Tracking of individual nanocrystals using diffracted x rays

Simultaneous Recording of Remote Domain Dynamics in Membrane Proteins Using the Double-Labeled DXB/DXT Technique

Protein dynamics play important roles in biological functions, which accompany allosteric structure changes. Diffracted X-ray blinking (DXB) uses monochromatic X-rays and nanocrystal probes. The intramolecular motion of target proteins is analyzed from the intensity changes in detector signals at the diffraction rings. In contrast, diffracted X-ray tracking (DXT) elucidates molecular dynamics by analyzing the trajectories of Laue spots. In this study, we have developed a dual-labeling technique for DXB and DXT, allowing the simultaneous observation of motions at different domains in proteins. We identified zinc oxide (ZnO) crystals as promising candidates for the second labeling probes due to their excellent diffraction patterns, high chemical stability, and favorable binding properties with proteins. The diffraction spots from the ZnO crystals are sufficiently separated from those of gold, enabling independent motion analysis at different domains. Dual-labeling DXB was employed for the motion analysis of the 5-HT2A receptor in living cells. Simultaneous motion recording of the N-terminus and the second extracellular loop demonstrated ligand-induced motion suppression at both domains. The dual-labeling DXT technique demonstrated a capsaicin-induced peak shift in the two-dimensional motion maps at the N-terminus of the TRPV1 protein, but the peak shift was not obvious in the C-terminus. The capsaicin-induced motion modulation was recovered by the addition of the competitive inhibitor AMG9810.

Real-time tilting and twisting motions of ligand-bound states of α7 nicotinic acetylcholine receptor

The α7 nicotinic acetylcholine receptor is a member of the nicotinic acetylcholine receptor family and is composed of five α7 subunits arranged symmetrically around a central pore. It is localized in the central nervous system and immune cells and could be a target for treating Alzheimer's disease and schizophrenia. Acetylcholine is a ligand that opens the channel, although prolonged application rapidly decreases the response. Ivermectin was reported as one of the positive allosteric modulators, since the binding of Ivermectin to the channel enhances acetylcholine-evoked α7 currents. One research has suggested that tilting motions of the nicotinic acetylcholine receptor are responsible for channel opening and activation. To verify this hypothesis applies to α7 nicotinic acetylcholine receptor, we utilized a diffracted X-ray tracking method to monitor the stable twisting and tilting motion of nAChR α7 without a ligand, with acetylcholine, with Ivermectin, and with both of them. The results show that the α7 nicotinic acetylcholine receptor twists counterclockwise with the channel transiently opening, transitioning to a desensitized state in the presence of acetylcholine and clockwise without the channel opening in the presence of Ivermectin. We propose that the conformational transition of ACh-bound nAChR α7 may be due to the collective twisting of the five α7 subunits, resulting in the compression and movement, either downward or upward, of one or more subunits, thus manifesting tilting motions. These tilting motions possibly represent the transition from the resting state to channel opening and potentially to the desensitized state.

Visualization of the Dynamics of Photoinduced Crawling Motion of 4-(Methylamino)Azobenzene Crystals via Diffracted X-ray Tracking

The photoinduced crawling motion of crystals is a continuous motion that azobenzene molecular crystals exhibit under light irradiation. Such motion enables object manipulation at the microscale with a simple setup of fixed LED light sources. Transportation of nano-/micromaterials using photoinduced crawling motion has recently been reported. However, the details of the motion mechanism have not been revealed so far. Herein, we report visualization of the dynamics of fine particles in 4-(methylamino)azobenzene (4-MAAB) crystals under light irradiation via diffracted X-ray tracking (DXT). Continuously repeated melting and recrystallization of 4-MAAB crystals under light irradiation results in the flow of liquid 4-MAAB. Zinc oxide (ZnO) particles were introduced inside the 4-MAAB crystals to detect diffracted X-rays. The ZnO particles rotate with the flow of liquid 4-MAAB. By using white X-rays with a wide energy width, the rotation of each zinc oxide nanoparticle was detected as the movement of a bright spot in the X-ray diffraction pattern. It was clearly shown that the ZnO particles rotated increasingly as the irradiation light intensity increased. Furthermore, we also found anisotropy in the rotational direction of ZnO particles that occurred during the crawling motion of 4-MAAB crystals. It has become clear that the flow perpendicular to the supporting film of 4-MAAB crystals is enhanced inside the crystal during the crawling motion. DXT provides a unique means to elucidate the mechanism of photoinduced crawling motion of crystals.

Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study

Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

Molecular Dynamics Mappings of the CCT/TRiC Complex-Mediated Protein Folding Cycle Using Diffracted X-ray Tracking

The CCT/TRiC complex is a type II chaperonin that undergoes ATP-driven conformational changes during its functional cycle. Structural studies have provided valuable insights into the mechanism of this process, but real-time dynamics analyses of mammalian type II chaperonins are still scarce. We used diffracted X-ray tracking (DXT) to investigate the intramolecular dynamics of the CCT complex. We focused on three surface-exposed loop regions of the CCT1 subunit: the loop regions of the equatorial domain (E domain), the E and intermediate domain (I domain) juncture near the ATP-binding region, and the apical domain (A domain). Our results showed that the CCT1 subunit predominantly displayed rotational motion, with larger mean square displacement (MSD) values for twist (χ) angles compared with tilt (θ) angles. Nucleotide binding had a significant impact on the dynamics. In the absence of nucleotides, the region between the E and I domain juncture could act as a pivotal axis, allowing for greater motion of the E domain and A domain. In the presence of nucleotides, the nucleotides could wedge into the ATP-binding region, weakening the role of the region between the E and I domain juncture as the rotational axis and causing the CCT complex to adopt a more compact structure. This led to less expanded MSD curves for the E domain and A domain compared with nucleotide-absent conditions. This change may help to stabilize the functional conformation during substrate binding. This study is the first to use DXT to probe the real-time molecular dynamics of mammalian type II chaperonins at the millisecond level. Our findings provide new insights into the complex dynamics of chaperonins and their role in the functional folding cycle.

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.

Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking

Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.

Visualizing Intramolecular Dynamics of Membrane Proteins

Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented.

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.

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.

Structural basis for the coiled-coil architecture of human CtIP

The DNA repair factor CtIP has a critical function in double-strand break (DSB) repair by homologous recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here, we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, small-angle X-ray scattering (SAXS) and diffracted X-ray tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during the recombinational repair. The zinc-binding motif in the CtIP N-terminus alters dynamically the coiled-coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.

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.

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-based living-cell motion analysis of individual serotonin receptors

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins, which transmit extracellular signals inside cells via activating G proteins. GPCRs are involved in a wide variety of physiological functions, such as signal sensing, immune system processes, and neurotransmission. Although the structures and functions of GPCRs have been well studied, little has been known about their real-time dynamics on live cells. In this study, we used Diffracted X-ray Tracking (DXT) and Diffracted X-ray Blinking (DXB) techniques for analysis. These methods are very precise single-molecular analytical techniques that elucidate protein dynamics by analyzing the diffraction spots from the gold nanocrystals labeled on the protein surface. DXT tracks diffraction spot movements, whereas DXB analyzes continuation of signals by calculating the autocorrelation function of each pixel from the recorded data. Serotonin receptor subtype 2A (5-HT_2A receptors) were transiently expressed on HEK 293 cells, and the gold nanocrystals were attached to the N-terminally introduced FLAG-tag via anti-FLAG antibodies. Fast- and mid-range motions were recorded by DXT with 100μs and 1.25 ms/frame rate, respectively. Slow-range motion was obtained using the DXB method with 100 ms/frame rate. An agonist interestingly suppressed the fluctuations of 5-HT_2A receptors at the microsecond-ranged fast measurement. On the contrary, the motion was enhanced by the agonist in the hundred-millisecond-ranged slow time scale. These dual-natured data may suggest that we succeeded in extracting different modes of receptor's motion on live cells; microsecond ranged fluctuation on the cell membrane, and millisecond-ranged dynamic movement comprising interactions with intracellular signaling molecules.

Diffracted X-ray tracking method for recording single-molecule protein motions

BACKGROUND

Proteins change their conformation depending on function. Although a vast number of static pictures of proteins have been accumulated, information regarding their dynamics in function is limited. Diffracted X-ray tracking (DXT) is a good candidate to obtain the missing data.

SCOPE OF REVIEW

A gold nanocrystal was attached to the target protein as a probe and the motion of the X-ray diffraction spots from the crystal corresponded to the motion of the target. Although it has advantages of high temporal (sub-millisecond) and spatial (approximately 0.1°) resolutions, it is not extensively utilized. This review focused on its effective application from a user's perspective. We also present an example with the KcsA channel and the status of recent developments to show the future possibilities of the method.

MAJOR CONCLUSIONS

DXT is a powerful method to investigate intramolecular structural changes. For instance, in the KcsA channel, the method revealed a wave of conformational changes transmitted from the gate region to the end of the molecule. The method is continuously being developed, and users can choose an appropriate measurement system depending on the condition of their sample.

GENERAL SIGNIFICANCE

Revealing the protein structural changes with respect to function is an important frontier. The most distinctive feature of the DXT method is that both high temporal and spatial resolutions are achievable, and it is possible to track the motions of multiple molecules at the same time. This feature is an advantage for screening molecules associated with the target proteins (e.g., ligands and medicines).

Diffracted X-ray Blinking Tracks Single Protein Motions

Single molecule dynamics studies have begun to use quantum probes. Single particle analysis using cryo-transmission electron microscopy has dramatically improved the resolution when studying protein structures and is shifting towards molecular motion observations. X-ray free-electron lasers are also being explored as routes for determining single molecule structures of biological entities. Here, we propose a new X-ray single molecule technology that allows observation of molecular internal motion over long time scales, ranging from milliseconds up to 10³ seconds. Our method uses both low-dose monochromatic X-rays and nanocrystal labelling technology. During monochromatic X-ray diffraction experiments, the intensity of X-ray diffraction from moving single nanocrystals appears to blink because of Brownian motion in aqueous solutions. X-ray diffraction spots from moving nanocrystals were observed to cycle in and out of the Bragg condition. Consequently, the internal motions of a protein molecule labelled with nanocrystals could be extracted from the time trajectory using this diffracted X-ray blinking (DXB) approach. Finally, we succeeded in distinguishing the degree of fluctuation motions of an individual acetylcholine-binding protein (AChBP) interacting with acetylcholine (ACh) using a laboratory X-ray source.

Radiation-driven rotational motion of nanoparticles

Focused synchrotron beams can influence a studied sample via heating, or radiation pressure effects due to intensity gradients. The high angular sensitivity of rotational X-ray tracking of crystalline particles via their Bragg reflections can detect extremely small forces such as those caused by field gradients. By tracking the rotational motion of single-crystal nanoparticles embedded in a viscous or viscoelastic medium, the effects of heating in a uniform gradient beam and radiation pressure in a Gaussian profile beam were observed. Changes in viscosity due to X-ray heating were measured for 42 µm crystals in glycerol, and angular velocities of 10-6 rad s-1 due to torques of 10-24 N m were measured for 340 nm crystals in a colloidal gel matrix. These results show the ability to quantify small forces using rotation motion of tracer particles.

Single-molecule motions of MHC class II rely on bound peptides

The major histocompatibility complex (MHC) class II protein can bind peptides of different lengths in the region outside the peptide-binding groove. Peptide-flanking residues (PFRs) contribute to the binding affinity of the peptide for MHC and change the immunogenicity of the peptide/MHC complex with regard to T cell receptor (TCR). The mechanisms underlying these phenomena are currently unknown. The molecular flexibility of the peptide/MHC complex may be an important determinant of the structures recognized by certain T cells. We used single-molecule x-ray analysis (diffracted x-ray tracking (DXT)) and fluorescence anisotropy to investigate these mechanisms. DXT enabled us to monitor the real-time Brownian motion of the peptide/MHC complex and revealed that peptides without PFRs undergo larger rotational motions than peptides with PFRs. Fluorescence anisotropy further revealed that peptides without PFRs exhibit slightly larger motions on the nanosecond timescale. These results demonstrate that peptides without PFRs undergo dynamic motions in the groove of MHC and consequently are able to assume diverse structures that can be recognized by T cells.

Channel function reconstitution and re-animation: a single-channel strategy in the postcrystal age

The most essential properties of ion channels for their physiologically relevant functions are ion-selective permeation and gating. Among the channel species, the potassium channel is primordial and the most ubiquitous in the biological world, and knowledge of this channel underlies the understanding of features of other ion channels. The strategy applied to studying channels changed dramatically after the crystal structure of the potassium channel was resolved. Given the abundant structural information available, we exploited the bacterial KcsA potassium channel as a simple model channel. In the postcrystal age, there are two effective frameworks with which to decipher the functional codes present in the channel structure, namely reconstitution and re-animation. Complex channel proteins are decomposed into essential functional components, and well-examined parts are rebuilt for integrating channel function in the membrane (reconstitution). Permeation and gating are dynamic operations, and one imagines the active channel by breathing life into the 'frozen' crystal (re-animation). Capturing the motion of channels at the single-molecule level is necessary to characterize the behaviour of functioning channels. Advanced techniques, including diffracted X-ray tracking, lipid bilayer methods and high-speed atomic force microscopy, have been used. Here, I present dynamic pictures of the KcsA potassium channel from the submolecular conformational changes to the supramolecular collective behaviour of channels in the membrane. These results form an integrated picture of the active channel and offer insights into the processes underlying the physiological function of the channel in the cell membrane.

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.

Brownian motion studies of viscoelastic colloidal gels by rotational single particle tracking

Colloidal gels have unique properties due to a complex microstructure which forms into an extended network. Although the bulk properties of colloidal gels have been studied, there has been difficulty correlating those properties with individual colloidal dynamics on the microscale due to the very high viscosity and elasticity of the material. We utilize rotational X-ray tracking (RXT) to investigate the rotational motion of component crystalline colloidal particles in a colloidal gel of alumina and decanoic acid. Our investigation has determined that the high elasticity of the bulk is echoed by a high elasticity experienced by individual colloidal particles themselves but also finds an unexpected high degree of rotational diffusion, indicating a large degree of freedom in the rotational motion of individual colloids even within a tightly bound system.

Tracking 3D picometer-scale motions of single nanoparticles with high-energy electron probes

We observed the high-speed anisotropic motion of an individual gold nanoparticle in 3D at the picometer scale using a high-energy electron probe. Diffracted electron tracking (DET) using the electron back-scattered diffraction (EBSD) patterns of labeled nanoparticles under wet-SEM allowed us to super-accurately measure the time-resolved 3D motion of individual nanoparticles in aqueous conditions. The highly precise DET data corresponded to the 3D anisotropic log-normal Gaussian distributions over time at the millisecond scale.

Combined measurement of X-ray photon correlation spectroscopy and diffracted X-ray tracking using pink beam X-rays

Combined X-ray photon correlation spectroscopy (XPCS) and diffracted X-ray tracking (DXT) measurements of carbon-black nanocrystals embedded in styrene-butadiene rubber were performed. From the intensity fluctuation of speckle patterns in a small-angle scattering region (XPCS), dynamical information relating to the translational motion can be obtained, and the rotational motion is observed through the changes in the positions of DXT diffraction spots. Graphitized carbon-black nanocrystals in unvulcanized styrene-butadiene rubber showed an apparent discrepancy between their translational and rotational motions; this result seems to support a stress-relaxation model for the origin of super-diffusive particle motion that is widely observed in nanocolloidal systems. Combined measurements using these two techniques will give new insights into nanoscopic dynamics, and will be useful as a microrheology technique.

ATP dependent rotational motion of group II chaperonin observed by X-ray single molecule tracking

Group II chaperonins play important roles in protein homeostasis in the eukaryotic cytosol and in Archaea. These proteins assist in the folding of nascent polypeptides and also refold unfolded proteins in an ATP-dependent manner. Chaperonin-mediated protein folding is dependent on the closure and opening of a built-in lid, which is controlled by the ATP hydrolysis cycle. Recent structural studies suggest that the ring structure of the chaperonin twists to seal off the central cavity. In this study, we demonstrate ATP-dependent dynamics of a group II chaperonin at the single-molecule level with highly accurate rotational axes views by diffracted X-ray tracking (DXT). A UV light-triggered DXT study with caged-ATP and stopped-flow fluorometry revealed that the lid partially closed within 1 s of ATP binding, the closed ring subsequently twisted counterclockwise within 2–6 s, as viewed from the top to bottom of the chaperonin, and the twisted ring reverted to the original open-state with a clockwise motion. Our analyses clearly demonstrate that the biphasic lid-closure process occurs with unsynchronized closure and a synchronized counterclockwise twisting motion.

Dynamical regulations of protein-ligand bindings at single molecular level

We present new quantitative regulations of the binding-affinity using dynamical single-molecule detection system with X-rays. In the study of antigen-antibody interactions, we found that structural fluctuations of single-molecules were negatively regulated by antigen-binding. Although strategies to produce ligand-induced stability have been well studied from the macro aspect both theoretically and experimentally, our dynamical single-molecular experimental results are first observations with angstrom accuracy in the real-time and space. It is considered that those negative regulations of protein structural fluctuations with binding event are related to biological functions. In addition, we clarified that ratio between antigen-binding condition and no-binding one in observed structural fluctuations are extremely relative to the binding-affinity. These results indicate that the phenomena of protein-ligand interactions considered as stable states can be defined as results of dynamical processes at the single-molecule level. Such new quantifications from angstrom-level structural fluctuations can be applied to various biological science and biotechnologies.

Single protein molecular dynamics determined with ultra-high precision

We have successfully observed dynamical Brownian motions in an individual protein molecule and other biological ones in real-time with one-hundredth the atomic-scale precision (picometer-scale precision) using X-rays of the super photon ring-8 (SPring-8).

Picometer-scale dynamical observations of individual membrane proteins: the case of bacteriorhodopsin

In vivo measurements of dynamical conformational changes in single biomolecules under functional conditions have had a tremendous impact on molecular and cell biology. However, even single-molecule fluorescent resonance energy transfer cannot easily monitor the intramolecular dynamics in cell systems due to shortcomings in monitoring precision. Here, we report dynamical observations of irreversible intramolecular conformational changes in a single-membrane protein [bacteriorhodopsin (BR)] using diffracted x-ray tracking. The light-driven proton pump BR is the best-characterized membrane protein. The position of BR's 35th amino acid, which is located farthest from retinal, exhibits a momentary positional jump of 0.73+/-0.48 A due to the expression of its function. Following that, we observed Brownian motion without the diffracted spots returning to their initial positions. The average width of this jump is about 14 times larger than that of thermal Brownian motion and agrees with estimated movements from known x-ray crystallography data. This result is an important step toward realizing in vivo observations of single-molecular conformational changes in membrane proteins.

Force generation by recombinant myosin heads trapped between two functionalized surfaces

Fluorescence resonance energy transfer measurements have revealed that the lever-arm domain of myosin swings when it hydrolyzes Mg-ATP. It is generally accepted that this swing of the lever arm of myosin is the molecular basis of force generation. On the other hand, the possibility that the force might be generated at the interface between actin and myosin cannot be ignored. However, there is a third possibility, namely, that myosin itself generates force without actin. Thus, using recombinant subfragment 1 molecules of Dictyostelium myosin II that were trapped between two functionalized surfaces of a surface-force apparatus, we determined whether myosin itself could actually generate force. Here, we report that, despite the absence of actin, myosin heads themselves have a capacity to generate a force (at least approximately 0.2 pN/molecule) that is coupled to the structural changes. Although the role of actin should not be neglected because muscle physiologically shortens as a result of the interaction between actin and myosin, in this work the focus is on the question of whether the catalytic domain of myosin has the capacity to generate force.

Picometer-scale dynamical x-ray imaging of single DNA molecules

Time-resolved dynamical x-ray imaging of individual DNA molecules with picometer-scale precision is demonstrated for the first time. Diffracted x-ray tracking (DXT), a single-molecule experiment with x rays, monitors the rotating motions, rather than the translational motions, of a labeled nanocrystal. DXT can obtain information about the dynamics of single molecules through a quantitative analysis, since the signals from DXT are independent of the chemical conditions.