Crystal Melting by Light: X‑ray Crystal Structure Analysis of an Azo Crystal Showing Photoinduced Crystal-Melt Transition

<i>Trans</i>–<i>cis</i> photoisomerization in an azo compound containing azobenzene chromophores and long alkyl chains leads to a photoinduced crystal-melt transition (PCMT). X-ray structure analysis of this crystal clarifies the characteristic coexistence of the structurally ordered chromophores through their π···π interactions and disordered alkyl chains around room temperature. These structural features reveal that the PCMT starts near the surface of the crystal and propagates into the depth, sacrificing the π···π interactions. A temporal change of the powder X-ray diffraction pattern under light irradiation and a two-component phase diagram allow qualitative analysis of the PCMT and the following reconstructive crystallization of the <i>cis</i> isomer as a function of product accumulation. This is the first structural characterization of a compound showing the PCMT, overcoming the low periodicity that makes X-ray crystal structure analysis difficult

Determination of the Structural Features of a Long-Lived Electron-Transfer State of 9-Mesityl-10-methylacridinium Ion

Extensive efforts have been devoted to developing electron donor–acceptor systems that mimic the utilization of solar energy that occurs in photosynthesis. X-ray crystallographic analysis shows how absorbed photon energy is stabilized in those compounds by structural changes upon photoinduced electron transfer (ET). In this study, structural changes of a simple electron donor–acceptor dyad, 9-mesityl-10-methylacridinium cation (Acr⁺–Mes), upon photoinduced ET were directly observed by laser pump and X-ray probe crystallographic analysis. The <i>N</i>-methyl group in Acr⁺ was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO₄) was generated by photoinduced ET. These structural changes correspond to reduction and oxidation due to photoinduced ET and directly elucidate the mechanism in Acr⁺–Mes for mimicking photosynthesis efficiently

Determination of the Structural Features of a Long-Lived Electron-Transfer State of 9-Mesityl-10-methylacridinium Ion

Extensive efforts have been devoted to developing electron donor–acceptor systems that mimic the utilization of solar energy that occurs in photosynthesis. X-ray crystallographic analysis shows how absorbed photon energy is stabilized in those compounds by structural changes upon photoinduced electron transfer (ET). In this study, structural changes of a simple electron donor–acceptor dyad, 9-mesityl-10-methylacridinium cation (Acr⁺–Mes), upon photoinduced ET were directly observed by laser pump and X-ray probe crystallographic analysis. The <i>N</i>-methyl group in Acr⁺ was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO₄) was generated by photoinduced ET. These structural changes correspond to reduction and oxidation due to photoinduced ET and directly elucidate the mechanism in Acr⁺–Mes for mimicking photosynthesis efficiently

ATP Dependent Rotational Motion of Group II Chaperonin Observed by X-ray Single Molecule Tracking

<div><p>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.</p></div

Angular diffusion coefficient of the group II chaperonin in the tilting (θ) direction.

<p>The values were obtained from the slope of the MSD versus time plot (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064176#pone-0064176-g003" target="_blank">Figure 3</a>-C). The lines in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064176#pone-0064176-g003" target="_blank">Figure 3</a>-C were fitted with least-squares fitting to the following equation: <i>MSD = 4Dt</i>, where <i>MSD</i> is the mean square angular displacement, <i>D</i> is the angular diffusion constant, and <i>t</i> is time interval.</p

Schematic model of the conformational changes in the group II chaperonin.

<p>Schematic model of the conformational changes in the group II chaperonin.</p

ATP-dependent rotational motion of a group II chaperonin tracked by DXT.

<p>(A) Conformational changes of the group II chaperonin in the absence (left) and presence (right) of ATP. (B) Schematic illustration of the detection of internal motions of group II chaperonins by DXT. (C) Typical DXT traces of gold nanocrystals immobilized on the ring of the group II chaperonin in the absence (upper panel) and presence of ATP (lower panel). (D) The distribution of the absolute angular displacement of the group II chaperonin in the twisting (χ) direction. About 500 DXT trajectories are used to make histogram. The trajectories with an angular displacement greater than 30 mrad in the χ direction were counted as inset bar-graph.</p

ATP-triggered rotational analysis of group II chaperonins in the θ direction.

<p>(A) Time-series histograms of the absolute angular displacement in the θ direction per frame (36 ms). (B) Tryptophan fluorescence changes for a group II chaperonin (TKS1-Cpn L265W) in a mixture of ATP, as measured with a stopped-flow spectrofluorometer. (C) Mean square angular displacement (MSD) in the θ direction as a function of time interval in the presence of 0 mM ATP, 2 mM ATP, or 1 mM ATP-AlFx.</p

Visualization 1: MHz frame rate hard X-ray phase-contrast imaging using synchrotron radiation

Electric arc ignition Originally published in Optics Express on 12 June 2017 (oe-25-12-13857

Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump–Probe X-ray Solution Scattering

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I₁, I₂, and I₃) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme–heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I₁ intermediate is generated within 100 ps and transforms to the R-like I₂ intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I₃ intermediate is formed via subunit rotation, a decrease in the heme–heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I₃ intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme–heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics