Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray

The Blinking of Small-Angle X-ray Scattering Reveals the Degradation Process of Protein Crystals at Microsecond Timescale

X-ray crystallography has revolutionized our understanding of biological macromolecules by elucidating their three-dimensional structures. However, the use of X-rays in this technique raises concerns about potential damage to the protein crystals, which results in a quality degradation of the diffraction data even at very low temperatures. Since such damage can occur on the micro- to millisecond timescale, a development in its real-time measurement has been expected. Here, we introduce diffracted X-ray blinking (DXB), which was originally proposed as a method to analyze the intensity fluctuations of diffraction of crystalline particles, to small-angle X-ray scattering (SAXS) of a lysozyme single-crystal. This novel technique, called the small-angle X-ray blinking (SAXB) method, analyzes the fluctuation in SAXS intensity reflecting the domain fluctuation in the protein crystal caused by the X-ray irradiation, which could be correlated with the X-ray-induced damage on the crystal. There was no change in the protein crystal's domain dynamics between the first and second X-ray exposures at 95K, each of which lasted 0.7 s. On the other hand, its dynamics at 295K increased remarkably. The SAXB method further showed a dramatic increase in domain fluctuations with an increasing dose of X-ray radiation, indicating the significance of this method.

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.

Ligand-Dependent Intramolecular Motion of Native Nicotinic Acetylcholine Receptors Determined in Living Myotube Cells via Diffracted X-ray Tracking

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that play an important role in signal transduction at the neuromuscular junction (NMJ). Movement of the nAChR extracellular domain following agonist binding induces conformational changes in the extracellular domain, which in turn affects the transmembrane domain and opens the ion channel. It is known that the surrounding environment, such as the presence of specific lipids and proteins, affects nAChR function. Diffracted X-ray tracking (DXT) facilitates measurement of the intermolecular motions of receptors on the cell membranes of living cells, including all the components involved in receptor function. In this study, the intramolecular motion of the extracellular domain of native nAChR proteins in living myotube cells was analyzed using DXT for the first time. We revealed that the motion of the extracellular domain in the presence of an agonist (e.g., carbamylcholine, CCh) was restricted by an antagonist (i.e., alpha-bungarotoxin, BGT).

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

The dynamic properties of crystalline materials are important for understanding their local environment or individual single-grain motions. A new time-resolved observation method is required for use in many fields of investigation. Here, we developed in situ diffracted X-ray blinking to monitor high-resolution diffraction patterns from single-crystal grains with a 50 ms time resolution. The diffraction spots of single grains of silver halides and silver moved in the θ and χ directions during the photolysis chemical reaction. The movements of the spots represent tilting and rotational motions. The time trajectory of the diffraction intensity reflecting those motions was analysed by using single-pixel autocorrelation function (sp-ACF). Single-pixel ACF analysis revealed significant differences in the distributions of the ACF decay constants between silver halides, suggesting that the motions of single grains are different between them. The rotational diffusion coefficients for silver halides were estimated to be accurate at the level of approximately 0.1 to 0.3 pm²/s. Furthermore, newly formed silver grains on silver halides correlated with their ACF decay constants. Our high-resolution atomic scale measurement—sp-ACF analysis of diffraction patterns of individual grains—is useful for evaluating physical properties that are broadly applicable in physics, chemistry, and materials science.

X-ray observations of single bio-supramolecular photochirogenesis

The binding and photochirogenic behaviour of 2-anthracenecarboxylate (AC) with human serum albumin (HSA) have hitherto been investigated and comprehended as time-averaged statistical events by spectroscopic examinations and product analyses. In this study, we employed a diffracted X-ray tracking (DXT) technique to visualize the single-molecular dynamics of free and AC-loaded HSA (AC:HSA = 0, 1, 5 and 10), as well as the AC-HSA complex under photoirradiation, all of which were tethered to gold nanocrystals and hence traceable in real time by DXT. This enabled us to draw a more dynamic picture of the bio-supramolecular photochirogenesis at a single-molecule resolution, detailing the softening and flexibility enhancement of HSA upon binding of ACs to its inter-subdomain IIA-IIB site and the dynamic extrusion of AC dimers produced upon photoirradiation.

Time-resolved X-ray Tracking of Expansion and Compression Dynamics in Supersaturating Ion-Networks

Supersaturation of a solution system is a metastable state containing more solute than can be normally solubilized. Moreover, this condition is thermodynamically important for a system undergoing a phase transition. This state plays critical roles in deposition morphology in inorganic, organic, polymer and protein solution systems. In particular, microscopic solution states under supersaturated conditions have recently received much attention. In this report, we observed the dynamic motion of individual ion-network domains (INDs) in a supersaturated sodium acetate trihydrate solution (6.4 M) by using microsecond time-resolved and high accuracy (picometre scale) X-ray observations (diffracted X-ray tracking; DXT). We found that there are femto-Newton (fN) anisotropic force fields in INDs that correspond to an Angstrom-scale relaxation process (continuous expansion and compression) of the INDs at 25 μs time scale. The observed anisotropic force-field (femto-Newton) from DXT can lead to new explanations of how material crystallization is triggered. This discovery could also influence the interpretation of supercooling, bio-polymer and protein aggregation processes, and supersaturated systems of many other materials.

Nonequilibrium magnetic response of anisotropic superparamagnetic nanoparticles and possible artifacts in magnetic particle imaging

Magnetic responses of superparamagnetic nanoparticles to high-frequency AC magnetic fields with sufficiently large amplitudes are numerically simulated to exactly clarify the phenomena occurring in magnetic particle imaging. When the magnetic anisotropy energy inevitable in actual nanoparticles is taken into account in considering the magnetic potential, larger nanoparticles exhibit a delayed response to alternations of the magnetic fields. This kind of delay is rather remarkable in the lower-amplitude range of the field, where the assistance by the Zeeman energy to thermally activated magnetization reversal is insufficient. In some cases, a sign inversion of the third-order harmonic response was found to occur at some specific amplitude, despite the lack in DC bias magnetic field strength. Considering the attenuation of the AC magnetic field generated in the human body, it is possible that the phases of the signals from nanoparticles deep inside the body and those near the body surface are completely different. This may lead to artifacts in the reconstructed image. Furthermore, when the magnetic/thermal torque-driven rotation of the anisotropic nanoparticles as well as the magnetic anisotropy energy are taken into account, the simulated results show that, once the easy axes are aligned toward the direction of the DC bias magnetic field, it takes time to randomize them at the field-free point. During this relaxation, the third-order harmonic response depends highly upon the history of the magnetic field. This is because non-linearity of the anhysteretic magnetization curve for the superparamagnetic nanoparticles varies with the orientations of the easy axes. This history dependence may also lead to another artifact in magnetic particle imaging, when the scanning of the field-free point is faster than the Brownian relaxations.

Real time ligand-induced motion mappings of AChBP and nAChR using X-ray single molecule tracking

We observed the dynamic three-dimensional (3D) single molecule behaviour of acetylcholine-binding protein (AChBP) and nicotinic acetylcholine receptor (nAChR) using a single molecule tracking technique, diffracted X-ray tracking (DXT) with atomic scale and 100 μs time resolution. We found that the combined tilting and twisting motions of the proteins were enhanced upon acetylcholine (ACh) binding. We present the internal motion maps of AChBP and nAChR in the presence of either ACh or α-bungarotoxin (αBtx), with views from two rotational axes. Our findings indicate that specific motion patterns represented as biaxial angular motion maps are associated with channel function in real time and on an atomic scale.