Diamond Light Source - Annual Review 2022/23

70 71 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 2 / 2 3 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 2 / 2 3 Integrated Facilities and Collaborations A s a world-leading centre for synchrotron science and a cornerstone of a world-class site for scientific discovery and innovation at Harwell, Diamond Light Source has powerful synergies with its neighbouring research institutes and beyond the campus, through collaborations and shared visions. The integrated facilities at Diamond present academic and industrial users with a one-stop-shop for research opportunities, enabling them to combine cutting-edge techniques and capabilities to advance their studies. During the period 2022/23, Diamond was active on over 75 grant funded projects (20 of which were Diamond led). Our grant portfolio involves projects with over 65 national and international collaborators, where Diamond has contributed to projects worth over £316m. The Membrane Protein Lab The Membrane Protein Laboratory (MPL), at Diamond is a Wellcome funded resource that supports integrated membrane protein structural biology. Located within the Research Complex at Harwell the MPL enables membrane protein research through the delivery of high-quality samples to Diamond’s beamlines and microscopes as well as providing a platform to support membrane protein biochemistry. Membrane proteins are found at the junctions between the outside world and the inner workings of the cell. Multicellular organisms such as humans use membrane proteins for communication, to acquire nutrients and detect threats. Membrane proteins are important targets for biomedicine with over half of all medicines altering membrane protein function. Understanding the structure and function of these proteins in isolation as well as within the wider cellular context will helps us to develop new therapeutics to tackle disease. Visiting scientists to the MPL can spend anywhere between a day and year in our labs supported by state-of -the art equipment and our experienced support scientists. Working with researchers from Brazil, MPL and eBIC scientists have solved two new single-particle cryo-EM structures from yeast; Ach1p (PDB: 8DH7) and cytochrome C oxidase (complex IV) (PDB: 8DH8) were deposited in the protein databank. In collaboration with the Rosalind Franklin Institute MPL scientists contributed to a publication in the journal Science which looked at new nuclear magnetic resonance (NMR) based methods to quantify interactions between host glycan-proteins and pathogens 1 . Specifically, the authors revealed a distinctive sugar-binding mode mediated by the unusual N-terminal domain from B-origin-lineage SARS-CoV-2 spike protein which is lost in later variants. In other work MPL and eBIC scientists have published a review of cryo- EM structures of membrane proteins smaller than 100kDa and provided an analysis of the sample preparation routes, data collection methods and processing approaches that were taken 1 in an effort to highlight successful approaches to understanding these difficult proteins. 1. Buchanan CJ, et al. Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science 377 (6604): eabm3125. (2022) DOI: 10.1126/science.abm3125. 2. Harrison PJ, et al. A review of the approaches used to solve sub-100 kDa membrane proteins by cryo-electron microscopy. J Struct Biol. 215 , 107959. (2023) DOI: 10.1016/j.jsb.2023.107959. XChem Installation of the new insertion device on I04-1 has increasedworking flux by 10x. Alongside the EIGER2 X 9 M detector installed previously, this allows us to collect high-quality data collection in 7.2 seconds exposure time. This has had themost impact on the industrial XChemprogramme who were previously collecting 60 seconds collections, saving up to 53 seconds per dataset. The XChem platform has also expanded the sample preparation facility to accommodate increased activity driven by user demand (from both academia and industry), grant funded projects and delivery on new collaborations (EUbOpen and Infratec). Investment in the facility, coupled with growth of the XChem team, enabled a 50% increase in the number of samples produced in Q1 2023 with almost 13,000 crystals mounted for academic user experiments and grant-funded research alone. Alongside capital investment in the platform, work is ongoing in collaboration with Scientific Software at Diamond to improve the robustness and reliability of the XChem software pipeline ahead of future redevelopment of the software stack to meet the demands of Diamond-II. As part of this work a new deep learning model (Crystal Hits in My Plate (CHiMP)) and user interface (EchoLocator) has been developed to automate crystal identification and selection of coordinates for dispensing compounds. Following the success of the COVID Moonshot’s development of a pre- clinical candidate for the SARS-CoV-2 Main protease, the XChem team and collaborators at Diamond have contributed to two successful National Institute of Health (NIH) grants funding the establishment of Antiviral Drug Discovery (AViDD) Centers for Pathogens of Pandemic Concern: the AI-driven Structure- enabled Antiviral Platform (ASAP) and the Rapidly Emerging Antiviral Drug Development Initiative (READDI). The XChem fragment screening platform is central to both Centers’ pipeline for identifying chemical starting points for drug discovery projects. Furthermore, ASAP will also leverage the platform’s approach to high-throughput structural biology to enable the rapid development from hit to lead-like molecules. Both centres are also committed to open-science and sharing their data to further enable drug discovery projects and methodology development elsewhere. Key publications: Skaist Mehlman T, et al. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B eLife 12 , e84632 (2023) DOI: 10.7554/eLife.84632 Saar K L, et al. Turning high-throughput structural biology into predictive inhibitor design PNAS 120 , (11) e2214168120 (2023) DOI: 10.1073/ pnas.2214168120 Zaho Y, et al. Structural analysis and development of notum fragment screening hits ACS Chem. Neurosci. 2022 , 13 (2022) DOI: 10.1021/ acschemneuro.2c00325 XFEL-Hub The XFEL Hub at Diamond continues to provide expertise and support to the UK community engaged in serial crystallography and XFEL-related life science research. This ranges from experimental conception to beamtime proposals, through sample preparations and testing, to XFEL data collection, analysis, and publication. Our Diamond-based activities continue to include organizing and running the block allocation group “Dynamic Structural Biology at Diamond and XFELs” for serial crystallography and time-resolved studies at various MX beamlines at Diamond. This fiscal year, members of the Hub participated in 9 XFEL experiments at the LCLS in the USA, SACLA in Japan, PAL-XFEL in Korea, or the European XFEL in Germany, as well as a site visit to SwissFEL in Switzerland. Highlighting the synergistic overlap and technology transfer between XFEL and synchrotron facilities, the XFEL Hub spearheads two major projects at Diamond, funded roughly 50:50 by Dr Orville’sWellcome grant and the STFC/ UKRI, that will establish methods for time-resolved serial crystallography studies using on-demand sample delivery and reaction initiation strategies that can be correlated with time-resolved X-ray emission spectroscopy (tr-XES) too. Commissioning activities for these two projects are progressing at Diamond beamline VMXi and is a world’s first installation at a synchrotron. Our plans also include a collaboration with SwissFEL, which along with the Hub plans to host the Diamond sample delivery capabilities and XES capabilities. The Hub has been testing prototypes for sample delivery and XES data collection with von Expanded XChem/I04-1 team. The XFEL Hub and collaborators in Pohang South Korea in December 2022 at PAL-XFEL for experiments. Left to right: Dr Pierre Aller, Dr Matin Maly, Mr Jack Stubbs, Ms Charlotte Cordery, Dr Ivo Tews, Allen M. Orville, Dr Anastasya Shilova, Dr Sam Horrell, Dr Philip Hincliffe, Dr Jos Kamps.