Tilting and rotational motions of silver halide crystal with diffracted X-ray blinking

Time-Resolved X-ray Observation of Intracellular Crystallized Protein in Living Animal

Understanding the cellular environment as molecular crowding that supports the structure-specific functional expression of biomolecules has recently attracted much attention. Time-resolved X-ray observations have the remarkable capability to capture the structural dynamics of biomolecules with subnanometre precision. Nevertheless, the measurement of the intracellular dynamics within live organisms remains a challenge. Here, we explore the potential of utilizing crystallized proteins that spontaneously form intracellular crystals to investigate their intracellular dynamics via time-resolved X-ray observations. We generated transgenic Caenorhabditis elegans specifically expressing the crystallized protein in cells and observed the formation of the protein aggregates within the animal cells. From the toxic-effect observations, the aggregates had minimal toxic effects on living animals. Fluorescence observations showed a significant suppression of the translational diffusion movements in molecules constituting the aggregates. Moreover, X-ray diffraction measurements provided diffraction signals originating from these molecules. We also observed the blinking behaviour of the diffraction spots, indicating the rotational motion of these crystals within the animal cells. A diffracted X-ray blinking (DXB) analysis estimated the rotational motion of the protein crystals on the subnanometre scale. Our results provide a time-resolved X-ray diffraction technique for the monitoring of intracellular dynamics.

Diffracted X-ray Tracking for Observing the Internal Motions of Individual Protein Molecules and Its Extended Methodologies

In 1998, the diffracted X-ray tracking (DXT) method pioneered the attainment of molecular dynamics measurements within individual molecules. This breakthrough revolutionized the field by enabling unprecedented insights into the complex workings of molecular systems. Similar to the single-molecule fluorescence labeling technique used in the visible range, DXT uses a labeling method and a pink beam to closely track the diffraction pattern emitted from the labeled gold nanocrystals. Moreover, by utilizing X-rays with extremely short wavelengths, DXT has achieved unparalleled accuracy and sensitivity, exceeding initial expectations. As a result, this remarkable advance has facilitated the search for internal dynamics within many protein molecules. DXT has recently achieved remarkable success in elucidating the internal dynamics of membrane proteins in living cell membranes. This breakthrough has not only expanded our knowledge of these important biomolecules but also has immense potential to advance our understanding of cellular processes in their native environment.

Observation of molecular motions in polymer thin films by laboratory grazing incidence diffracted X-ray blinking

Research on polymer surfaces has shown that the mobilities of polymer chains, which affect the aggregation state and thus the physical properties of the material, differ between the surface and bulk. However, the mobilities of the surface polymers have not been fully characterized. Therefore, we propose a time-resolved method for evaluating surface mobility. This measurement scheme is called grazing incidence diffracted X-ray blinking (GI-DXB) and can be used to evaluate the molecular motions occurring at polymer surfaces by continuously measuring X-ray diffraction patterns near the total reflection angle over small time periods. In this study, the crystallized polymer poly{2-(perfluorooctyl)ethyl acrylate}(PC8FA) was measured. The decay constants, which are indexes of molecular motions, were calculated to be 3.98 × 10−3 s−1 for the fluoroalkyl groups in the side chains observed along the in-plane direction and 3.36 × 10−3 s−1 for the lamellar structure observed along the out-of-plane direction when 2000 diffraction profiles of 500 ms were recorded and the incident angle was 0.07°. In contrast, transmission DXB indicated decay constants of 2.63 × 10−3 s−1 for the side chains and 2.87 × 10−3 s−1 for the lamellar structures. These results suggested that the PC8FA surface is mobile, because a larger decay constant indicates a higher mobility. GI-DXB can be used to measure surface dynamics. The authors contend that GI-DXB is a highly versatile tool because it allows the evaluation of local motions with a laboratory X-ray system, and these motions cannot be detected by conventional surface analyses. This measurement scheme may facilitate the development of high-performance polymers and discovery of new physical properties.

Dynamic observations of various oligomers in amyloid β isoforms using laboratory diffracted X-ray blinking

Acceleration of societal ageing has increased the global incidence of geriatric diseases such as Alzheimer's disease (AD), and the demands for proper diagnosis and monitoring of those diseases are also increasing daily. We utilized diffracted X-ray blinking (DXB) for amyloid β (Aβ) isoforms, which are thought to be closely related to AD, to discriminate among the dynamics of individual particles in early and long-term oligomerisation and aggregation inhibiting environments. Among the various Aβ isoforms, the dynamics of Aβ (1–42), which is known to be the most toxic form, were the slowest (the dynamics were lower by 78% com-pared with short-term incubation), and the dynamics were restored (the dynamics increased by 105% compared with normal aggregation) in an environment that suppressed oligomerisation of Aβ (1–42). It has been confirmed that the use of DXB allows measurements of dynamics related to the functional states of the target molecules.

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The Dynamics of Amyloid β in early oligomerisation was measured by Diffracted X-ray Blinking, pico-meter scale method.

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The dynamics of Amyloid β was shrinked in more oligomerisation.

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The dynamics of Amyloid β (1–42) on Pd surface were recovered by 105% compared with that of normal oligomerisation.

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Dynamical measurement captured the recovery of Amyloid β (1–42); it is important to measure the dynamics of the oligomer.

Green Synthesis and Characterization of Antimicrobial Synergistic AgCl/BAC Nanocolloids

All over the world, one of the major challenges is the green synthesis of potential materials against antimicrobial resistance and viruses. This study demonstrates a simple method like chemistry lab titration to synthesize green, facile, scalable, reproducible, and stable synergistic silver chloride/benzyldimethylhexadecyl-ammonium chloride (AgCl/BAC) colloidal Nanoantimicrobials (NAMs). Nanocolloidal dispersions of AgCl in an aqueous medium are prepared by using silver nitrate (AgNO₃) as precursor and BAC as both sources of chloride and stabilizer, holding an asymmetric molecular structure. The synthetic approach is scalable and green. Both the morphology and stability of AgCl/BAC nanocolloids (NCs) were investigated as a function of different molar fractions of the reagents. AgCl/BAC NCs were characterized by transmission electron microscopy (TEM) and X-ray photoelectron and UV–vis spectroscopies. Zeta potential measurements revealed increasing positive potential values at every stage of the synthesis. Size distribution and hydrodynamic diameter of the particles were measured by dynamic light scattering (DLS), which predicted the formation of BAC layered structures associated with the AgCl nanoparticles (NPs). Small-angle X-ray scattering (SAXS) experiments verify the thickness of the BAC bilayer around AgCl. The produced AgCl/BAC NCs probably have synergistic antimicrobial properties from the AgCl core and the biocide BAC shell. AgCl/BAC NCs stability over months was investigated. The experimental evidence supports the morphological stability of the AgCl/BAC NCs, while higher positive zeta potential values anticipate a long-term antimicrobial effect: a higher surface charge causes NPs to be potentially more lethal to bacteria. AgCl/BAC antimicrobial aqueous colloidal suspensions will be used as additives for the industrial production of antimicrobial coatings.

Diffracted X-ray Tracking Method for Measuring Intramolecular Dynamics of Membrane Proteins

Membrane proteins change their conformations in response to chemical and physical stimuli and transmit extracellular signals inside cells. Several approaches have been developed for solving the structures of proteins. However, few techniques can monitor real-time protein dynamics. The diffracted X-ray tracking method (DXT) is an X-ray-based single-molecule technique that monitors the internal motion of biomolecules in an aqueous solution. DXT analyzes trajectories of Laue spots generated from the attached gold nanocrystals with a two-dimensional axis by tilting (θ) and twisting (χ). Furthermore, high-intensity X-rays from synchrotron radiation facilities enable measurements with microsecond-timescale and picometer-spatial-scale intramolecular information. The technique has been applied to various membrane proteins due to its superior spatiotemporal resolution. In this review, we introduce basic principles of DXT, reviewing its recent and extended applications to membrane proteins and living cells, respectively.

Superelasticity of a photo-actuating chiral salicylideneamine crystal

Superelasticity is a type of elastic response to an applied external force, caused by a phase transformation. Actuation of materials is also an elastic response to external stimuli such as light and heat. Although both superelasticity and actuation are deformations resulting from stimulus-induced stress, there is a phenomenological difference between the two with respect to whether force is an input or an output. Here, we report that a molecular crystal manifests superelasticity during photo-actuation under light irradiation. The crystal exhibits stepwise twisted actuation due to two effects, photoisomerization and photo-triggered phase transition, and the actuation behavior is simulated based on a dynamic multi-layer model. The simulation, in turn, reveals how the photoisomerization and phase transition progress in the crystal, indicating superelasticity induced by modest stress due to the formation of photoproducts. This work provides not only a successful simulation of stepwise twisted actuation, but also to the best of our knowledge the first indication of superelasticity induced by light.

Laboratory diffracted x-ray blinking to monitor picometer motions of protein molecules and application to crystalline materials

In recent years, real-time observations of molecules have been required to understand their behavior and function. To date, we have reported two different time-resolved observation methods: diffracted x-ray tracking and diffracted x-ray blinking (DXB). The former monitors the motion of diffracted spots derived from nanocrystals labeled onto target molecules, and the latter measures the fluctuation of the diffraction intensity that is highly correlated with the target molecular motion. However, these reports use a synchrotron x-ray source because of its high average flux, resulting in a high time resolution. Here, we used a laboratory x-ray source and DXB to measure the internal molecular dynamics of three different systems. The samples studied were bovine serum albumin (BSA) pinned onto a substrate, antifreeze protein (AFP) crystallized as a single crystal, and poly{2-(perfluorooctyl)ethyl acrylate} (PC₈FA) polymer between polyimide sheets. It was found that not only BSA but also AFP and PC₈FA molecules move in the systems. In addition, the molecular motion of AFP molecules was observed to increase with decreasing temperature. The rotational diffusion coefficients (D_R) of BSA, AFP, and PC₈FA were estimated to be 0.73 pm²/s, 0.65 pm²/s, and 3.29 pm²/s, respectively. Surprisingly, the D_R of the PC₈FA polymer was found to be the highest among the three samples. This is the first report that measures the molecular motion of a single protein crystal and polymer by using DXB with a laboratory x-ray source. This technique can be applied to any kind of crystal and crystalline polymer and provides atomic-order molecular information.

Living-Cell Diffracted X-ray Tracking Analysis Confirmed Internal Salt Bridge Is Critical for Ligand-Induced Twisting Motion of Serotonin Receptors

Serotonin receptors play important roles in neuronal excitation, emotion, platelet aggregation, and vasoconstriction. The serotonin receptor subtype 2A (5-HT_2AR) is a Gq-coupled GPCR, which activate phospholipase C. Although the structures and functions of 5-HT_2ARs have been well studied, little has been known about their real-time dynamics. In this study, we analyzed the intramolecular motion of the 5-HT_2AR in living cells using the diffracted X-ray tracking (DXT) technique. The DXT is a very precise single-molecular analytical technique, which tracks diffraction spots from the gold nanocrystals labeled on the protein surface. Trajectory analysis provides insight into protein dynamics. The 5-HT_2ARs were transiently expressed in HEK 293 cells, and the gold nanocrystals were attached to the N-terminal introduced FLAG-tag via anti-FLAG antibodies. The motions were recorded with a frame rate of 100 μs per frame. A lifetime filtering technique demonstrated that the unliganded receptors contain high mobility population with clockwise twisting. This rotation was, however, abolished by either a full agonist α-methylserotonin or an inverse agonist ketanserin. Mutation analysis revealed that the “ionic lock” between the DRY motif in the third transmembrane segment and a negatively charged residue of the sixth transmembrane segment is essential for the torsional motion at the N-terminus of the receptor.

Diffracted X-ray blinking measurements of interleukin 15 receptors in the inner/outer membrane of living NK cells

Interleukin 15 receptor (IL-15R) is a transmembrane signalling protein consisting of 3 subsets: α, β (IL-15Rβ), and γ (γ_c). IL-2 and IL-15 share the signalling domains IL-15Rβ and γ_c, although they bind to intrinsic α-subsets and non-signalling domains. Additionally, IL-2 and IL-15 play different roles; therefore, there have been many observations of the dynamic behaviours of IL-15R, which are linked to physiological functions. For more practical discrimination between IL-2 and IL-15, a study was designed and carried out in which α-subsets were removed and a cytoplasmic inhibitor was applied to create a simplified environment in which secondary signalling molecules were reduced. We also applied a new measurement method, diffracted X-ray blinking (DXB), to achieve higher accuracy (<0.01 Å). The dynamics of IL-2 binding (confined motion, max range = 0.71 Å) and IL-15 binding (normal motion) in live natural killer cells were different. We also confirmed. that DXB was a suitable method to quantitatively evaluate the transmembrane protein dynamics of inner/outer live cell membranes by labeling the extracellular domain since the measurements were dependent on the cytosolic environment.