The UK’s synchrotron: Life sciences at Diamond Light Source

Images to demonstrate life sciences at Diamond Light Source
© Sealand Aerial Photography Limited

Professor David Stuart FRS, Director of Life Sciences at the UK’s synchrotron, Diamond Light Source, spoke to SciTech Europa about his work on protein structures and the fundamental role of facilities like Diamond in the life sciences sector.

Professor Dave Stuart FRS has been the Director of Life Sciences at Diamond Light Source since 2008. He is also the MRC Professor of Structural Biology at the University of Oxford, and Deputy Head of the Division of Structural Biology at the Department of Clinical Medicine.

Stuart is a true world-leader in structural biology, mapping the Foot and Mouth Virus disease structure, discovering the first structure of an enveloped virus, and advancing the understanding of viral assembly, replication, and infection. He is also known for pushing technological developments that drive innovative science forward as a key player in the case for funding Diamond itself, as well as its new national Electron Bio-Imaging Centre (eBIC).

He has numerous firsts and awards to his name. He was elected a Fellow to the Royal Society at the early age of 43, and is a fellow of the Academy Of Medical Sciences. In 2006, Stuart was awarded the Aminoff prize of the Royal Swedish Academy of Science for his remarkable contributions in virus crystallography.

SciTech Europa asked Stuart about his research, his role at Diamond, and how facilities such as this are shaping the future of research in the life sciences.

Given your varied positions at Diamond, how would you describe the role that you play there?

My job here is the Life Science Director, which means that I spend about half my time here doing that job, and I try to do some science as well. When I am here, I try to make sure that Diamond is as good as anywhere in the world for doing synchrotron radiation, and beyond that trying to make sure that the methods used here at the synchrotron are as good as possible at solving problems for biology and biomedical science. And while that is mainly basic science, there are increasing opportunities for therapeutic developments.

What sparked your interest in researching the structure of viruses?

That is a good question. I started off looking at protein structures which, compared with viruses, are rather simpler. I guess I was intrigued by the idea of seeing something like a virus, which some people argue are alive, and other argue are not, but which nevertheless have many properties of living things. They evolve according to Darwinian evolution, and yet they are also sufficiently simple that you can see their complete structure in atomic detail.

I think that is what really interested me; the idea of something that had a lot of biological properties, but you could imagine that, one day, you might be able to completely understand the whole thing and how it worked.

Perhaps one of the most interesting aspects of structural biology is using it to design medicines based around those structures you are able to observe. This has grown significantly over the last couple of decades, as technology development and innovation has resulted in ever-more detailed observations. How has Diamond in particular contributed to this?

It is very difficult to make new drugs, and if you look at the work that goes on in the pharmaceutical companies, in many instances the work on a new drug fails, and so never actually becomes an effective therapy.

The great thing about the developments that have happened at Diamond and other synchrotrons is that they have enabled the process of getting structural information on the therapeutic targets and on the complexities of a drug with its target to be speeded up by orders of magnitude. Over the past 20 years, that has been a significant change within drug companies, many of which now see structure as a central part of the development pipeline.

This speed has been enhanced with automation, meaning that it is now possible to respond quickly enough in terms of providing structural information to hook directly into pipelines for developing new chemistries. The timescale is fast enough to make the most of chemical discovery, linked, and fed by, structural insight. This has had a fundamental impact on the way people think about drug discovery.

How would you describe your work on mapping the Foot and Mouth Virus disease structure?

I started working on viruses at the time when it was becoming possible to think about doing virus structures, and this was a challenge I wanted to take on. I then got to know, via David Philips, who was the head of the laboratory at the time, a virologist called Fred Brown. He was working on Foot and Mouth Disease at the contained labs at Pirbright – the only place in the country where the work could be done.

Brown was something of a forward-looking virologist, and he was convinced that it should be possible to use structure to help make better vaccines against the Foot and Mouth Disease Virus.

Even in the 2001 epidemic, which was devastating to the UK, the UK did not vaccinate – for various complicated reasons. This epidemic saw the massive destruction of cattle, and there was huge economic loss to the country. But Brown thought that there must be a better way of doing this, and he thought that structure could illuminate that. This was fantastic because it was somebody in a different field, a virologist, who could see that structure would be useful.

We thus started the work and the virus was grown in the contained category four laboratories where, because we were working on an animal pathogen, it was relatively easy to work inside the labs, but we had to be extremely careful when we came out – everybody showers etc.

It took a very long time to put in place precautions that were acceptable. And every time we wanted to do a data collection, we had to get a specific licence to make the trip, and this included being escorted by disease security officers; we had to have all the viruses locked up, and all the virus crystals had to be destroyed after they were worked with. But it was a very interesting time. It was great fun. And we were very careful.

You mentioned that mapping the virus was a challenge. Do you think you were drawn to work with Foot and Mouth Disease also because of the high profile nature of it? Or was it just because it was a convenient opportunity that presented itself?

I was drawn to it because it was a problem that was worth looking at. At the time I started work on it, there hadn’t been a serious outbreak in the UK for a number of years. In fact, when we got the structure it was not that easy to make the case for developing – or trying to work to develop –vaccines from that point.

This was made a little more difficult because Brown was then working for a company which decided to move out of animal vaccines, and so he had to change fields; it was very difficult to try and build on the structure as we hoped we would.

It was only after the very serious outbreak of the disease that we were then able to make some new collaborations and really start again on trying to do something useful with the structure.

Is there perhaps something of a disconnect between the speed of drug development and real-world progress after you have made the necessary discoveries?

The scientific experiments get much faster, and you can obtain scientific insights very quickly. This can then make it very tempting to cherry-pick, to do one experiment and then move on to something else. As such, the lesson here is that even if you get a structure of a virus or very positive experimental results, to actually build on that and to convert it into something useful will take years. Indeed, there are often 20 years between doing a piece of work to seeing it converted into an application, and that was certainly the case with Foot and Mouth.

You were a champion for scientific funding for Diamond when it was being originally conceived. Why is it important that Diamond focuses funding on technological advances and continues to look at developing the facility going forwards?

My first degree was in biophysics, and a place like Diamond is somewhere where you get the physical sciences, engineering, physics, and so on all coming together with biology. If you look at the history of development of the biological sciences, often it is insights from the physical sciences that have really driven the methodological and technological advances. That is at least as true today as it ever was. And in some ways it is more true because of the technical capabilities that we now have.

The developments in speeding up the structure determination for proteins and viruses have come through technical developments at places like Diamond, but also spin-offs from detector developments at CERN, and elsewhere. Bringing people with insights from physical science together with people who are really driven by tough biological problems is a very productive way of advancing science and allowing science to develop more quickly.

For me, structural biology is a good example of that. When I was starting out, it was a small-scale activity and people didn’t really think that it would do very much. I remember one very famous scientist saying to me, “Why do you want to do protein crystallography? They have already determined the structure of a protein”. And in a sense, that’s a physicist’s answer because the thing that is amazing about biology is that it is so diverse. It is rich and there are all sorts of solutions to problems and many different protein structures. There is a basic difference between biology and physics, so you need an appreciation of both of those things to really make it work and that is what’s so great about somewhere like Diamond, because you can bring that together.

Moving forwards, we are going to be having the Rosalind Franklin Institute on site, which should increase the critical mass even further and allow us to broaden out beyond just the synchrotron activities to other related things – this may also potentially bring some sort of chemical developments in, for instance. There is a very good reason for having this concentration of diverse expertise.

The new eBIC facility has recently opened at Diamond. What will the main capabilities of this be?

eBIC is a centre for electron microscopy. An electron microscope doesn’t require a synchrotron, and in recent years there have been massive developments in this area, with the capability of the method increasing enormously. Now, what an electron microscope can produce stands alongside the methods of crystallography at the synchrotron and X-ray tomography and others; it is a very major way of looking at biological structure.
This is being driven by the technical developments that we have already discussed. One of the downsides, however, is that the kit is quite expensive to purchase and maintain and, moreover, is still not 100% reliable all of the time.

One of the great things about the use of Diamond as a synchrotron for X-ray crystallography is that by making efficient beamlines that can provide a significant amount of data to a large number of scientists democratises the science. This means that smaller groups around the country that simply cannot afford millions of pounds for a microscope or a beamline can access really good experimental facilities, do great science, and so be competitive on the world stage.

That was effectively the driver for setting up eBIC: to try and provide a centre with enough critical mass to be efficient, to help develop the necessary methods to establish the throughput of electron microscopy, and provide that through the same peer-reviewed access procedure that we use at Diamond – so that it is open to everybody on the basis of the quality of the science.

How would you like to see this facility develop moving forwards?

It is very hard to read the future, of course, but it is clear that there is still a lot of potential development in the area of electron microscopy and, for me, one of the really interesting possibilities is to do a different sort of science.

Traditionally with crystallography and electron microscopy, we work with purified proteins or complexes usually after breaking open the cells in which they are produced. In the future with electron tomography, however, it should be possible to look at those structures in their native context.

Now, for instance, we are able to take a mammalian cell that is alive, flash-freeze it, and then cut away some of the cell to make it thin enough to look at in an electron microscope and so then start to get to molecular resolution and actually look inside the cell.
What is fantastic is the possibility that it should be feasible to join up structural biology with cell biology, meaning that we will not only be able to understand molecules in isolation, but understand what they are doing in a very crowded environment of a living cell. There are, however, numerous technical issues which remain to be solved for this to become a reality.

Would you say that the fact that eBIC is accessible to a much wider element of the scientific community increases the likelihood of novel discoveries?

Yes, I think so. But while that it easy in theory, it is not so straightforward to make happen.

Techniques such as electron microscopy and X-ray crystallography are quite complicated. When I began working with crystallography it was necessary to spend a lot of time getting to grips with all the details of the theory, and that can place something of a barrier for people outside of the field to use it.

However, new data processing techniques are changing that. That is, X-ray diffraction data collected at a Diamond beamline is processed by software which will often arrive at a result without any intervention. That significantly lowers that barrier, at least once the user has become familiar with the method. Of course, this takes a number of years. But once I has been achieved then you are able to open up methods to a much broader community.

The same is going to be true for electron microscopy. This is at an earlier stage, and the methods are still changing quite rapidly, but one of the challenges that people at Diamond and elsewhere are trying to address is include whether it is possible to make pipelines so that people can come with a sample and very quickly get some sort of feedback on the quality of the data and help with its analysis.

At the American Association for the Advancement of Science meeting in Washington in February, you chaired a meeting on ‘Cryo-Electron Tomography: The Promises and Challenges of Structural Biology in situ’ which also included other high profile names in the field, such as Wolfgang Baumeister from the Max Planck Institute of Biochemistry, Bridget Carragher from the New York Structural Biology Center, and Peijun Zhang from the University of Oxford and also from Diamond. What were you most looking forward to with regard to this meeting?

It was great to be able to meet with these experts and to chat with them; to find out where they think things are going and what is exciting for them.

Carragher is a pioneer of automation in electron microscopy. She worked at the Scripps Research Institute in California, USA, and took a method that required you to look at each picture individually and then move on to the next and made it work so that one could collect data automatically on an electron microscope overnight, which was a huge step forward. Even traditional microscopists who were sceptical of this were converted when they actually saw it working. She is continuing to develop exciting new methods of automating sample preparation and other things.

Baumeister is a real hero who has been pushing for years to try and work out how you can do the in situ analysis of cells and get to the point where you can see individual molecules in them. He has pioneered that over the last 10 years more than anyone else in the field, and it was great to catch up with him.

Looking back on your own research, how you have worked to expand the applications of technologies of structural genomics for biomedical applications such as developing new medicines. How would you describe this and why is it is so important?

Structural genomics is an interesting area. It arose when people started to be able to sequence the DNA of whole genomes, meaning that there was a massive amount of information produced. We were then presented with the genome sequence and we knew that that coded for proteins.

For me, the really interesting aspect of biology is how those proteins fold up into molecules that interact and actually do things – whether that is chemistry in the cell, or whether it is communication. We were getting a flood of information when genome sequencing began to take off, but we couldn’t really understand or interpret it.

Structural genomics was a response to that and was an effort towards obtaining a more comprehensive view of the structure of the key elements of cells. This was tackled in different ways. In the USA, for instance, it was often tackled by looking at where gaps in the knowledge existed and by try and fill them in. In Europe, there was a slightly different approach. Here, we looked at biological systems and tried to understand them.
In the USA, people would sometimes work on proteins without knowing their function, but afterwards it made sense. Whereas in Europe, we would tend to focus on proteins we knew were of biomedical importance, and then go on to develop a more comprehensive knowledge of it.

Nevertheless, what was common across the globe was the idea that by trying to be more systematic in the science, to try to move it to something that was not just one individual in a lab trying to solve one protein but to look across a whole number of proteins, a whole number of organisms, and try and work out methodologies that are of general applicability, then it was possible to make discoveries much faster.

There was thus an interest in automation and parallelisation, and also in having a big enough number of results so that you could understand what was statistically significant and what was not. That has made a big difference, from producing the samples to then crystallising them, or getting them ready for statistical analysis, through to the analysis at a synchrotron, and so on. All of those things together have made a huge difference.

Given the varied research that you have conducted throughout your career, what is one thing you would want people to know?

At the moment, I am thinking a lot about the idea of using structure for vaccine development. It is interesting to note that we determined the structure of the Foot and Mouth Disease Virus many years ago, but now using that structure we have been able to provide clues about how to make something, which will be hopefully a safe vaccine. There is a sense that this has a real chance of making a difference.

The take-home message here is that you can obtain great results, but sometimes looking at them and trying to understand the simple things about them – the simple things that stabilise the structure – can actually give you information that is useful and that you couldn’t obtain in any other way.

Professor David Stuart FRS
Director of Life Sciences
Diamond Light Source
Tweet @DiamondLightSou
www.diamond.ac.uk/Home.html

Laboratory Supplies Directory - Now Live

LEAVE A REPLY

Please enter your comment!
Please enter your name here