A Coordinated Infrastructure for NMR for the Physical and Life Sciences: Upgrade to the Ultra-high Field 950 MHz Spectrometer at Oxford

Lead Research Organisation: University of Oxford
Department Name: Biochemistry

Abstract

Uncovering the dynamics and three-dimensional arrangements of the millions of biological macromolecules in a cell remains a formidable task. Yet we need to know how these molecules assemble and interact if we are to understand the emergent property called life. Although large-scale efforts, such as the human genome project, have provided us with the sets of components that make up living organisms, we are still some way from comprehending how these components come together to form the molecular machines that carry out all the basic biological functions.

Similar to engineers, we need to "see" the shape of components to understand their role and place in functional assemblies. Nuclear Magnetic Resonance (NMR) spectroscopy is currently the only method that can provide us with detailed views of biological components under conditions similar to those that occur in living organisms, or even in the living cell itself. As such, NMR studies complement other structural methods which rely on creating immobilised assemblies, such as crystallography and electron microscopy. As well as structural information NMR gives unique information about the dynamic behavior of these components over time, which can be related to events such as chemical catalysis, and insight about associations occurring between components that complements information from other biophysical methods.

NMR instrumentation consists of large, powerful, and very expensive magnets, and electronics that transmit and record experimental signals. In this proposal, the University of Oxford requests support from the UK Research Councils to upgrade our existing ultra-high field 950 MHz NMR system, which features the most powerful magnet in the UK, with the latest generation of high-sensitivity electronics for signal detection. This so-called "cryoprobe" upgrade will boost the measured signal by a factor of ~2-4 enhancing the quality of experimental data collected and enabling more challenging molecular systems to be studied. Coupled to an automation accessory that will allow round-the-clock use of the upgraded NMR system, our proposal represents the most cost-effective and efficient means of increasing cutting-edge NMR capacity and capability in the UK (~£535K for the proposed upgrade versus ~£5M for a similar new system).

Once upgraded, 50% of the time on the 950 MHz NMR system will be made available to external users from other UK academic institutions and from industry. In particular, we aim to assist users from the south of England and Wales, for which Oxford is well placed to serve as an easily accessible regional NMR hub.

Planned Impact

We expect the proposed equipment upgrade to have societal and economic impact through two distinct pathways: direct relevance to life sciences, and the training of researchers.

NMR is an established analytical method for characterising the properties of biological macromolecules. Contrary to X-ray crystallography, however, solution-state NMR can provide information under near physiological conditions, in membrane-mimicking environments or even in living cells. Thus, NMR-derived information is uniquely important not just for structural biologists but more broadly for researchers interested in mechanistic aspects of life. We believe that this wide group, which nowadays includes cell biologists, biochemists, chemists and physicists, will directly benefit from the improved data quality afforded by the upgraded instrumentation.

Scientists based in industry will also benefit from the upgraded NMR spectrometer at Oxford. NMR is widely used in the UK biotechnology and pharmaceutical industries for screening libraries of potential drug molecules and for characterisation of the structure and dynamics of 'druggable' target proteins. Because of the high cost of investment, pharma companies generally do not have in-house ultra-high field NMR systems that are required for studies of some of the most challenging systems. We are aware of demand for access to ultra-high field NMR time from pharma companies including UCB Celltech and Vernalis and will welcome such industrial users on our upgraded 950 MHz system.

Thus, the upgraded 950 MHz spectrometer at Oxford will provide novel opportunities for UK researchers working in both academia and industry to describe challenging biological systems and thereby contribute to our understanding of molecular mechanisms underpinning health and disease.

In addition to basic research considerations, the availability of cutting edge tools directly impacts on the education and training of students and staff in the UK. The Oxford Biochemistry solution-state NMR facility provides opportunities for training and experimentation for undergraduate and graduate students, as well as postdoctoral and early career researchers. We expect that researchers using the upgraded system will gain insights into novel, powerful NMR methods, and they will then be able to re-use this experience in other facilities, whether in academia or industry. Moreover, the structural biology groups using the 950 MHz spectrometer have established interdisciplinary collaborations with molecular and cell biologists, thereby facilitating two-way transfer of ideas and opportunities between NMR researchers and those from collaborating laboratories.

Publications

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Description This award is an equipment grant for the upgrade of a 950 MHz NMR spectrometer with a SampleJet sample changer and a 5mm TCI cryoprobe. Both of these hardware items were ordered in May 2018. The SampleJet was delivered in late December 2018 and installed in January 2019. It is working well and significantly enhances throughput of samples on the 950 MHz spectrometer. The availability of the SampleJet is already attracting new users for the spectrometer.

The 5mm TCI cryoprobe was delivered in April 2019 and a partial installation was carried out. Some modifications to the NMR room were required for the full installation and for health & safety reasons; these took several months to complete. The cryoprobe was up and running early in the autumn of 2019. Once test data had been collected and various problems had been troubleshooted, we were able to start welcoming external users to the facility in November 2019. This initial group of users included the Pfuhl group (KCL), the Hansen group (UCL), the Crump group (Bristol) and the Christodoulou group (UCL/Crick). In late February, free time on the 950 for external users (25% of total time) for the year beginning around April 15th, 2020 was allocated in conjuction with the Crick MRC NMR Facility using their established application process.

Unfortunately, the Covid pandemic beginning in March 2020 and the resulting series of lockdowns made it very difficult for external users to collect data on the 950 and for this reason the amount of time used on the 950 by external users has been much lower than we had anticipated during the period 2020-2022. This is because travel to Oxford was not always possible during several periods in 2020-2021 and also because external research groups were not able to produce the isotope-labelled samples required for NMR due to laboratory closures or to reduced capacity in laboratories. In a small number of cases, external users were able to ship samples to Oxford for data collection but the majority of external users have samples which can not easily be shipped by courier.

A positive outcome of the Covid pandemic has been the use of the 950 for experiments designed to screen small molecule/SARS-CoV-2 protein interactions in solution. At least two different research consortia, based in and around Oxford have used the 950 during the past year for this type of experiment.

The EPSRC funding for NMR in 2018 has led to the establishment of ConnectNMR UK, a network of UK NMR researchers. A network grant to fund the activities of ConnectNMR UK was approved by the EPSRC in March (Ref: EP/S036067/1). Prof Christina Redfield is one of the co-applicants on this grant (representing the biomolecular solution-state NMR community) and has been involved with ConnectNMR UK collaborations with the CCPN project. The grant started on October 1st, 2019. Because activities supported by this network grant were not possible during the Covid pandemic, the end date of the grant has been extended to 31 Jan 2024 (no cost extension).

During 2021/2022 the ongoing pandemic (Delta and Omicron variants) continued to be responsible for a decrease in the demand for 950 MHz NMR time in Oxford. Restrictions on lab occupancy and requirements for self-isolation and social distancing have meant that research groups in the UK have produced fewer protein samples requiring ultra-high field NMR. The Crick NMR Facility also experienced a lower demand during 2020-2022 and were able to accommodate all the requirements from many of the London-based groups. As a result these groups did not need to travel to Oxford for 950 MHz NMR time. However, in Feb 2022 we have begun to see an increase in demand for NMR time. A further allocation of 88 days of time for external users of the 950 MHz started on 31 Oct 2022. There has been some take-up of this 'free' time but there still seems to be adequate capacity at the Crick to accommodate many of the London-based groups. The funding for this time for external users has come from a grant from within the University of Oxford and this funding is due to expire at the end of 2023 and is very unlikely to be renewed. Enquiries have been made to the MRC (who fund the Crick NMR facility) about the possibility of funding the 88 days of 950 time provided at Oxford (at a cost of ~£25K per annum) but the response from the MRC is that there 'no mechanism' to provide this type of funding. This will mean from 2024 onwards, it will not be possible to provide 'free' access to the 950 at Oxford for external users. There is no indication that academic users in the UK biomolecular NMR community are willing to or have the resources to pay for ultra-high-field NMR access charges, particularly with free time available at the Crick and Birmingham.

As a result of the pandemic, we have made remote access to our spectrometers possible; this means that users can operate the spectrometer from their own computers once samples are in the magnet. This increase in remote operation across Europe has resulted in a successful Horizon-Infra-2021 application called Remote NMR: Moving NMR Infrastructures To Remote Access Capabilities". The funding for the Oxford part of this grant has been provided by Innovate UK because of delays in the 'association' of the UK with Horizon funding. Professor Christina Redfield is a member of the Steering Board of the R-NMR project and also coordinates one of the work packages (see https://r-nmr.eu).
Exploitation Route Access by the UK NMR community to the upgraded 950 MHz spectrometer was severely limited by the Covid pandemic. During 2020-2022 we were not able to have as many external users as we would have expected due to Covid restrictions. The situation has improved during 2022-2023 but the demand for ultra-high-field NMR in the UK does not appear to have returned yet to pre-pandemic levels. The feedback from users so far has been positive with publication quality data being collected. At least 9 papers including data from the 950 MHz spectrometer have been published and these involve ~5 different research groups. It can be challenging to ensure that external users acknowledge this equipment grant when they publish their work.
Sectors Education,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Access to Ultra-high Field Nuclear Magnetic Resonance (NMR) Spectroscopy for Biomedical Scientists in Oxford (Wellcome Institutional Strategic Support Fund)
Amount £9,210 (GBP)
Funding ID BRD00062 
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 08/2019 
End 07/2023
 
Description Connect NMR UK: A National NMR Network for the Physical and Life Sciences
Amount £17,770 (GBP)
Funding ID EP/S036067/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2019 
End 09/2022
 
Description Expanding Access to the 950 MHz Solution-State NMR Spectrometer at Oxford (EPA Cephalosporin Fund)
Amount £28,160 (GBP)
Funding ID ALR02140 
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 06/2020 
End 12/2023
 
Description Ultra-high field nuclear magnetic resonance (NMR) spectroscopy for the physical sciences (John Fell Fund)
Amount £7,298 (GBP)
Funding ID ALD00080 
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 06/2019 
End 06/2023
 
Description NMRDG/BBS meeting on NMR in Biophysics and Molecular Biology, Leeds, April 2019. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I gave a scientific talk entitled "Interactions and Conformational Dynamics of the Bacterial Oxidoreductase DsbD". During my talk I also described the EPSRC-funded upgrade of the Oxford 950 MHz NMR spectrometer describing the equipment that had been ordered, the timeline for delivery/installation and details of possible access mechanisms for external users from UK academic groups.

I gave a second short talk about the ConnectNMR UK network grant that was approved for funding by EPSRC in March 2019. This outlined the plans that we had for activities to engage with the wider UK NMR community.
Year(s) Of Engagement Activity 2019