Japan Partnering Award -XFEL and dynamic heme enzymology

Lead Research Organisation: University of Leicester
Department Name: Molecular and Cell Biology

Abstract

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Publications

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Kwon H (2021) XFEL Crystal Structures of Peroxidase Compound II in Angewandte Chemie

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Kwon H (2021) XFEL Crystal Structures of Peroxidase Compound II. in Angewandte Chemie (International ed. in English)

 
Description Experimental: By trapping a key intermediate (Compound II) in the catalytic pathway of the enzymes cytochrome c peroxidase and ascorbate peroxidase using the femtosecond pulses of the SACLA X-ray free electron laser to avoid the chemical effects of X-rays, we have shown that there is a key difference in the distances between the iron and oxygen atom in this state of these enzymes. This means the details of the chemistry needs to be re-evaluated.
By visiting our partners in Japan we have not only enabled the collection of the necessary experimental data, we have also widened the collaborations between the UK and Japan-based group. The hosting of a UK-Japan meeting at Leicester in September 2023 facilitated knowledge exchange and collaboration. One of the participants (Dr Hitomi Sawai of Nakaski Unversity)) has joined the Leicester-centred LINXS Theme "Chemistry of Life" (https://www.linxs.se/chemistry-of-life), the inaugural meeting of the sub-theme on the role of metals in biology was held immediately preceding the UK-Japan meeting.
A further outcome from the meeting is that we have been commissioned to assemble and edit a volume of Methods in Enzymology on time resolved methods in structural biology.
Exploitation Route Use of XFELs to avoid seeing X-ray induced reduction of redox-sensitive sates will be applicable to the investigation of many other redox enzymes. The consolidation of links between the XFELs and synchotrons is expanding the methodology and scope for time-resolved analysis of enzyme mechanisms
Sectors Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

URL https://timeresolved23.le.ac.uk/
 
Title Raw XFEL diffraction data from compound II of Ascorbate peroxidase 
Description raw X-ray data deposition for publication 10.1002/anie.202103010 and PDB ID 7BI1 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact making data publicly available will enable improvement in processing 
 
Title Raw diffraction images of CCP by SF-ROX at SACLA 
Description Diffraction images of cytochrome c peroxidase (CcP, PDB code: 7BIU). They were collected using X-ray free electron laser from SACLA at 15 keV with the serial femtosecond rotation crystallography (SF-ROX) method. The MX300-HS CCD detector was used to record images. CcP crystals belong to P212121 space group with a=50.81, b=75.54, c=106.57 Å. 10303 images were collected from 147 crystals, and 9145 images were merged at 1.06 Å resolution using CrystFEL 0.9.1 in the published result. The experiment was carried out on BL2. Images were converted to HDF5 files with measured photon energies. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact public availably of data will enable improvement of data processing methods 
URL https://zenodo.org/record/4484116
 
Description Diamond Light Source 
Organisation Diamond Light Source
Country United Kingdom 
Sector Private 
PI Contribution Provided material for X-ray crystallography and X-ray fluorescence measurements, conducted or helped to conduct experiments
Collaborator Contribution provided facilities and expert advice (including hands-on help) when requested
Impact Nature Communications article (2016) listed in outputs
Start Year 2014
 
Description 2023 International Joint Meeting of the 23rd International Conference on Cytochrome P450 and the 38th Annual Meeting of the Japanese Society for the study of Xenobiotics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk was given at an International (but Japan -focused) meeting on the study of and uses for heme enzymes.
Year(s) Of Engagement Activity 2023
URL https://www.2023iccp450-jssx.org/En/index.html
 
Description LINXS Reboot After the pandemics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk given as contribution to meeting "to discuss the LINXS science and development in the past four years and the future ambitions in expanding the LINXS community."
Lund Sweden.
Establishing contacts with ESS. MAXIV and Lund University community
Year(s) Of Engagement Activity 2022
URL https://www.linxs.se/events/2022/2/2/linxs-science-day-the-development-and-future-vision-of-linxs
 
Description UK Japan meeting on Dynamic and Time resolved crystallography 2 day meeting held in Leicester 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact An open meeting was held bringing together UK- (as well as European-) and Japan-based researchers using time -resolved methods at synchrotrons and XFELs to study enzyme mechanisms. Speakers wereinvited from Japan, Germany and Sweden as well as the UK. The program is available on https://timeresolved23.le.ac.uk/programme/
The two-day event was held at the University of Leicester, with most of the sessions also made available on-line. There were 70 in-person registrants.
Year(s) Of Engagement Activity 2023
URL https://timeresolved23.le.ac.uk/dynamic-crystallography-xfels-and-synchrotrons-to-study-enzyme-react...
 
Description Visit to PAL (Pohang Accelerator Laboratory) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Visit to XFEL to discuss collaboration and developments in methods of sample delivery for time-resolved enzyme studies
Year(s) Of Engagement Activity 2023