Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light

2021 ◽  
Vol 51 (1) ◽  
Author(s):  
Mark A. Wilson
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Enzyme Catalysis ◽  
Energy Landscape ◽  
Annual Review ◽  
Publication Date ◽  
Ambient Conditions ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography

Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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 Two mirror X-ray pulse split and delay instrument for femtosecond time resolved investigations at the LCLS free electron laser facility

2016 ◽  
Vol 24 (11) ◽  
pp. 11768 ◽  
Author(s):  
Nora Berrah ◽  
Li Fang ◽  
Brendan F Murphy ◽  
Edwin Kukk ◽  
Timur Y. Osipov ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Time Resolved ◽  
X Ray ◽  
Laser Facility

scholarly journals Direct autocorrelation of soft-x-ray free-electron-laser pulses by time-resolved two-photon double ionization of He

2009 ◽  
Vol 80 (2) ◽  
Author(s):  
R. Mitzner ◽  
A. A. Sorokin ◽  
B. Siemer ◽  
S. Roling ◽  
M. Rutkowski ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Laser Pulses ◽  
Double Ionization ◽  
Time Resolved ◽  
X Ray ◽  
Two Photon

In Situ X-Ray Techniques for Electrochemical Interfaces

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Bruna F. Baggio ◽  
Yvonne Grunder
Keyword(s):  
Annual Review ◽  
Publication Date ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Recent Developments ◽  
In Operando ◽  
Electrochemical Interfaces ◽  
Ray Scattering

This article reviews progress in the study of materials using X-ray-based techniques from an electrochemistry perspective. We focus on in situ/in operando surface X-ray scattering, X-ray absorption spectroscopy, and the combination of both methods. The background of these techniques together with key concepts is introduced. Key examples of in situ and in operando investigation of liquid–solid and liquid–liquid interfaces are presented. X-ray scattering and spectroscopy have helped to develop an understanding of the underlying atomic and molecular processes associated with electrocatalysis, electrodeposition, and battery materials. We highlight recent developments, including resonant surface diffraction and time-resolved studies. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 14 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

2015 ◽  
Vol 71 (7) ◽  
pp. 856-860 ◽  
Author(s):  
Wenting Wu ◽  
Przemyslaw Nogly ◽  
Jan Rheinberger ◽  
Leonhard M. Kick ◽  
Cornelius Gati ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Second Harmonic ◽  
Night Vision ◽  
Salt Crystallization ◽  
Time Resolved ◽  
Batch Crystallization ◽  
X Ray ◽  
Vapour Diffusion ◽  
Serial Crystallography

Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallization conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.

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 Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA

2020 ◽  
Vol 1864 (2) ◽  
pp. 129466 ◽  
Author(s):  
Michihiro Suga ◽  
Atsuhiro Shimada ◽  
Fusamichi Akita ◽  
Jian-Ren Shen ◽  
Takehiko Tosha ◽  
...  
Keyword(s):  
Laser Radiation ◽  
Free Electron ◽  
Free Electron Laser ◽  
Time Resolved ◽  
X Ray
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