The Edinburgh Protein Production Facility (EPPF) in Edinburgh, Scotland, UK, is one of Europe’s largest and best resourced protein research facilities. Affiliated to the University of Edinburgh, it was opened in 2008 to provide a set of custom designed, managed facilities to support a variety of protein-related life science projects. Since then, the EPPF has contributed to the research behind more than 350 scientific publications on a wide range of subjects. The EPPF has accommodated over 650 registered users from 170 research groups from Edinburgh and beyond, that span Physics, Chemistry and Medicine, as well as Biology.
Dr. Martin Wear is Manager of the EPPF, and also Senior Lecturer in Biochemistry at the University of Edinburgh’s School of Biological Sciences.
“The Edinburgh Protein Production Facility is a ‘research hotel’,” he remarked. “The researchers that use it book time and space on our equipment and have access to our staff expertise, if needed. We have developed the EPPF to provide all the facilities necessary for protein research in one place. We train students, postdoctoral researchers, Principle Investigators (PIs): from high-school work-placement students, right the way through to established researchers. As we train, we encourage them to do a lot of the work themselves.”
Roots in molecular biology
The idea and the framework behind the EPPF originated from work in developing analytical methodologies for producing, purifying, screening and analysing proteins and protein ligand complexes carried out by Professor Walkinshaw and Dr. Wear. This work underpinned a large body of research related to the field of molecular recognition, drug design, and protein production. The primary investors in the EPPF and research projects have been the University of Edinburgh and the Wellcome Trust. The current core staff team consists of five experienced postdoctoral scientists covering a broad set of expertise that includes molecular biology, structural biology, traditional biochemistry, small molecule chemistry, protein production and biophysics.
“Right from the very beginning, we knew that the research hotel would need to have really experienced postdoctoral scientists that had been involved in their own research projects, and in driving both their own and other research themes forward, as staff,” explained Dr. Wear. “Our core scientists are not just good technicians; they are interested in the ‘nuts and bolts’ of the equipment and the experiments that people are using and performing, but at the same time, they have a really high-level understanding of theory and academic input. Therefore, they understand the limitations of the equipment in the Facility, and how to make the best use of it and the reagents. This means that the output from the downstream research, using the best quality reagents, the best quality proteins, is more effective and efficient with far better quality results. It's also informative from the user's point of view, because they're working on the project with genuine experts and they pick up invaluable tips and insight.”
Aside from the restrictions posed by the Covid-19 pandemic, the biggest challenge for the EPPF is in maintaining and upgrading its equipment to the latest specification.
“This is critical, but it is expensive. To maintain this world class output from the biomedical scientific community we need to constantly be at the edge of what the equipment and science can do, and make sure that the platforms are coming online to enable people to achieve that,” said Dr. Wear. One of the unique things about the EPPF, is that we try to keep the costs for users as low as possible. However, strategic support from the funding bodies, institutions, and the University is then vital to keep the Facility running. Overall though, the outputs and the value from it are far greater than the sum of the parts.”
Continued support from the Wellcome Trust and the University of Edinburgh have enabled the EPPF to invest significantly in equipment that is varied enough to support a wide range of research requirements. “The research hotel model was designed to create access to as varied a platform and user as possible,” said Dr. Wear.
The EPPF has modern liquid chromatography systems configured in slightly different ways to give as much flexibility for production and purification as possible; capacity for the culture of bacteria, yeast, and mammalian cells; a comprehensive suite of analytical instruments for examining the biophysical state of proteins and protein complexes - surface plasmon resonance (SPR) instruments for studying kinetics, calorimetry instruments for studying thermodynamics, and a series of spectroscopy and light scattering technologies, which can be used to define and determine the size and the shape and the activity of proteins or protein reagents in their native solution states.
“It’s really important to have all the equipment in one place, because it allows people to either ‘cherry-pick‘ a particular platform for their workflow, or essentially, use us as a proxy for their own lab, for the whole pipeline of work.” Dr. Wear commented.
The research environment itself is also crucial for success.
“The core equipment won't function, unless there is a good supporting infrastructure around it,” said Dr. Wear. “Our essentials are centrifuges, incubators, and -80°C freezers, core consumables and reagents, as well as the building itself. If you don't have these in place, it doesn't really matter how much high-end equipment you've got, you can't use it effectively.”
“Our new PHCbi equipment was acquired with a set of resources and funds that exist to support efforts to innovatively increase the sustainability of the University’s infrastructure, the core equipment, and the way that it runs, with a view to really seriously reducing the energy costs and carbon footprint of the whole University. The University of Edinburgh has set a target to be carbon neutral by 2040. We calculated that the energy saving on the new PHCbi cabinets versus old ones, was approximately £6,000 a year on electricity alone, and about 11 tonnes of CO2 equivalent.” he explained. “In addition, people have commented that the new PHCbi cabinets are really quiet and run very smoothly. It's actually nice to be in the labs now, whereas before, it was really quite noisy. They make the work environment more conducive, which is really good for everyone,” he added.
“We calculated that the energy saving on the new PHCbi cabinets versus old ones, was approximately £6,000 a year on electricity alone, and about 11 tonnes of CO2 equivalent.”
While Dr. Wear’s opinion is that there are several alternative suppliers on the market, with relatively similar equipment specs and prices, he feels PHCbi equipment has several advantages.
“Taking into account the build quality, the cost per unit efficiency, and any bespoke alterations that you might want, the PHCbi units have always featured in the top 20%. It is their reliability however, that makes them stand out. For price, performance and reliability, PHCbi rank in the top 10% of instrumentation when it comes to considering what to buy,” he said. “PHC Europe have achieved a balance that includes providing real service to the customer, whether it's on technical advice, pricing or reliability. And because we've had a long-term relationship with them, and my PHC rep, Cheryl Swinton-Aitken, has always been really amenable, it just makes that relationship much more productive, both for them and for us.”
Trends in protein research
The EPPF has a long history of working with the immunophilin proteins. These are a large family of small proteins that are involved in the immune response and the activation of T-cells. In connection, it is known for its work on analysis of the molecular details of the interaction between the cyclophilins and the drug, cyclosporine, administered to organ transplant patients to prevent organ rejection, and is directly mediated by this family of proteins. They are also somehow implicated in the infectious cycle of viruses, like HIV and hepatitis.
MPR-1412-PE: While the EPPF has used PHCbi equipment for many years, it has most recently acquired 6 x PHCbi MPR-1412 Medical/ Pharmaceutical Refrigerators to provide refrigeration in the temperature range 2°C to 23°C. The units have been specifically purchased to support work with the ÄKTATM protein purification equipment.
“There is a lot of interest in developing novel inhibitors for these proteins to develop new therapeutics and treatments. As we have a long history of working on them, we have also developed a worldwide reputation as being the best source for getting hold of those proteins as reagents for research, and also for their detailed biophysical characterization,” explained Dr. Wear. “Big biopharma has preferentially come to us for these proteins and for the work.”
One international trend in protein science is the miniaturisation of protein production and characterization work flows in cryo-electron microscopy analysis. Significant technological advances in the last few years, mean that it is now possible to obtain atomic resolution structures using the technique. Less material is needed compared to the two traditional atomic resolution techniques: X-Ray crystallography and NMR.
“There’s been a general shift in the scale for production to meet that demand, which means that the equipment, as well as the up- and downstream processing, has become more sensitive and higher throughput, because less sample is needed to process. In the next five years, I can see that technique becoming routine,” he continued.
The Covid-19 pandemic has also influenced research in proteins in many ways.
“We were involved in rapid response Covid-19 research and part of a Covid-19 protein production consortium, which comprised of a network of 10 laboratories across the country set up by the Wellcome Trust UK and the Rosalind Franklin Institute. The consortium was designed to try and provide a set of laboratories and resources to produce reagents for Covid-19 research, especially for those people who were busy with research, but didn't necessarily have the facilities to make the viral proteins or the expertise. The consortium was there to provide quality regents to facilitate novel ideas to try and address certain questions about the virus’ replication, or the pandemic, or distribution of new therapeutics etc,” said Dr. Wear
However, the pandemic has also affected access to
“We were allowed to stay open, but with restrictions on, for example, how many people could be in the lab, in each room, etc. This has delayed some of our training and teaching activities, but we have taken on much more service work than we would normally do and have worked 24/7 in shifts right the way through the pandemic to try and push projects through,” he added.
The proteins and the protein complexes that researchers want and need to study have become increasingly complex.
“Proteins that we are now trying to research tend to be multi-component and are large and complicated, and can't be made simply anymore,” remarked Dr. Wear. “It’s become more expensive to make them. More complex production platforms, mammalian cells or insect cells are needed. It is just getting harder and harder to make the materials required to carry out research with. Without lots of experience in doing that, a lot of these projects would never get off the ground without having access to a core facility like the EPPF.”
For more information visit www.ed.ac.uk/biology/research/facilities/edinburgh-protein-production-facility-eppf
Key research carried out in conjunction with the Edinburgh Protein Production Facility
2021. Fast acting allosteric inhibitors of phosphofructokinase block trypanosome glycolysis and can cure acute African trypanosomiasis in mice. Nat Commun. Feb 16;12(1):1052.doi: 10.1038/s41467-021-21273-6. Iain W. McNae, James Kinkead, Divya Malik, Li-Hsuan Yen, Martin K. Walker, Chris Swain, Scott P. Webster, Nick Gray, Peter M. Fernandes, Elmarie Myburgh, Elizabeth A. Blackburn, Ryan Ritchie, Carol Austin, Martin A. Wear, Adrian J. Highton, Andrew J. Keats, Antonio, Jacqueline Dornan, Jeremy C. Mottram, Paul A.M. Michels, Simon Pettit, Malcolm D. Walkinshaw.
2020. A helminth-derived suppressor of ST2. Elife. May 18;9:e54017. doi: 10.7554/eLife.54017. Vacca F, Chauché C, Jamwal A, Hinchy EC, Heieis G, Webster H, Ogunkanbi A, Sekne Z, Gregory WF, Wear M, PeronaWright G, Higgins MK, Nys JA, Cohen ES, McSorley HJ.
2017. Molecular Basis for Cell Cycle Control of Mis18 Complex Assembly, an Essential Regulator of Centromere Inheritance. EMBO Rep. 2017 Apr 4. pii: e201643564. doi: 10.15252/embr.201643564. Frances Spiller, Bethan Medina-Pritchard, Maria Alba Abad, Martin A. Wear, Oscar Molina, William C. Earnshaw and A. Arockia Jeyaprakash.
2017. Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions; identification of a new non-peptide inhibitor using Biacore™ T200. FEBS Open Bio. 23;7(4):533-549. M.A. Wear, M. Nowicki, I. McNae and MD. Walkinshaw.
2016 Biophysical characterization and activity of lymphostatin, a multifunctional virulence factor of attaching & effacing Escherichia coli. J. Biol. Chem. 11;291(11):5803-16. Robin L. Cassady-Cain, Elizabeth A. Blackburn, Husam Alsarraf, Emil Dedic, Andrew G. Bease, Bettina Bouttcher, Ren Joslashrgensen, Martin Wear, and Mark P. Stevens.
2015 A Streamlined, Automated Protocol for the Production of Milligram Quantities of Untagged Recombinant Rat Lactate Dehydrogenase A Using ÄKTAxpressTM. PLoS One. 2015 Dec 30;10(12):e0146164. doi: 10.1371/journal.pone.0146164. eCollection. Nowicki MW, Blackburn EA, McNae IW, Wear MA.
2007. Experimental determination of van der waals energies in a biological system. Angew Chem Int Ed Engl. 2007;46(34):6453-6. doi: 10.1002/anie.200702084. Wear MA, Kan D, Rabu A, Walkinshaw MD.