scholarly journals Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 728-736
Author(s):  
Sylvain Aumonier ◽  
Gianluca Santoni ◽  
Guillaume Gotthard ◽  
David von Stetten ◽  
Gordon A. Leonard ◽  
...  
Keyword(s):  
Blue Light ◽  
Room Temperature ◽  
Intermediate Species ◽  
Time Resolved ◽  
X Ray ◽  
Blue Light Photoreceptor ◽  
Intermediate States ◽  
Serial Crystallography ◽  
Protein Reaction ◽  
Monochromatic Synchrotron

The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.

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 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 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow

IUCrJ ◽  
2020 ◽  
Vol 7 (2) ◽  
pp. 207-219 ◽  
Author(s):  
Diana C. F. Monteiro ◽  
David von Stetten ◽  
Claudia Stohrer ◽  
Marta Sans ◽  
Arwen R. Pearson ◽  
...  
Keyword(s):  
Data Collection ◽  
Room Temperature ◽  
Time Resolved ◽  
X Ray ◽  
Biologically Relevant ◽  
3D Printed ◽  
Serial Crystallography ◽  
Low X ◽  
Very High

Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX.

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 X-ray reflectivity with a twist: Quantitative time-resolved X-ray reflectivity using monochromatic synchrotron radiation

2019 ◽  
Vol 114 (8) ◽  
pp. 081904 ◽  
Author(s):  
Howie Joress ◽  
Shane Q. Arlington ◽  
Timothy P. Weihs ◽  
Joel D. Brock ◽  
Arthur R. Woll
Keyword(s):  
Synchrotron Radiation ◽  
Time Resolved ◽  
X Ray ◽  
Monochromatic Synchrotron

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 Room temperature hidden state in a manganite observed by time-resolved X-ray diffraction

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Haijuan Zhang ◽  
Yuanyuan Zhang ◽  
Runze Li ◽  
Junxiao Yu ◽  
Wenxia Dong ◽  
...  
Keyword(s):  
Room Temperature ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray

Stable sample delivery in viscous media via a capillary for serial crystallography

2020 ◽  
Vol 53 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Ki Hyun Nam
Keyword(s):  
Room Temperature ◽  
Capillary Tube ◽  
Glucose Isomerase ◽  
Low Flow ◽  
Innovative Technology ◽  
Delivery Method ◽  
Crystal Sample ◽  
X Ray ◽  
Serial Crystallography ◽  
Delivery Medium

Serial crystallography (SX) is an innovative technology in structural biology that enables the visualization of the molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample-delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques, drastically reducing sample consumption. In serial millisecond crystallography using a viscous medium via a capillary, crystals of lysozyme embedded in agarose, which produce an unstable injection stream at atmospheric pressure, and crystals of glucose isomerase embedded in gelatin, which is known to be problematic for open-extruder operation, were stably delivered at a flow rate of 100 nl min−1. The room-temperature crystal structures of lysozyme and glucose isomerase were successfully determined at 1.85 and 1.70 Å resolutions, respectively. This simple but highly efficient sample-delivery method can allow researchers to deliver crystals precisely to an X-ray beam in SX experiments.

scholarly journals Breaking Simple Scaling Relations Through Metal-Oxide Interactions: Understanding Room Temperature Activation of Methane on M-CeO2 (M= Pt, Ni or Co) Interfaces

2020 ◽  
Author(s):  
Pablo Lustemberg ◽  
Feng Zhang ◽  
Ramón A. Gutiérrez ◽  
Pedro J. Ramírez ◽  
Sanjaya D. Senanayake ◽  
...  
Keyword(s):  
Photoelectron Spectroscopy ◽  
Density Functional ◽  
Room Temperature ◽  
Elevated Temperatures ◽  
Ambient Pressure ◽  
Scaling Relations ◽  
Time Resolved ◽  
X Ray ◽  
Metal Support ◽  
Simple Scaling

The clean activation of methane at low temperatures remains an eminent challenge and a field of competitive research. In particular, on late transition metal surfaces such as Pt(111) or Ni(111), elevated temperatures are necessary to activate the hydrocarbon molecule, but a massive deposition of carbon makes the metal surface useless for catalytic activity. However, on very low-loaded M/CeO2 (M= Pt, Ni, or Co) surfaces, the dissociation of methane occurs at room temperature, which is unexpected considering simple linear scaling relationships. This intriguing phenomenon has been studied using a combination of experimental techniques (ambient-pressure X-ray photoelectron spectroscopy, time-resolved X-ray diffraction and X-ray absorption spectroscopy) and density functional theory-based calculations. The experimental and theoretical studies show that the size and morphology of the supported nanoparticles together with strong metal-support interactions are behind the deviations from the scaling relations. These findings point toward a possible strategy to circumvent scaling relations, producing active and stable catalysts which can be employed for methane activation and conversion. <br>

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