE at various temperatures (20–35°C) and pressures (0.1–200 MPa), to characterize the dissociation equilibrium of disulfide‐deficient variant of hen lysozyme amyloid protofibril. Based on the density profiles, the partial molar volume and thermal expansibility changes for dissociation, Δv_D and Δe_D, were obtained to be ?74 cm³/mol at 25°C and ?2.3 cm³ mol^?1 K^?1, respectively. The dissociation of amyloid fibril destroys the cross β‐structure, and such conformational destruction in native protein fold rarely accompanies negative thermal expansibility change. We discussed the negative thermal expansibility change in terms of hydration and structural packing of the amyloid protofibril.     

Physical properties of the nonlinear optical material Li2B4O7 studied by static NMR and MAS NMR

The mechanisms behind the nonlinear optical (NLO) properties of Li₂B₄O₇ are characterized by ⁷Li static nuclear magnetic resonance (NMR) and magic-angle spinning (MAS) NMR. Furthermore, the structural nature of 3-coordinate BO₃ and 4-coordinate BO₄ groups is also characterized by the same method. For ⁷Li and ¹¹B, the spin-lattice relaxation time T₁ in laboratory frame gradually decreases with increasing temperature, whereas the spin-lattice relaxation time T_1ρ in rotating frame, which differs from T₁, is nearly constant. In addition, the activation energies of ⁷Li and ¹¹B, which are obtained via the values of T₁ and T_1ρ, are also compared.     

Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data

Functional motions of ¹⁵N‐labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R_1ρ and CPMG‐type experiments. CEST also simultaneously reports on site‐specific R₁ and R₂ parameters. It is shown here how CEST‐derived R₁ and R₂ relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a “lean” version of the model‐free approach S² order parameters can be determined that match those from the standard model‐free approach applied to ¹⁵N R₁, R₂, and {¹H}‐¹⁵N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond‐to‐millisecond timescales.     

Solid-state 13C-NMR studies of the aging of poly(vinylidene fluoride)/poly(methyl methacrylate) blends

Solid state ¹³C-NMR was used to investigate the miscibility and subsequent separation of solution-cast blends of poly(vinylidene fluoride) (PVF₂) and poly(methyl methacrylate) (PMMA) with aging for a range of compositions. It was found that one amorphous phase and intimate mixing of the polymer chains in this phase existed for all compositions of the blends, even after 2 months of aging at room temperature as determined by the proton spin lattice relaxation time T_1ρH in the rotating frame, and the time constant T_CH for transfer of magnetization. The T_1ρH is sensitive to the spatial homogeneity of the blend via spin diffusion and would indicate the presence of phases or domains in the amorphous component of the blend larger than approximately 19 Å. The T_CH is proportional to the inverse sixth power of the interatomic distances needed for transfer of magnetization from proton to carbon and would be sensitive to a separation of polymer chains in the amorphous phase with aging on the order of 4–5 Å. There was an increase of the T_1ρH and T_CH values with aging, indicating that a subtle separation between unlike chains in the amorphous phase was occurring although a single amorphous phase was present.     

Tumbling motions of NH2(CH3)2 ions in [NH2(CH3)2]2ZnCl4 studied using 1H MAS NMR and 13C CP/MAS NMR

The structure and the phase transition temperatures of [NH₂(CH₃)₂]₂ZnCl₄ were determined using X-ray diffraction and DSC, respectively. The temperature dependence of chemical shifts and the spin–lattice relaxation time T_1ρ in the rotating frame were measured for the ¹H and ¹³C nuclei in [NH₂(CH₃)₂]₂ZnCl₄. From these results, it was observed that the structural change by chemical shifts does not occur with temperature. However, T_1ρ for ¹H and ¹³C in [NH₂(CH₃)₂]₂ZnCl₄ showed a minimum, and it is apparent that both T_1ρ values are governed by the same tumbling motions. The activation energies of tumbling motions for ¹H and ¹³C are nearly the same owing to the connection between CH₃ and NH₂ ions in the [NH₂(CH₃)₂]⁺ group.     

Correlation between local mobility and mechanical properties of high‐speed melt‐spun nylon‐6 fibers

This article establishes the processing–microstructure–motion–property relationship of high‐speed melt‐spun nylon‐6 fibers. From solid‐state ¹H NMR T_1ρ (spin–lattice relaxation time in the rotating frame) relaxation studies, all nylon‐6 fibers spun at 4500–6100 m/min showed three‐component exponential decay with the time constants T_1ρ,I, T_1ρ,II, and T_1ρ,III, indicating that there existed three different motional phases. These phases were assigned to immobile crystalline, intermediate rigid amorphous, and mobile amorphous regions. The determination of the correlation time (τ_c) of the respective phases provided information about the local molecular mobility of each phase with respect to the spinning speed. As the spinning speed increased, τ_c of the crystalline region increased (4500–5200 m/min) and then reached a plateau. However, τ_c for the rigid amorphous region increased from 5200 m/min onward, indicating that the rigid amorphous chains were more oriented and constrained in the spinning speed range of 5500–6100 m/min. The drastic increase of the maximum thermal stress for all fibers from 5500 to 6100 m/min was coincident with the τ_c characteristics of the rigid amorphous region. The significant increase in tenacity and Young's modulus and the large decrease in elongation at break at 5500–6100 m/min were also in good agreement with the local molecular motion of the intermediate rigid amorphous phase in the nylon‐6 fibers. © 2001 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 993–1000, 2001