New technique recovers more ‘hard-to-get’ proteins

Key points:

• Researchers at the Institute have developed a new technique called SP4 which captures more of the proteins from cells than existing methods.
• The new method is not only more efficient than previous techniques, but also cheaper, making large scale protein studies more accessible.
• Their next steps are to use this new technique to understand how misfolded protein accumulation is managed by cells.

Researchers from the Institute’s Signalling research programme have published a new method of protein collection called SP4 in the journal Analytical Chemistry. Collecting proteins for analysis is key to understanding many of the processes that happen in cells, both healthy ones and those implicated in disease. Compared to its predecessor, SP4 is better at recovering fragile protein aggregates such as those found in the cell membrane, and toxic misfolded proteins that accumulate in old cells. By sharing their improved technique, the team will not only be able to apply them in their own research, but scientists around the world will be able to streamline their studies and gain new insights into the proteome.

Proteomics is the study of the entire collection of proteins in a biological sample, much like genomics is to genes. Due to their diversity, the comprehensive extraction and purification of proteins presents challenges and no 100% effective method exists. ‘SP3’ is a method that comes very close to achieving this, by forcing proteins out of solution onto the surface of chemically-enhanced magnetic beads for researchers to process further. The new research shows that the reliance on magnetism for SP3 means some proteins, which don’t fully bind to the beads, can get lost when the beads are washed.

Dr Harvey Johnston, the postdoctoral researcher in the Samant lab who led the work, said: “We set out to see whether magnetic beads could be removed from the equation. We managed to demonstrate that the beads are not essential and that proteins can bind to each other in the same way as they bind beads. Using centrifugal force to capture the aggregated proteins, recovery for proteomics was consistently either greater or equivalent to SP3 across a broad range of sample types and inputs, and relative to other methods.”

Some proteins are of higher interest to researchers, especially in the Samant lab where they investigate how misfolded protein accumulation is managed by cells. Importantly, SP4 increases the recovery of proteins with lower solubility – ones that can contribute to the accumulation of toxic misfolded proteins in older cells and those that exist in the cell membrane. A greater understanding of transmembrane proteins is essential for many diagnostic tests, immunotherapy targets, and for gaining insight into how cells interact with their environment.

Harvey and the team recognised that simplicity is key to ensuring the new method. This led to them adding a higher surface area, in the form of cheap inert silica beads, into the methodology. Using glass beads—1/1000^th the cost of magnetic beads—and centrifugation allowed them to capture the aggregated proteins for proteomics, boosting protein recovery amounts compared to SP3 and other methods.

Harvey concluded: “There is huge potential for this technique; from offering better characterisation of diagnostic and immunotherapy targets, to insight into how cells interact with their environment. We’ve already heard that others have made the swap from SP3 to SP4 and can’t wait to see the impact this technical development has for labs around the world.”

Notes to Editors

Publication reference

Johnston et al., Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics 2 Sample Preparation without Magnetic Beads, Analytical Chemistry 2022.

Press contact

Honor Pollard, Communications Officer, honor.pollard@babraham.ac.uk

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Affiliated authors (in author order):

Harvey Johnston, postdoctoral researcher, Samant lab

Kranthikumar Yadav, postdoctoral researcher, Mass Spectrometry facility

David Oxley, Head of Mass Spectrometry facility

Rahul Samant, Group leader, Signalling research programme

Research funding

This research was funded by the BBSRC.

About the Babraham Institute

The Babraham Institute undertakes world-class life sciences research to generate new knowledge of biological mechanisms underpinning ageing, development and the maintenance of health. Our research focuses on cellular signalling, gene regulation and the impact of epigenetic regulation at different stages of life. By determining how the body reacts to dietary and environmental stimuli and manages microbial and viral interactions, we aim to improve wellbeing and support healthier ageing. The Institute is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through Institute Strategic Programme Grants and an Institute Core Capability Grant and also receives funding from other UK research councils, charitable foundations, the EU and medical charities.

About BBSRC

The Biotechnology and Biological Sciences Research Council (BBSRC) is part of UK Research and Innovation, a non-departmental public body funded by a grant-in-aid from the UK government.

BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.

Funded by government, BBSRC invested £451 million in world-class bioscience in 2019-20. We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.