Tetsunari Kimura

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL

Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350u2009kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9u2009Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, ‘distorted-chair’ form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the ‘radiation damage-free’ structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35u2009Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5u2009Å from the Mn4CaO5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ4-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5u2009Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.

A three-dimensional movie of structural changes in bacteriorhodopsin

Snapshots of bacteriorhodopsin Bacteriorhodopsin is a membrane protein that harvests the energy content from light to transport protons out of the cell against a transmembrane potential. Nango et al. used timeresolved serial femtosecond crystallography at an x-ray free electron laser to provide 13 structural snapshots of the conformational changes that occur in the nanoseconds to milliseconds after photoactivation. These changes begin at the active site, propagate toward the extracellular side of the protein, and mediate internal protonation exchanges that achieve proton transport. Science, this issue p. 1552 Time-resolved serial crystallography using an x-ray free electron laser reveals structural changes in bacteriorhodopsin. Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.

Dynamics of Dangling Bonds of Water Molecules in pharaonis Halorhodopsin during Chloride Ion Transportation.

Ion transportation via the chloride ion pump protein pharaonis halorhodopsin (pHR) occurs through the sequential formation of several intermediates during a photocyclic reaction. Although the structural details of each intermediate state have been studied, the role of water molecules in the translocation of chloride ions inside of the protein at physiological temperatures remains unclear. To analyze the structural dynamics of water inside of the protein, we performed time-resolved Fourier transform infrared (FTIR) spectroscopy under H2O or H2(18)O hydration and successfully assigned water O-H stretching bands. We found that a dangling water band at 3626 cm(-1) in pHR disappears in the L1 and L2 states. On the other hand, relatively intense positive bands at 3605 and 3608 cm(-1) emerged upon the formation of the X(N) and O states, respectively, suggesting that the chloride transportation is accompanied by dynamic rearrangement of the hydrogen-bonding network of the internal water molecules in pHR.

New Insights into Metal Ion-Crown Ether Complexes Revealed by SEIRA Spectroscopy

We demonstrate a powerful spectroscopic technique, surface-enhanced infrared absorption (SEIRA) spectroscopy, not only for detecting host–guest complexes in solution but also for examining the relationship between the guest selectivity, complex structure, and solvent effect. We synthesize thiol derivatives of 15-crown-5 and 18-crown-6 [2-(6-mercaptohexyloxy)methyl-15-crown-5 (15C5-C1OC6-SH) and 2-(6-mercaptohexyloxy)methyl-18-crown-6 (18C6-C1OC6-SH)], which are adsorbed on gold surfaces through S–Au bonds. The IR difference spectra of the M+·15C5-C1OC6 (M = Li, Na, K, Rb, and Cs) complexes on gold are observed using aqueous solutions of MCl by SEIRA spectroscopy. The spectra show a noticeable change in the C–O stretching vibration at around 1100 cm−1. The spectral patterns of M+·15C5-C1OC6 are similar for Li+ and Na+, and for K+, Rb+, and Cs+; the interaction between the metal ions and 15C5-C1OC6 changes drastically between Na+ and K+ in the series of alkali metal ions. On the other hand, the equilibrium constant for complex formation determined by the IR intensity shows clear preference for Na+ ions. We also observe the IR difference spectra of M+·18C6-C1OC6 in methanol and compare them with those in water. The spectral patterns in methanol are almost the same as those in water, but the equilibrium constant in methanol does not show preference for any ion, different from the K+ preference in water. From these findings we attribute the origin of the ion selectivity of 15C5 and 18C6 in solution to the interaction between the metal ions and the crown ethers in the complexes or the solvation energy of free ions. In the case of 15C5-C1OC6 in water, the preference of Na+ over K+, Rb+, and Cs+ can be attributed to the strength of the interaction or the size matching between metal ions and 15C5-C1OC6; the Na+ selectivity over Li+ ions is dominated by the solvation energy of free ions. For 18C6-C1OC6 in methanol, the equilibrium constant for complex formation becomes much bigger in methanol than that in water and loses the selectivity in methanol, because the solvation energy in methanol is fairly smaller than that in water, predominating the contribution from the strength of the interaction between metal ions and 18C6-C1OC6. The IR spectra measured by SEIRA spectroscopy are quite sensitive to properties of host–guest complexes such as the intermolecular interaction, the structure, and the orientation against the gold surface. However, the evidence for guest selectivity emerges primarily in the intensity of the spectra, rather than band positions or spectral patterns in the IR spectra.

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome C oxidase

XFEL and IR analyses suggest that O2 bound at CuB blocks proton backflow for unidirectional H+ transport by water channel closure. Bovine cytochrome c oxidase (CcO), a 420-kDa membrane protein, pumps protons using electrostatic repulsion between protons transferred through a water channel and net positive charges created by oxidation of heme a (Fea) for reduction of O2 at heme a3 (Fea3). For this process to function properly, timing is essential: The channel must be closed after collection of the protons to be pumped and before Fea oxidation. If the channel were to remain open, spontaneous backflow of the collected protons would occur. For elucidation of the channel closure mechanism, the opening of the channel, which occurs upon release of CO from CcO, is investigated by newly developed time-resolved x-ray free-electron laser and infrared techniques with nanosecond time resolution. The opening process indicates that CuB senses completion of proton collection and binds O2 before binding to Fea3 to close the water channel using a conformational relay system, which includes CuB, heme a3, and a transmembrane helix, to block backflow of the collected protons.

Nanosecond pump–probe device for time-resolved serial femtosecond crystallography developed at SACLA

A nanosecond pump–probe device for time-resolved serial femtosecond crystallography has been developed at SACLA.

The Impact of the Polymer Chain Length on the Catalytic Activity of Poly( N -vinyl-2-pyrrolidone)-supported Gold Nanoclusters

Poly(N-vinyl-2-pyrrolidone) (PVP) of varying molecular weight (Mwu2009=u200940-360u2009kDa) were employed to stabilize gold nanoclusters of varying size. The resulting Au:PVP clusters were subsequently used as catalysts for a kinetic study on the sized-dependent aerobic oxidation of 1-indanol, which was monitored by time-resolved in situ infrared spectroscopy. The obtained results suggest that the catalytic behaviour is intimately correlated to the size of the clusters, which in turn depends on the molecular weight of the PVPs. The highest catalytic activity was observed for clusters with a core size of ~7u2009nm, and the size of the cluster should increase with the molecular weight of the polymer in order to maintain optimal catalytic activity. Studies on the electronic and colloid structure of these clusters revealed that the negative charge density on the cluster surface also strongly depends on the molecular weight of the stabilizing polymers.

A nearly on-axis spectroscopic system for simultaneously measuring UV–visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline

A nearly on-axis UV–visible absorption spectrometer was developed at SPring-8 that enables spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection.

A Study of the Dynamics of the Heme Pocket and C-helix in CooA upon CO Dissociation Using Time-Resolved Visible and UV Resonance Raman Spectroscopy.

CooA is a CO-sensing transcriptional activator from the photosynthetic bacterium Rhodospirillum rubrum that binds CO at the heme iron. The heme iron in ferrous CooA has two axial ligands: His77 and Pro2. CO displaces Pro2 and induces a conformational change in CooA. The dissociation of CO and/or ligation of the Pro2 residue are believed to trigger structural changes in the protein. Visible time-resolved resonance Raman spectra obtained in this study indicated that the ν(Fe-His) mode, arising from the proximal His77-iron stretch, does not shift until 50 μs after the photodissociation of CO. Ligation of the Pro2 residue to the heme iron was observed around 50 μs after the photodissociation of CO, suggesting that the ν(Fe-His) band exhibits no shift until the ligation of Pro2. UV resonance Raman spectra suggested structural changes in the vicinity of Trp110 in the C-helix upon CO binding, but no or very small spectral changes in the time-resolved UV resonance Raman spectra were observed from 100 ns to 100 μs after the photodissociation of CO. These results strongly suggest that the conformational change of CooA is induced by the ligation of Pro2 to the heme iron.

1P097 Development of micro-channel flow-flash method for time-resolved spectroscopic study of enzymatic reactions(02.Heme proteins,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Time-resolved spectroscopy is powerful to clarify the molecular mechanism of enzymes. Although the solution-mixing is a general technique to trigger the reaction, high sample consumption and limited time-resolution have prevented its extensive application for enzymatic reactions. To improve the time-resolution, we choose the flow-flash method with caged-compounds, where the flash can quickly release substrates. In addition, based on the approach reported by Nakashima et al. at this Society meeting (3I1034 in 2012), we are developing a microchannel flow-cell connected with pulse-synchronized syringe-pump. Only 1 nl sample volume is required to obtain a time-resolved spectrum. The latest developments of the devices will be reported in this presentation.