scholarly journals Serial X-ray Crystallography

Crystals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 99
Author(s):  
Ki Hyun Nam
Keyword(s):  
Room Temperature ◽  
X Rays ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
X Ray Crystallography ◽  
Target Molecules ◽  
Serial Crystallography ◽  
Pump Probe Experiment ◽  
Serial Femtosecond Crystallography

Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.

scholarly journals Approach of Serial Crystallography

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 854
Author(s):  
Ki Hyun Nam
Keyword(s):  
Radiation Damage ◽  
Room Temperature ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Wide Range ◽  
Experimental Limitation ◽  
Serial Crystallography ◽  
Collection Strategies

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

scholarly journals Sample Delivery Media for Serial Crystallography

2019 ◽  
Vol 20 (5) ◽  
pp. 1094 ◽  
Author(s):  
Ki Nam
Keyword(s):  
Radiation Damage ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Interaction Point ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography ◽  
Delivery Medium

X-ray crystallographic methods can be used to visualize macromolecules at high resolution. This provides an understanding of molecular mechanisms and an insight into drug development and rational engineering of enzymes used in the industry. Although conventional synchrotron-based X-ray crystallography remains a powerful tool for understanding molecular function, it has experimental limitations, including radiation damage, cryogenic temperature, and static structural information. Serial femtosecond crystallography (SFX) using X-ray free electron laser (XFEL) and serial millisecond crystallography (SMX) using synchrotron X-ray have recently gained attention as research methods for visualizing macromolecules at room temperature without causing or reducing radiation damage, respectively. These techniques provide more biologically relevant structures than traditional X-ray crystallography at cryogenic temperatures using a single crystal. Serial femtosecond crystallography techniques visualize the dynamics of macromolecules through time-resolved experiments. In serial crystallography (SX), one of the most important aspects is the delivery of crystal samples efficiently, reliably, and continuously to an X-ray interaction point. A viscous delivery medium, such as a carrier matrix, dramatically reduces sample consumption, contributing to the success of SX experiments. This review discusses the preparation and criteria for the selection and development of a sample delivery medium and its application for SX.

Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Deepshika Gilbile ◽  
Megan L. Shelby ◽  
Artem Y. Lyubimov ◽  
Jennifer L. Wierman ◽  
Diana C. F. Monteiro ◽  
...  
Keyword(s):  
Room Temperature ◽  
Microfluidic Chips ◽  
Fixed Target ◽  
Plug And Play ◽  
X Ray ◽  
X Ray Crystallography ◽  
Serial Crystallography

This work presents our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial X-ray crystallography measurements.

scholarly journals Lard Injection Matrix for Serial Crystallography

2020 ◽  
Vol 21 (17) ◽  
pp. 5977
Author(s):  
Ki Hyun Nam
Keyword(s):  
Flow Rate ◽  
Room Temperature ◽  
Glucose Isomerase ◽  
Viscous Medium ◽  
Cubic Phase ◽  
Time Resolved ◽  
Crystal Sample ◽  
X Ray ◽  
Serial Crystallography ◽  
Delivery Medium

Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject experiments. Delivering a crystal sample using a viscous medium decreases sample consumption by lowering the flow rate while being extruded from the injector or syringe as compared to a liquid jet injector. Since the environment of crystal samples varies, continuous development of the delivery medium is important for extended SX applications. Herein, I report the preparation and characterization of a lard-based sample delivery medium for SX. This material was obtained using heat treatment, and then the soluble impurities were removed through phase separation. The lard injection medium was highly stable and could be injected via a syringe needle extruded at room temperature with a flow rate < 200 nL/min. Serial millisecond crystallography experiments were performed using lard, and the room temperature structures of lysozyme and glucose isomerase embedded in lard at 1.75 and 1.80 Å, respectively, were determined. The lard medium showed X-ray background scattering similar or relatively lower than shortenings and lipidic cubic phase; therefore, it can be used as sample delivery medium in SX experiments.

scholarly journals X-rays only when you want them: optimized pump–probe experiments using pseudo-single-bunch operation

2015 ◽  
Vol 22 (3) ◽  
pp. 729-735 ◽  
Author(s):  
M. P. Hertlein ◽  
A. Scholl ◽  
A. A. Cordones ◽  
J. H. Lee ◽  
K. Engelhorn ◽  
...  
Keyword(s):  
Laser Excitation ◽  
Ccd Camera ◽  
Single Shot ◽  
X Rays ◽  
Time Resolved ◽  
Pump Probe ◽  
Charge Coupled Device ◽  
X Ray ◽  
X Ray Absorption ◽  
Sample Damage

Laser pump–X-ray probe experiments require control over the X-ray pulse pattern and timing. Here, the first use of pseudo-single-bunch mode at the Advanced Light Source in picosecond time-resolved X-ray absorption experiments on solutions and solids is reported. In this mode the X-ray repetition rate is fully adjustable from single shot to 500 kHz, allowing it to be matched to typical laser excitation pulse rates. Suppressing undesired X-ray pulses considerably reduces detector noise and improves signal to noise in time-resolved experiments. In addition, dose-induced sample damage is considerably reduced, easing experimental setup and allowing the investigation of less robust samples. Single-shot X-ray exposures of a streak camera detector using a conventional non-gated charge-coupled device (CCD) camera are also demonstrated.

Design of a fast rotational chopper for X-ray pump–probe experiments at Diamond Light Source

2010 ◽  
Vol 1 (MEDSI-6) ◽  
Author(s):  
Luis Varandas ◽  
Andrew Peach ◽  
Kevin Collins ◽  
Brian Nutter
Keyword(s):  
Single Crystal Diffraction ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Structures ◽  
Advanced Control ◽  
Speed Stability ◽  
Exceptional Stability ◽  
Energy Activation

New trends in X-ray crystallography are concerned with the study of transient conditions of atomic structures, which take place after an energy activation agent is introduced. These time-resolved experiments require a fast mechanical shutter to interrupt the X-ray beam in a pump–probe cycle, with the aim to generate a stroboscopic effect. Thus, only diffraction data that are representative of the activated structure are actually collected. A rotating type of shutter, also known as chopper, is presented with the purpose to enable time-resolved experiments to be performed at I19 small-molecule single-crystal diffraction beamline. Exceptional stability in the rotational speed is critical to achieve the desired stroboscopic effect with minimum jitter. This requirement can be addressed only through design by the specification of suitable components and implementation of high-precision methods in manufacturing. The proposed equipment is comprised of a spindle supported on air bearings coupled to a slotted disc rotating inside a vacuum enclosure and driven by a brushless servo motor. Advanced control features are proposed to ensure that speed stability is achieved. Preliminary tests produced very encouraging results, giving strong indication that the chopper satisfies the specifications required for time-resolved experiments.

scholarly journals Demonstration of a picosecond Bragg switch for hard X-rays in a synchrotron-based pump–probe experiment

2019 ◽  
Vol 26 (4) ◽  
pp. 1253-1259 ◽  
Author(s):  
Mathias Sander ◽  
Roman Bauer ◽  
Victoria Kabanova ◽  
Matteo Levantino ◽  
Michael Wulff ◽  
...  
Keyword(s):  
Epitaxial Films ◽  
High Repetition Rate ◽  
X Rays ◽  
Sound Waves ◽  
Optical Pump ◽  
Pump Probe ◽  
X Ray ◽  
Benchmark Experiment ◽  
Probe Experiment ◽  
Pump Probe Experiment

A benchmark experiment is reported that demonstrates the shortening of hard X-ray pulses in a synchrotron-based optical pump–X-ray probe measurement. The pulse-shortening device is a photoacoustic Bragg switch that reduces the temporal resolution of an incident X-ray pulse to approximately 7.5 ps. The Bragg switch is employed to monitor propagating sound waves in nanometer thin epitaxial films. From the experimental data, the pulse duration, diffraction efficiency and switching contrast of the device can be inferred. A detailed efficiency analysis shows that the switch can deliver up to 109 photons s−1 in high-repetition-rate synchrotron experiments.

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.

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.

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