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.

Time-Resolved Serial Femtosecond Crystallography at the European X-ray Free Electron Laser

2019 ◽  
Author(s):  
Marius Schmidt ◽  
Suraj Pandey ◽  
Adrian Mancuso ◽  
Richard Bean
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Crystallographic Data ◽  
Time Resolved ◽  
X Ray ◽  
Serial Femtosecond Crystallography

Abstract This protocol introduces step by step into the collection of time resolved crystallographic data and their analysis at the European Free Electron Laser.

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

2017 ◽  
Vol 24 (5) ◽  
pp. 1086-1091 ◽  
Author(s):  
Minoru Kubo ◽  
Eriko Nango ◽  
Kensuke Tono ◽  
Tetsunari Kimura ◽  
Shigeki Owada ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Free Electron ◽  
Good Choice ◽  
Cubic Phase ◽  
Liquid Droplets ◽  
Optical Pump ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
Serial Femtosecond Crystallography

X-ray free-electron lasers (XFELs) have opened new opportunities for time-resolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TR-SFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.

scholarly journals Approach of Serial Crystallography II

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 655
Author(s):  
Ki-Hyun Nam
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Cryogenic Temperature ◽  
Research Trends ◽  
Special Issue ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Fluctuation Dynamics ◽  
Serial Crystallography

Serial crystallography (SX) is an emerging X-ray crystallographic method for determining macromolecule structures. It can address concerns regarding the limitations of data collected by conventional crystallography techniques, which require cryogenic-temperature environments and allow crystals to accumulate radiation damage. Time-resolved SX studies using the pump-probe methodology provide useful information for understanding macromolecular mechanisms and structure fluctuation dynamics. This Special Issue deals with the serial crystallography approach using an X-ray free electron laser (XFEL) and synchrotron X-ray source, and reviews recent SX research involving synchrotron use. These reports provide insights into future serial crystallography research trends and approaches.

scholarly journals Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 628
Author(s):  
Suraj Pandey ◽  
Ishwor Poudyal ◽  
Tek Narsingh Malla
Keyword(s):  
Free Electron ◽  
Reaction Dynamics ◽  
Reaction Coordinate ◽  
Biological Macromolecules ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Recent Developments ◽  
Serial Femtosecond Crystallography

With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.

SAXS Instrumentation

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
Data Collection ◽  
Free Electron ◽  
Free Electron Laser ◽  
Sample Volume ◽  
Time Resolved ◽  
Sample Handling ◽  
X Ray ◽  
Efficient Data ◽  
Laser Sources ◽  
Efficient Data Collection

SAXS instrumentation is available for the laboratory, at the synchrotron, and at X-ray free electron laser sources. This chapter deals with SAXS instrumentation. It covers laboratory systems, synchrotron beamlines and newer sources. Multiple synchrotron facilities have SAXS beamlines and the ability to perform SAXS studies on free electron laser sources is growing. Sample handling has adopted automation and in some cases microfluidics to reduce sample volume requirements. Sensitive detectors efficient data collection software and rapid analysis allow real time decisions to be made during data collection. Specialized apparatus enables time resolved studies. Each component is described.

scholarly journals X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis

2021 ◽  
Vol 7 (34) ◽  
pp. eabh0250
Author(s):  
Patrick Rabe ◽  
Jos J. A. G. Kamps ◽  
Kyle D. Sutherlin ◽  
James D. S. Linyard ◽  
Pierre Aller ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Free Electron ◽  
Free Electron Laser ◽  
Enzyme Dynamics ◽  
Time Resolved ◽  
X Ray ◽  
Unique Reaction ◽  
Solution Studies ◽  
Correlated Motion ◽  
Serial Femtosecond Crystallography

Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.

scholarly journals Double chirp-taper x-ray free-electron laser for attosecond pump-probe experiments

2019 ◽  
Vol 22 (5) ◽  
Author(s):  
Zhen Zhang ◽  
Joseph Duris ◽  
James P. MacArthur ◽  
Zhirong Huang ◽  
Agostino Marinelli
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Pump Probe ◽  
X Ray
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