Ayana Tomita

Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin

Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.

Developing 100 ps-resolved X-ray structural analysis capabilities on beamline NW14A at the Photon Factory Advanced Ring

NW14A is a newly constructed undulator beamline for 100 ps time-resolved X-ray experiments at the Photon Factory Advanced Ring. This beamline was designed to conduct a wide variety of time-resolved X-ray measurements, such as time-resolved diffraction, scattering and X-ray absorption fine structure. Its versatility is allowed by various instruments, including two undulators, three diffractometers, two pulse laser systems and an X-ray chopper. The potential for the detection of structural changes on the 100 ps time scale at NW14A is demonstrated by two examples of photo-induced structural changes in an organic crystal and photodissociation in solution.

Direct Probing of Spin State Dynamics Coupled with Electronic and Structural Modifications by Picosecond Time-Resolved XAFS

The first direct observation of the transient spin-state in a disordered magnetic system with time-resolved XAFS is reported. By observing the evolution of the Fe(II) 1s-3d transition, the spin crossover transition from the (1)A(1) low spin state to (5)T(2) high spin state has been directly observed on a picosecond time scale. Moreover, observation of the transient spin state with time-resolved XAFS allows for the investigation of the variations in the electronic state and molecular structure. This unique experimental technique probes the excited states involved in the ultrafast photoinduced reactions in disordered magnetic systems.

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

Trans-cis 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 cis 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 N-methyl group in Acr(+) was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO(4)) 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.

'It's hollow': the function of pores within myoglobin.

SUMMARY Despite a century of research, the cellular function of myoglobin (Mb), the mechanism regulating oxygen (O2) transport in the cell and the structure–function relationship of Mb remain incompletely understood. In particular, the presence and function of pores within Mb have attracted much recent attention. These pores can bind to Xe as well as to other ligands. Indeed, recent cryogenic X-ray crystallographic studies using novel techniques have captured snapshots of carbon monoxide (CO) migrating through these pores. The observed movement of the CO molecule from the heme iron site to the internal cavities and the associated structural changes of the amino acid residues around the cavities confirm the integral role of the pores in forming a ligand migration pathway from the protein surface to the heme. These observations resolve a long-standing controversy – but how these pores affect the physiological function of Mb poses a striking question at the frontier of biology.

Capturing molecular structural dynamics by 100 ps time-resolved X-ray absorption spectroscopy

An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented.

Shock-induced lattice deformation of CdS single crystal by nanosecond time-resolved Laue diffraction

We report a single-shot nanosecond time-resolved Laue diffraction measurement of cadmium sulfide (CdS) single crystal under laser-induced shock compression. The observed Laue diffraction pattern maintains sixfolding axis of the wurtzite structure for 10ns at a shock pressure of 3.92GPa, which is above the threshold pressure of phase transition to a rocksalt structure. This result shows that a transient wurtzite structure is observed above its threshold pressure to a rocksalt structure on a nanosecond time scale. Uniaxial compression was confirmed by the c∕a value of the transient structure obtained from the (201) and (302) peaks.We report a single-shot nanosecond time-resolved Laue diffraction measurement of cadmium sulfide (CdS) single crystal under laser-induced shock compression. The observed Laue diffraction pattern maintains sixfolding axis of the wurtzite structure for 10ns at a shock pressure of 3.92GPa, which is above the threshold pressure of phase transition to a rocksalt structure. This result shows that a transient wurtzite structure is observed above its threshold pressure to a rocksalt structure on a nanosecond time scale. Uniaxial compression was confirmed by the c∕a value of the transient structure obtained from the (201) and (302) peaks.

100 ps time-resolved solution scattering utilizing a wide-bandwidth X-ray beam from multilayer optics

A new method of time-resolved solution scattering utilizing X-ray multilayer optics is presented.

OPTICAL PROPERTIES OF TRANSITION-METAL DOPED SPINELS

Strong blue emission is observed from Ti-doped MgAl2O4, yellow emission from a Mn-doped one and white light emission from a V-doped one. The optimum condition to obtain the strongest emission was studied by changing the doping density and growing atmosphere. The microscopic models for these emission processes are proposed from observation of other optical responses and electron spin resonance spectra both in the electronic ground and excited states.