Structural Studies on Viruses, Viral Proteins and Cell Interactions

Lead Research Organisation: University of Oxford
Department Name: Wellcome Trust Centre for Human Genetics

Abstract

Viruses outnumber all other organisms on the globe. These nano-parasites reproduce inside our cells, so they are often very difficult to combat. Some 33 million people are infected with HIV and many other human viruses also have a terrible impact on human health. Viruses include hundreds of major human pathogens and are responsible for millions of deaths every year. Nevertheless many of these diseases can in principle be prevented or treated - smallpox was declared eradicated in 1979 and this year or next the United Nations Food and Agriculture Organisation is likely to declare the global eradication of rinderpest, a devastating scourge of cloven footed animals. This is encouraging and suggests that the closely related measles virus might also succumb to a concerted vaccination campaign. Despite these successes there are still many viruses which we are unable to control by vaccination. Drugs play a complementary role, for treating people already infected. The pharmaceutical and biotechnology industries pump considerable money into anti-viral research and development and the range of drugs now available to combat HIV shows that this strategy can be very effective. However the unexpected emergence of SARS and swine ?flu shows that we cannot predict the next major virus outbreak so it is sensible to support basic research - to be better prepared to respond to the unexpected. This proposal for such underpinning research comes from David Stuart, a Medical Research Council Professor based at the Nuffield Department of Medicine at Oxford University. The work will deliver new information about viruses, in the form of portraits in atomic detail, made freely available in public databases for use by academic or commercial experts in drug and vaccine design. We think that there is a real chance that this knowledge will eventually allow safer and more robust vaccines to be designed. This work is only possible using the very bright X-ray beams provided by the UK synchrotron, Diamond, allowing us to see these particles that are invisible through a normal microscope. The first aim of the work is to improve the experimental technology to facilitate data collection from pathogens and then to investigate several viruses which represent major burdens on global health, including the three major hepatitis viruses A, B and C. For some of the simpler viruses we will see if structural knowledge can be used to guide the development of improved vaccines.

Technical Summary

This application is for the renewal of a programme focused on virus structure analysis which includes technical development, and spans from basic research into fundamental questions of function and taxonomy, through to work to underpin the development of improved vaccines and anti-viral drugs.

Technical developments comprise the first aim: novel methods for X-ray structure determination in situ (i.e. avoiding any handling of crystals), the investigation of novel crystal freezing methods and exploration of the limits of X-ray analysis for small arrays of virus particles in cells using diffraction and imaging.

These methods underpin three biomedical themes: (i) to tackle some major outstanding questions concerning picornaviruses, (ii) to understand a major vaccine particle, that of hepatitis B, and to determine novel structures to map the landscape of the viral universe, and (iii) to work towards a more comprehensive view of virus fusion.

Theme (i) includes the investigation of the atomic structures of hepatitis A, EV71 and a newly assigned nonclassical picornavirus (Ljungan or a parechovirus); investigation of assembly /disassembly pathways including analysis of a representative picornavirus heavy particle; and the design and structure determination for recombinant mutant picornavirus capsids with increased stability, to establish rules for improved vaccines.

For theme (ii) we will work towards the high resolution X-ray structure of the hepatitis B surface antigen particle and initiate crystallographic analyses of novel viruses from a virus ecology pipeline.

Theme (iii) builds on existing work on viral fusion proteins, with a particular focus on hepatitis C E1 and E2 proteins and E2 of the bovine viral diarrhoea pestivirus. We will also initiate work on a markedly different and complex fusion system from vaccinia virus.

The programme includes the analysis of viruses responsible for major global health burdens (including hepatitis A, B and C viruses) and will contribute to the body of structural information freely available in the public domain, which can be used both by academics and commercial organisations for structure-guided drug discovery. In addition we will work in a more translational fashion on vaccine design. As appropriate we will form collaborations to maximise exploitation of the results, a strategy exemplified by our current work on foot-and-mouth disease virus vaccine (with Intervet/Schering-Plough Animal Health).

Publications


10 25 50
Abrescia NG (2012) Structure unifies the viral universe. in Annual review of biochemistry
Aller P (2015) Application of in situ diffraction in high-throughput structure determination platforms. in Methods in molecular biology (Clifton, N.J.)
Axford D (2014) In cellulo structure determination of a novel cypovirus polyhedrin. in Acta crystallographica. Section D, Biological crystallography
Axford D (2012) In situ macromolecular crystallography using microbeams. in Acta crystallographica. Section D, Biological crystallography
Bahar MW (2011) How vaccinia virus has evolved to subvert the host immune response. in Journal of structural biology
 
Description Gates Polio initiative
Amount £76,138 (GBP)
Organisation World Health Organization (WHO) 
Sector Public
Country Global
Start 01/2011 
End 05/2012
 
Description Automation of protein crytallography 
Organisation European Molecular Biology Laboratory (EMBL)
Department EMBL Grenoble outstation
Country France, French Republic 
Sector Academic/University 
PI Contribution Harware and software development
Collaborator Contribution improvements to beamline design. Design comercialised by EMBL, recognising MRC imput. Now implemented at several sitesContibution to development of ispyb database implemented at ESRF and Diamond.
Impact publications and hardware and software installed at ESRF and Diamond
Start Year 2007
 
Description Automation of protein crytallography 
Organisation European Synchrotron Radiation Facility (ESRF)
Country European Union (EU) 
Sector Academic/University 
PI Contribution Harware and software development
Collaborator Contribution improvements to beamline design. Design comercialised by EMBL, recognising MRC imput. Now implemented at several sitesContibution to development of ispyb database implemented at ESRF and Diamond.
Impact publications and hardware and software installed at ESRF and Diamond
Start Year 2007
 
Description Fab Cloning and Expression 
Organisation University of Oxford
Department Sir William Dunn School of Pathology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution We have introduced a generic method for the production of antibody fragments
Collaborator Contribution Joint development
Impact Methods reported in 18662785 and Methods in Molecular Biology (in press)
Start Year 2006
 
Description Hand foot and mouth disease viruses 
Organisation Tsinghua University China
Department Laboratory of Structural Biology
Country China, People's Republic of 
Sector Academic/University 
PI Contribution Structural analysis, in silico drug design work
Collaborator Contribution virus production, shared expertise in structure work
Impact Nature Stuct biology paper Nature Communications paper
Start Year 2010
 
Description High Pressure Freezing 
Organisation DIAMOND Light Source Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution providing scientific questions samples and expretees
Collaborator Contribution development of protocols and provision of hardware
Impact not yet
Start Year 2011
 
Description Insect Cell Expression 
Organisation Oxford Brookes University
Department School of Life Sciences Oxford Brookes
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Testing and developing methods with Professor Linda King (Oxford Brookes University and Oxford Expression Technology Ltd)..
Collaborator Contribution Help in developing methods for insect cell expression
Impact Three publications in peer-reviewed journals: 19655260, 18781697, 20441568
 
Description Micro-Crystallography 
Organisation DIAMOND Light Source Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution providing scientific questions samples and expretees
Collaborator Contribution technical developments at I24 beamline
Impact scientific papers currently in preperation
Start Year 2008
 
Description Polio Vaccine 
Organisation Harvard University
Department Harvard Medical School
Country United States of America 
Sector Academic/University 
PI Contribution Working to design more stable vaccine
Collaborator Contribution Working to characterize particles and to produce them
Impact Too early
Start Year 2010
 
Description Polio Vaccine 
Organisation Public Health England
Department National Institute for Biological Standards and Control (NIBSC)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Public 
PI Contribution Working to design more stable vaccine
Collaborator Contribution Working to characterize particles and to produce them
Impact Too early
Start Year 2010
 
Description Polio Vaccine 
Organisation University of Leeds
Department Institute of Molecular and Cellular Biology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Working to design more stable vaccine
Collaborator Contribution Working to characterize particles and to produce them
Impact Too early
Start Year 2010
 
Description Polio Vaccine 
Organisation University of Reading
Department Microbiology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Working to design more stable vaccine
Collaborator Contribution Working to characterize particles and to produce them
Impact Too early
Start Year 2010
 
Description Vaccinia 
Organisation Imperial College London (ICL)
Department Imperial College of Science Technology and Medicine (ICSTM)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Protein production, structure determination
Collaborator Contribution Numerous joint publications
Impact Various publication with G Smith in author list.
Start Year 2006
 
Description Virus evolution 
Organisation University of Helsinki (Helsingin yliopisto)
Country Finland, Republic of 
Sector Academic/University 
PI Contribution Structure determination
Collaborator Contribution Numerous publications and joint avtivity
Impact A number of the publications fall in this category. These have Bamford as co-author
 
Description Virus structure 
Organisation The Pirbright Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution In silico analysis Biophysical analysis structural analysis
Collaborator Contribution Animal tests virus production
Impact Innivative vaccines
Start Year 2006
 
Description X-Ray Microscopy 
Organisation DIAMOND Light Source Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution providing scientific question samples and part of the required expertese
Collaborator Contribution Working with us on trips to Bessy Syncrotron
Impact nothing yet
Start Year 2009
 
Description Diamond Light Source Open Days 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact At Diamond's open days, visitors are able to engage with scientists and engineers as part of a visit to the facility. They encounter researchers discussing their work, and are able to see the potential future impact of the research activity, for example, the potential applications of solar technology. Families often bring children to the facility, who are exposed to a range of science and engineering careers outside of the usual lab environment.

The open days at Diamond aim to change the perception of scientists, and how different areas of science interact and support one another. Feedback is regularly received that visitors encounter new areas of science which they were previously unaware of, which they now express an interest in. Teacher feedback of our schools events reports that visiting the facility increases engagement with their subjects and enables students to consider careers in science.
Year(s) Of Engagement Activity 2013
 
Description Illuminating Atoms exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I was one of the scientists who was photographed by Max Alexander for his Illuminating Atoms exhibition, which is currently on display at the Royal Albert Hall, the Scottish Parliament and the National Assembly for Wales.

The exhibition will tour in 2015 and STFC are hoping to take it to Westminster.
Year(s) Of Engagement Activity 2009,2014
URL http://www.diamond.ac.uk/Home/News/LatestNews/09-10-16.html
 
Description Photography exhibition celebrating the International Year of Crystallography 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Reaching out to new audiences and raising the profile of crystallography and the important science it is achieving.

Celebrating the work of scientists involved in crystallography and the facilities and techniques they use. Raising awareness among people who might be more interested in art and photography prior to seeing the exhibition
Year(s) Of Engagement Activity 2011,2014
URL http://www.diamond.ac.uk/Home/News/LatestNews/09-10-16.html
 
Description Revealed: The surprising origins of Hepatitis A 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Highlighting the work of UK scientists in helping society tackle illnesses that currently affect millions of people.

Generating national and international news coverage in this important development, the work of the group and the role played by the UK's synchrotron.
Year(s) Of Engagement Activity 2014
URL http://www.diamond.ac.uk/Home/News/LatestNews/20-10-14.html
 
Description Revolutionary Biology 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact 2014 is the International Year of Crystallography and to celebrate this event NDM has produced a series of short films - 'Revolutionary Biology'. Revolutionary Biology shows how the field of structural biology has developed over the past 100 years, Oxford's involvement in that development, and where we go from here.

A panellist discussion will follow the film screening, with Professors David Stuart, Yvonne Jones and Michael Glazer, and BBC reporter Dr Jonathan Webb on Friday 14th November 2014

Questions will be asked after the launch party.
Year(s) Of Engagement Activity 2014
URL http://www.ndm.ox.ac.uk/part-1-the-building-blocks-of-life
 
Description Science and Society Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Presented at the annual Science and Society lecture - talk sparked questions and discussions afterwords.

Talk could lead to potential collaboration opportunists.
Year(s) Of Engagement Activity 2014
 
Description Scientists use Diamond to develop potential new drug treatment to tackle viruses 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Highlighting the work of UK scientists in helping society tackle illnesses that currently affect millions of people.

Generating national and international news coverage in this important development, the work of the group and the role played by the UK's synchrotron.
Year(s) Of Engagement Activity 2014
URL http://www.diamond.ac.uk/Home/News/LatestNews/10-02-14_5.html