Emergence of Debye Scaling in the Density of States of Liquids under Nanoconfinement.

In the realm of nanoscience, the dynamic behaviors of liquids at scales beyond the conventional structural relaxation time, τ, unfold a fascinating blend of solid-like characteristics, including the propagation of collective shear waves and the emergence of elasticity. However, in classical bulk liquids, where τ is typically of the order of 1 ps or less, this solid-like behavior remains elusive in the low-frequency region of the density of states (DOS). Here, we provide evidence for the emergent solid-like nature of liquids at short distances through inelastic neutron scattering measurements of the low-frequency DOS in liquid water and glycerol confined within graphene oxide membranes. In particular, upon increasing the strength of confinement, we observe a transition from a liquid-like DOS (linear in the frequency ω) to a solid-like behavior (Debye law, ∼ω2) in the range of 1-4 meV. Molecular dynamics simulations confirm these findings and reveal additional solid-like features, including propagating collective shear waves and a reduction in the self-diffusion constant. Finally, we show that the onset of solid-like dynamics is pushed toward low frequency along with the slowing-down of the relaxation processes upon confinement. This nanoconfinement-induced transition, aligning with k-gap theory, underscores the potential of leveraging liquid nanoconfinement in advancing nanoscale science and technology, building more connections between fluid dynamics and materials engineering.

Computational and spectroscopic |characterization of thianthrene.

In this work, we have carried out a comprehensive characterization of the vibrational spectroscopy of the non-planar molecule thianthrene. The combination of infrared, Raman and inelastic neutron scattering spectroscopies is highly complementary and allows all of the modes to be observed. Periodic density-functional theory calculations have provided unambiguous assignments of the spectra. The literature states that C-S stretch modes occur in the 600-800 cm-1 range. We find that while there are modes that involve sulfur motion in this region, this is a consequence of motion in the ortho-phenylene rings. The modes that are driven by the C-S stretches are found in the ~400-500 cm-1 range. The C-S-C bending modes occur in the 200-300 cm-1 range; these have not been previously characterized.

Cooperative Change in the Internal Dynamics of Streptavidin Caused by Biotin Binding.

Protein-ligand interactions are of vital importance for biological functions. The biological function of proteins, such as ligand-binding, is strongly influenced by their dynamics. Quasielastic neutron scattering (QENS) was used to investigate the internal molecular dynamics of streptavidin (STV). QENS experiments to probe the internal dynamics were performed on a ps and 50-100 ps timescale using inverted geometry time-of-flight spectrometers. At the 50-100 ps timescale, the internal equilibrium motions of streptavidin proved to be unaffected by biotin (B) binding. However, on the ps timescale, suppression of jump-diffusion is observed even upon partial ligand saturation. This change indicates that the entire STV protein was affected by the population of one of the four binding sites, thus supporting a cooperative effect.

Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations.

Inspired by the modular architecture of natural signaling proteins, ligand binding proteins are equipped with two fluorescent proteins (FPs) in order to obtain Förster resonance energy transfer (FRET)-based biosensors. Here, we investigated a glucose sensor where the donor and acceptor FPs were attached to a glucose binding protein using a variety of different linker sequences. For three resulting sensor constructs the corresponding glucose induced conformational changes were measured by small angle X-ray scattering (SAXS) and compared to recently published single molecule FRET results (Höfig et al., ACS Sensors, 2018). For one construct which exhibits a high change in energy transfer and a large change of the radius of gyration upon ligand binding, we performed coarse-grained molecular dynamics simulations for the ligand-free and the ligand-bound state. Our analysis indicates that a carefully designed attachment of the donor FP is crucial for the proper transfer of the glucose induced conformational change of the glucose binding protein into a well pronounced FRET signal change as measured in this sensor construct. Since the other FP (acceptor) does not experience such a glucose induced alteration, it becomes apparent that only one of the FPs needs to have a well-adjusted attachment to the glucose binding protein.

Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study.

By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein-protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and Å length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na+-selective ionophore monensin and the K+-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.

Thermophoresis: The Case of Streptavidin and Biotin.

Thermophoretic behavior of a free protein changes upon ligand binding and gives access to information on the binding constants. The Soret effect has also been proven to be a promising tool to gain information on the hydration layer, as the temperature dependence of the thermodiffusion behavior is sensitive to solute-solvent interactions. In this work, we perform systematic thermophoretic measurements of the protein streptavidin (STV) and of the complex STV with biotin (B) using thermal diffusion forced Rayleigh scattering (TDFRS). Our experiments show that the temperature sensitivity of the Soret coefficient is reduced for the complex compared to the free protein. We discuss our data in comparison with recent quasi-elastic neutron scattering (QENS) measurements. As the QENS measurement has been performed in heavy water, we perform additional measurements in water/heavy water mixtures. Finally, we also elucidate the challenges arising from the quantiative thermophoretic study of complex multicomponent systems such as protein solutions.

Strong Adverse Contribution of Conformational Dynamics to Streptavidin-Biotin Binding.

Molecular dynamics plays an important role for the biological function of proteins. For protein ligand interactions, changes of conformational entropy of protein and hydration layer are relevant for the binding process. Quasielastic neutron scattering (QENS) was used to investigate differences in protein dynamics and conformational entropy of ligand-bound and ligand-free streptavidin. Protein dynamics were probed both on the fast picosecond time scale using neutron time-of-flight spectroscopy and on the slower nanosecond time scale using high-resolution neutron backscattering spectroscopy. We found the internal equilibrium motions of streptavidin and the corresponding mean square displacements (MSDs) to be greatly reduced upon biotin binding. On the basis of the observed MSDs, we calculated the difference of conformational entropy ΔSconf of the protein component between ligand-bound and ligand-free streptavidin. The rather large negative ΔSconf value (-2 kJ mol-1 K-1 on the nanosecond time scale) obtained for the streptavidin tetramer seems to be counterintuitive, given the exceptionally high affinity of streptavidin-biotin binding. Literature data on the total entropy change ΔS observed upon biotin binding to streptavidin, which includes contributions from both the protein and the hydration water, suggest partial compensation of the unfavorable ΔSconf by a large positive entropy gain of the surrounding hydration layer and water molecules that are displaced during ligand binding.

The high-intensity option of the SANS diffractometer KWS-2 at JCNS - characterization and performance of the new multi-megahertz detection system.

A new detection system based on an array of 3He tubes and innovative fast detection electronics has been installed on the high-intensity small-angle neutron scattering (SANS) diffractometer KWS-2 operated by the Jülich Centre for Neutron Science (JCNS) at the Heinz Meier-Leibnitz Zentrum in Garching, Germany. The new detection system is composed of 18 eight-pack modules of 3He tubes that work independently of one another (each unit has its own processor and electronics). To improve the read-out characteristics and reduce the noise, the detection electronics are mounted in a closed case on the rear of the 3He tubes' frame. The tubes' efficiency is about 85% (for λ = 5 Å) and the resolution slightly better than 8 mm. The new detection system is characterized by a dead-time constant of 3.3 µs per tube and an overall count rate as high as 6 MHz at 10% dead-time loss. Compared with the old detector this is an improvement by a factor of 60. The much higher count rate will shorten the measurement times and thus increase the number of experiments possible in a given time period by the optimal use of the high flux of up to 2 × 108 n cm-2 s-1 at the sample position. Combined with the event-mode operation capability, this will enable new scientific opportunities in the field of structural investigations of small soft-matter and biological systems. The implementation of the detector in the high-intensity concept on KWS-2, its characterization and its performance based on test experiments are reported in this paper.