High hit-rate, high-throughput serial protein crystallography at SACLA using fixed target silicon nitride chips
Lead Research Organisation:
University of Essex
Department Name: Life Sciences
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Publications
Ebrahim A
(2019)
Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins.
in IUCrJ
Hough MA
(2023)
Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches.
in Frontiers in molecular biosciences
Hough MA
(2021)
Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis.
in Current opinion in structural biology
Lucic M
(2021)
Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeIV = O formation in bacterial dye-decolorizing peroxidases.
in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry
Lucic M
(2020)
Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in FeIV =O Formation.
in Angewandte Chemie (International ed. in English)
Moreno-Chicano T
(2022)
Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.
in IUCrJ
Moreno-Chicano T
(2019)
High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.
in IUCrJ
Worrall JAR
(2022)
Serial femtosecond crystallography approaches to understanding catalysis in iron enzymes.
in Current opinion in structural biology
| Description | BEORHN: Biological Enzymatic Oxidation of Reactive Hydroxylamine in Nitrification via Combined Structural Biology and Molecular Simulation |
| Amount | £441,577 (GBP) |
| Funding ID | BB/V01577X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2021 |
| End | 06/2024 |
| Description | Breaking the Cage: Transformative Time-resolved Crystallography using Fixed Targets at Synchrotrons and XFELs |
| Amount | £446,146 (GBP) |
| Funding ID | BB/W001950/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 01/2025 |
| Title | Chips with everything |
| Description | A current limitation of serial femtosecond crystallography using liquid jet sample delivery has been the relatively low throughput, especially given the scarcity and value of XFEL beamtime and protein samples. We propose to revolutionise metalloprotein SFX through the use of highly time and sample efficient chip-based sample delivery, exploiting a high degree of a priori sample and sample delivery characterisation at a synchrotron microfocus beamline. We anticipate that this will allow us to collect sufficient data in this proposal to determine the damage-free structures of more than 10 metalloproteins of interest, with highly efficient use of both X-rays and samples. Moreover, the comparatively short interval between loading of samples and measurement will allow us to characterise relatively long-lived intermediates. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | We demonstrated high throughput high hit-rate use of the chip technology, with partners from Diamond and SACLA (Japan) inOct 2017. 100s of Gigabytes of data were collected on 10 protein systems, and outputs will include a series of papers in due course. One output has been further funding by BBSRC for us to pursue this line of work by visits to SACAL XFEL in Japan for the next few years |
| Title | PDB entries |
| Description | Deposition of crystallographic coordinates and data for nitrite-bound Cu nitrite reductase obtained through serial femtosecond crystallography. PDB entry 6QWG |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Dissemination of experimental result, associated with publication: Chicano, TM, Ebrahim, A, Axford, D, Appleby, MV, Beale, JH, et al. & Hough, MA. (2019) High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. IUCr Journal, 6, 1074-1085. |
| URL | https://www.ebi.ac.uk/pdbe/entry/pdb/6qwg |
| Description | Collaboration with University of Southampton (Dr Ivo Tews) |
| Organisation | University of Southampton |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Our work on Cu nitrite reductase serial crystallography at Diamond and SACLA led to the establishment of a new collaboration with Dr Ivo Tews, University of Southampton to exploit our new methodology. |
| Collaborator Contribution | New samples & proteins to apply our methodology to (FutA iron transport system) Participation in SACLA and Diamond beamtime We have been granted SACLA beamtime jointly with Dr Tews for 2019 and 2020. |
| Impact | Multiple future publications from joint serial crystallography experiments are anticipated. |
| Start Year | 2018 |
| Description | SACLA-RIKEN |
| Organisation | RIKEN |
| Department | RIKEN SPring-8 Center |
| Country | Japan |
| Sector | Private |
| PI Contribution | The UK-based elements of the team from Essex University and Diamond will conduct regular experiments at Diamond to ensure optimal preparation for the work in Japan. This UK activity is funded by existing grant awards and with in-house collaborative beamtime. The in-kind contribution from Essex to the project will be protein and microcrystal samples, reagents, ligands and photocages, together with expertise in the structures and reactions to be characterised. |
| Collaborator Contribution | Diamond will contribute fixed-target chips, mounting systems, sample stages and control and access to cluster computing for data analysis. The Japanese-based team at Riken/SACLA (led by Dr Sugimoto) will contribute expertise in photocage experiments, access to the synchronised laser system, laboratory access and standard equipment for sample handling, reagents. |
| Impact | This project started in May 2018. Two experimental sessions by the Essex and Diamond (UK partners) have taken place with the Japanese partners at SACLA. Currently we are generating outcomes in the form of publications and data depositions, to be detailed later. |
| Start Year | 2018 |