scholarly journals Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography

IUCrJ ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 431-443
Author(s):  
Hongjie Li ◽  
Yoshiki Nakajima ◽  
Takashi Nomura ◽  
Michihiro Sugahara ◽  
Shinichiro Yonekura ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Water Oxidation ◽  
Structural Changes ◽  
Short Delay ◽  
Time Resolved ◽  
Pump Probe ◽  
Sample Flow Rate ◽  
Excitation Region ◽  
Pump And Probe ◽  
Serial Femtosecond Crystallography

Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump–probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

scholarly journals Capturing structural changes of photosystem II using time-resolved serial femtosecond crystallography with proper flash excitations

2020 ◽  
Author(s):  
Honjie Li ◽  
Yoshiki Nakajima ◽  
Takashi Nomura ◽  
Michihiro Sugahara ◽  
Shinichiro Yonekura ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Water Oxidation ◽  
Structural Changes ◽  
Light Condition ◽  
Enzymatic Reactions ◽  
Time Resolved ◽  
Pump Probe ◽  
State Cycle ◽  
S2 State ◽  
Serial Femtosecond Crystallography

Abstract Photosystem II (PSII) catalyzes light-induced water oxidation through an Si-state cycle, leading to the generation of di-oxygen, protons, and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture intermediate states of light-driven enzymatic reactions. In this approach, it is crucial to avoid contamination of light into the samples when analyzing a particular reaction intermediate. Here, we describe a method for determining a proper light condition that avoids light contamination to the PSII microcrystals while minimizing the sample consumption in TR-SFX. With the proper illumination conditions determined, we analyzed the S2-state structure of PSII at room temperature, revealing the structural changes during the S1-to-S2 transition at an ambient temperature. By comparing with the previous studies performed at a low temperature or with a different delay time, we reveal the possible channels for water inlet and proton egress, as well as structural changes important for the water-splitting reaction.

scholarly journals Extraction of Fast Changes in the Structure of a Disordered Ensemble of Photoexcited Biomolecules

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
H.-C. Poon ◽  
M. Schmidt ◽  
D. K. Saldin
Keyword(s):  
Structural Changes ◽  
Ultrashort Pulses ◽  
Fast Time ◽  
X Rays ◽  
Multiple Diffraction ◽  
Time Resolved ◽  
Pump Probe ◽  
Pump And Probe ◽  
Time Variations ◽  
Diffraction Patterns

Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation. We show here that quantities extractable from multiple diffraction patterns of dissolved molecules in random orientations, as measured using powerful ultrashort pulses of X-rays, also contain information about structural changes of a molecule on photoexcitation.

scholarly journals Selective time-dependent changes of Cu(DPPE)(DMP)·PF6on photoexcitation

2014 ◽  
Vol 70 (a1) ◽  
pp. C776-C776 ◽  
Author(s):  
Elzbieta Trzop ◽  
Bertrand Fournier ◽  
Katarzyna Jarzembska ◽  
Jesse Sokolow ◽  
Radoslaw Kaminski ◽  
...  
Keyword(s):  
Structural Changes ◽  
Dye Sensitized Solar Cells ◽  
Department Of Energy ◽  
Data Sets ◽  
Monoclinic System ◽  
Time Resolved ◽  
Pump Probe ◽  
Light Emitting Devices ◽  
Potential Applications ◽  
Photon Source

Thanks to their potential applications as light-emitting devices, chemical sensors and dye-sensitized solar cells, heteroleptic copper (I) complexes have been extensively studied. Cu(DPPE)(DMP)·PF6(dppe= 1,2-bis(diphenylphosphino)ethane; dmp = 2,9-dimethyl-1,10-phenanthroline) crystallizes in the monoclinic system, P21/c, with two independent molecules in the asymmetric unit. Previous studies on this system [1,2] show strong temperature-dependent emission. The complex was studied at 90K under 355nm laser excitation. At this temperature, the luminescence decay for Cu(DPPE)(DMP)·PF6is biexponential with lifetimes of ~3μs and ~28μs. Two time-resolved X-ray diffraction techniques were applied for studies: (1) a Laue technique at BioCARS ID-14 beamline at the Advanced Photon Source, and (2) monochromatic diffraction at a newly constructed in-house pump-probe monochromatic facility at the University at Buffalo. Structural changes determined with the two methods are in qualitative agreement; discrepancies in position of the Cu and P atoms were observed. The molecular distortions were smaller than those determined at 16K in the earlier synchrotron study by Vorontsov et al. [2]. Photodeformation maps (see Figure below), in which the increase in temperature on photoexcitation has been eliminated, clearly illustrate the photoinduced atomic shifts for both data sets. Results will be compared with those obtained for other studied heteroleptic copper (I) complexes, for instance Cu[(1,10-phenanthroline-N,N′) bis(triphenylphosphine)]·BF4[3]. The in-house pump-probe facility is discussed by Radoslaw Kaminski at this meeting. Research funded by the National Science Foundation (CHE1213223). BioCARS Sector 14 at APS is supported by NIH (RR007707). The Advanced Photon Source is funded by the Office of Basic Energy Sciences, U.S. Department of Energy, (W-31-109-ENG-38). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.

scholarly journals Simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II

2015 ◽  
Vol 112 (13) ◽  
pp. 3979-3984 ◽  
Author(s):  
Xichen Li ◽  
Per E. M. Siegbahn ◽  
Ulf Ryde
Keyword(s):  
Photosystem Ii ◽  
Water Oxidation ◽  
Density Functional ◽  
Structural Changes ◽  
Complete Agreement ◽  
Oxygen Evolving Complex ◽  
Chemical Modeling ◽  
Oxygen Evolving ◽  
High Degree ◽  
Exafs Spectra

Most of the main features of water oxidation in photosystem II are now well understood, including the mechanism for O–O bond formation. For the intermediate S2 and S3 structures there is also nearly complete agreement between quantum chemical modeling and experiments. Given the present high degree of consensus for these structures, it is of high interest to go back to previous suggestions concerning what happens in the S2–S3 transition. Analyses of extended X-ray adsorption fine structure (EXAFS) experiments have indicated relatively large structural changes in this transition, with changes of distances sometimes larger than 0.3 Å and a change of topology. In contrast, our previous density functional theory (DFT)(B3LYP) calculations on a cluster model showed very small changes, less than 0.1 Å. It is here found that the DFT structures are also consistent with the EXAFS spectra for the S2 and S3 states within normal errors of DFT. The analysis suggests that there are severe problems in interpreting EXAFS spectra for these complicated systems.

Fluorescence property of photosystem II protein complexes bound to a gold nanoparticle

2017 ◽  
Vol 198 ◽  
pp. 121-134 ◽  
Author(s):  
Kazuki Tahara ◽  
Ahmed Mohamed ◽  
Kousuke Kawahara ◽  
Ryo Nagao ◽  
Yuki Kato ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Gold Nanoparticle ◽  
Water Oxidation ◽  
Artificial Photosynthesis ◽  
Fluorescence Property ◽  
Light Illumination ◽  
Time Resolved Fluorescence ◽  
Strong Light ◽  
Time Resolved ◽  
Fluorescence Measurements

Development of an efficient photo-anode system for water oxidation is key to the success of artificial photosynthesis. We previously assembled photosystem II (PSII) proteins, which are an efficient natural photocatalyst for water oxidation, on a gold nanoparticle (GNP) to prepare a PSII–GNP conjugate as an anode system in a light-driven water-splitting nano-device (Noji et al., J. Phys. Chem. Lett., 2011, 2, 2448–2452). In the current study, we characterized the fluorescence property of the PSII–GNP conjugate by static and time-resolved fluorescence measurements, and compared with that of free PSII proteins. It was shown that in a static fluorescence spectrum measured at 77 K, the amplitude of a major peak at 683 nm was significantly reduced and a red shoulder at 693 nm disappeared in PSII–GNP. Time-resolved fluorescence measurements showed that picosecond components at 683 nm decayed faster by factors of 1.4–2.1 in PSII–GNP than in free PSII, explaining the observed quenching of the major fluorescence peak. In addition, a nanosecond-decay component arising from a ‘red chlorophyll’ at 693 nm was lost in time-resolved fluorescence of PSII–GNP, probably due to a structural perturbation of this chlorophyll by interaction with GNP. Consistently with these fluorescence properties, degradation of PSII during strong-light illumination was two times slower in PSII–GNP than in free PSII. The enhanced durability of PSII is an advantageous property of the PSII–GNP conjugate in the development of an artificial photosynthesis device.

scholarly journals Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction

2017 ◽  
Vol 4 (2) ◽  
pp. 024501 ◽  
Author(s):  
Krishnayan Basuroy ◽  
Yang Chen ◽  
Sounak Sarkar ◽  
Jason Benedict ◽  
Philip Coppens
Keyword(s):  
Structural Changes ◽  
Time Resolved ◽  
Pump Probe

scholarly journals On the assessment of time-resolved diffraction results

2014 ◽  
Vol 70 (3) ◽  
pp. 291-299 ◽  
Author(s):  
Bertrand Fournier ◽  
Philip Coppens
Keyword(s):  
Relative Intensity ◽  
Structural Changes ◽  
External Perturbation ◽  
Dynamic Structure ◽  
Intensity Change ◽  
Data Sets ◽  
Time Resolved ◽  
Pump Probe ◽  
Final Model ◽  
R Factors

Data collected during dynamic structure pump–probe crystallography experiments require appropriate indicators of agreement and tools to visualize the electron-density distribution changes. Agreement factors based on the ratio of intensitiesRwith and without the external perturbation are shown to be analogous to the {\cal R}1andw{\cal R}2{\cal R} factors widely used in standard crystallographic refinements. The η-based {\cal R} factors, normalized by the average relative intensity change, are significantly larger thanR-based values. It is shown that the relative intensity change η-based {\cal R} factors are not suitable for comparing different data sets. Fourier photodifference maps allow the visualization of the externally induced structural changes in the crystal, but also can be used during refinement to observe residual peaks not yet accounted for by the model and thus monitor the progress of the refinement. The photodeformation maps are a complementary tool to confirm the validity of the final model. Photodeformation maps with equalized laser-on and laser-off thermal motion are used to highlight the structural changes.

scholarly journals Pump-Probe Time-Resolved Serial Femtosecond Crystallography at SACLA: Current Status and Data Collection Strategies

2019 ◽  
Vol 9 (24) ◽  
pp. 5505 ◽  
Author(s):  
Eriko Nango ◽  
Minoru Kubo ◽  
Kensuke Tono ◽  
So Iwata
Keyword(s):  
Data Collection ◽  
Free Electron ◽  
Free Electron Laser ◽  
Current Status ◽  
Optical Pump ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Collection Strategies ◽  
Serial Femtosecond Crystallography

Structural information on protein dynamics is a critical factor in fully understanding the protein functions. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) is a recently established technique for visualizing the structural changes or reactions in proteins that are at work with high spatial and temporal resolution. In the pump-probe method, protein microcrystals are continuously delivered from an injector and exposed to an X-ray free-electron laser (XFEL) pulse after a trigger to initiate a reaction, such as light, chemicals, temperature, and electric field, which affords the structural snapshots of intermediates that occur in the protein. We are in the process of developing the device and techniques for pump-probe TR-SFX while using XFEL produced at SPring-8 Angstrom Compact Free-Electron Laser (SACLA). In this paper, we described our current development details and data collection strategies for the optical pump X-ray probe TR-SFX experiment at SACLA and then reported the techniques of in crystallo TR spectroscopy, which is useful in clarifying the nature of reaction that takes place in crystals in advance.

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