Visualising proteins in health and disease

Lead Research Organisation: MRC Laboratory of Molecular Biology

Abstract

We are intrigued by how proteins do their work in order to keep cells, and thereby ourselves, alive. Knowing how a protein looks like in 3D often helps in understanding how they work. Therefore, we focus our research on making 3D pictures of proteins. Because proteins are so small and we can get a lot of information from looking at details on the atomic scale, we need to use very large and powerful, electron microscopes. Our research focuses on two related topics. Firstly, we develop computer programs to process the images of proteins that we take in the electron microscope. This is needed because, without further processing in the computer, the images from an electron microscope are not clear enough to help us understand how proteins work. We give away all our computer programs for free in the form of a software package called RELION. Scientists around the world use RELION to visualise the proteins they are interested in. Secondly, we use our own software and the electron microscopes at MRC-LMB to visualise proteins that we are interested in ourselves. Instead of looking at proteins in their healthy, functional state, we visualise filamentous states of proteins (so-called amyloids), which are associated with neurodegenerative diseases. One protein we study, Tau, plays an important role in Alzheimer’s disease. This part of our research is done together with Michel Goedert's group, who is also at MRC-LMB.

Technical Summary

We are intrigued by how proteins work. The genetic code determines the amino acid sequence of proteins, which in turn determines their 3D-structure. The precise 3D-arrangement of different types of atoms inside proteins allows them to perform the many types of functions that are needed to keep the cell alive. Therefore, visualising the 3D-structures of proteins is a powerful way to find out more about how they work. Research in our lab focuses on different aspects of protein structure determination.
One line of research is the development of image processing methods to determine protein structures from electron cryo-microscopy (cryo-EM) images. We implement these methods in our open-source computer program RELION. This program is used to solve protein structures in many cryo-EM labs worldwide.
In another line of research, we use experimental cryo-EM together with our own image processing developments to discover new protein structures. Instead of solving structures of proteins in their healthy, functional state we focus on protein structures that are associated with disease. For this purpose, we extract amyloid filaments from the brains of individuals with different types of neurodegenerative diseases, like amyloid filaments made of the protein Tau from Alzheimer’s disease (image above) or chronic traumatic encephalopathy. This work has revealed that the same protein may adopt surprisingly different structures in different diseases, and ongoing efforts are aimed at understanding how this happens. This line of research is done in close collaboration with the Goedert group, also at MRC-LMB.

Publications

10 25 50
 
Description EC Marie Curie International Outgoing Fellowship
Amount £58,017 (GBP)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 03/2015 
End 02/2016
 
Description EMBO Long-term Fellowship
Amount € 74,100 (EUR)
Organisation European Molecular Biology Organisation 
Sector Charity/Non Profit
Country Germany
Start 03/2014 
End 02/2016
 
Description EU Marie Curie Fellowship
Amount € 231,283 (EUR)
Funding ID FP7-PEOPLE-2012-IIF 327937 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 03/2013 
End 02/2015
 
Description EU Marie Curie Fellowship
Amount € 121,210 (EUR)
Funding ID Project contract no: 657990 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 08/2015 
End 07/2017
 
Description Fidelity International Foundation
Amount £182,675 (GBP)
Organisation Fidelity UK Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2018 
End 12/2020
 
Description HFSP Long Term
Amount £87,780 (GBP)
Organisation Human Frontier Science Program (HFSP) 
Sector Charity/Non Profit
Country France
Start 12/2015 
End 11/2018
 
Description Japan Society for the Promotion of Science Fellowship
Amount ¥10,512,000 (JPY)
Funding ID JSPS/OT/290060 
Organisation Japan Society for the Promotion of Science (JSPS) 
Sector Public
Country Japan
Start 09/2018 
End 09/2020
 
Description Swiss National Science Foundation
Amount SFr. 100,550 (CHF)
Organisation Swiss National Science Foundation 
Sector Public
Country Switzerland
Start 05/2017 
End 04/2019
 
Title Video on how to prepare graphene-oxide coated cryo-EM grids 
Description We published a video describing how to cover cryo-EM specimen grids with a thin layer of graphene oxide on Figshare. 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact This video has been used by many colleagues around the world, who have reported back in person that they found it very useful. 
URL https://figshare.com/articles/Graphene_Oxide_Grid_Preparation/3178669
 
Description Characterizing 3D DNA origami objects by electron cryo-microscopy 
Organisation Technical University of Munich
Department Walter Schottky Institute
Country Germany 
Sector Academic/University 
PI Contribution We visualize DNA origami samples using electron cryo-microscopy
Collaborator Contribution The partner provides DNA origami samples
Impact http://dx.doi.org/10.1073/pnas.1215713109 http://dx.doi.org/10.1073/pnas.1612720113
Start Year 2011
 
Description Learning a prior for cryo-EM structure determination 
Organisation Royal Institute of Technology
Country Sweden 
Sector Academic/University 
PI Contribution We collaborate with Carola Schoenlieb at the dept of Applied Mathematics of the University of Cambridge and with Ozan Oktem at the KTH in Stockholm to develop the mathematics required for incorporating informative priors in cryo-EM structure determination through deep learning approaches. We implement such developments into our software package RELION.
Collaborator Contribution Carola and Ozan help with mathematical derivations and proofs.
Impact A publication is in preparation.
Start Year 2019
 
Description Learning a prior for cryo-EM structure determination 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution We collaborate with Carola Schoenlieb at the dept of Applied Mathematics of the University of Cambridge and with Ozan Oktem at the KTH in Stockholm to develop the mathematics required for incorporating informative priors in cryo-EM structure determination through deep learning approaches. We implement such developments into our software package RELION.
Collaborator Contribution Carola and Ozan help with mathematical derivations and proofs.
Impact A publication is in preparation.
Start Year 2019
 
Description Structure determination of Orb2 amyloid filaments 
Organisation Stowers Institute for Medical Research
Country United States 
Sector Academic/University 
PI Contribution Ruben Hervas Millan, postdoc from the lab of Kausik Si at the Stowers institute isolated Orb2 amyloid filaments from fly brain and took cryo-EM images. They then contacted us and we helped with the structure determination. Ruben then spent 2 weeks in our group to create an atomic model and figures for the paper.
Collaborator Contribution Ruben Hervas Millan, postdoc from the lab of Kausik Si at the Stowers institute isolated Orb2 amyloid filaments from fly brain and took cryo-EM images. They also performed biochemical experiments to show how these amyloids are involved in long-term memory formation in the fly.
Impact A paper describing the Orb2 filament structure has been submitted.
Start Year 2019
 
Description Structure determination of a bacterial Zinc transporter 
Organisation University of Groningen
Country Netherlands 
Sector Academic/University 
PI Contribution We solved the cryo-EM structure of the ZntB transporter
Collaborator Contribution Our collaborators prepared the protein sample
Impact A paper describing the structure has been published.
Start Year 2016
 
Description Structure determination of a bacterial efflux pump 
Organisation Manchester University NHS Foundation Trust
Department Biochemistry
Country United Kingdom 
Sector Hospitals 
PI Contribution We solved a cryo-EM structure of the MacA-MacB-tolC efflux pump
Collaborator Contribution Ben Luisi provided purified protein sample
Impact A paper describing this structure has been published.
Start Year 2015
 
Description Structure determination of human gamma-secretase 
Organisation Tsinghua University China
Country China 
Sector Academic/University 
PI Contribution We solved the cryo-EM structure of human gamma-secretase to 4.5A and 3.4A resolution, and also analysed the conformational space of its catalytic subunit
Collaborator Contribution They provided purified human gamma-secretase samples
Impact http://dx.doi.org/10.1038/nature14892 http://dx.doi.org/10.1038/nature13567 http://dx.doi.org/10.7554/eLife.11182
Start Year 2014
 
Description Structure determination of tau filaments 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Academic/University 
PI Contribution We solved cryo-EM structures of Tau filaments from the brain of an individual with Alzheimers disease
Collaborator Contribution Michel Goedert in Neurobiology organised brain material and performed biochemical analyses.
Impact A paper has been published. This paper was accompanied by a MRC headoffice press release, and was widely covered in national and international media.
Start Year 2016
 
Description Structure determination of the Plasmodium falciparum cytosolic ribosome 
Organisation The Walter and Eliza Hall Institute of Medical Research (WEHI)
Department Division of Infection and Immunity
Country Australia 
Sector Academic/University 
PI Contribution Determined a preliminary structure of the cytosolic ribosome from Plasmodium falciparum by cryo-EM single-particle analysis
Collaborator Contribution Provided purified ribosome samples
Impact http://dx.doi.org/10.7554/eLife.03080
Start Year 2013
 
Description structure determination of rabbit ryanodin receptor 
Organisation Tsinghua University China
Country China 
Sector Academic/University 
PI Contribution Structure determination by cryo-EM single particle analysis
Collaborator Contribution Sample preparation by purification from rabbit muscle.
Impact http://dx.doi.org/10.1038/nature14063
Start Year 2014
 
Title RELION 
Description Objective structure determination with cryo-EM data. 
Type Of Technology Software 
Year Produced 2011 
Open Source License? Yes  
Impact RELION is currently the most widely used cryo-EM structure determination software package in the world. It has been used for 30% of all structures in the EMDB and RELION-related papers attract more than 2000 citations every year. 
URL http://www2.mrc-lmb.cam.ac.uk/relion
 
Description Cambridge Science festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Hundreds of people attended a stand on crystals.

People were interested and asked lots of questions
Year(s) Of Engagement Activity 2013,2014,2015
URL http://www.cam.ac.uk/science-festival
 
Description EMBO workshop on cryo-EM image processing 
Form Of Engagement Activity Scientific meeting (conference/symposium etc.)
Part Of Official Scheme? Yes
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact ~30 students were trained on the use of my software RELION.
Year(s) Of Engagement Activity 2012,2013,2014
URL http://www.embl.de/training/events/2014/CRY14-01/
 
Description Experiment demonstration at street party in Cambridge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I performed an experiment and gave a small presentation about carbon dioxide
Year(s) Of Engagement Activity 2018
 
Description Lab tours of small groups of people 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I regularly do tours of the lab with interested people, most of them local to Cambridge, sometimes including international visitors too. I show them the electron microscopes and the computers we use to calculate cryo-EM structures. I also explain them what we study, why we do it, and what comes out of it.
Year(s) Of Engagement Activity 2018,2019,2020
 
Description Lecture at Perse School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact I gave a seminar on cryo-electron microscopy and structural biology to GCSE- and A-level students at the Perse school in Cambridge
Year(s) Of Engagement Activity 2019
 
Description MRC postdoc symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I gave a seminar, and sat in on a discussion panel, about postdoctoral career options (both inside and outside academia).
Year(s) Of Engagement Activity 2016,2017,2018,2019
URL https://twitter.com/MRCpostdocs
 
Description MRC-LMB open day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Type Of Presentation Workshop Facilitator
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I helped in the Nobel prize treasure hunt for children.

The kids loved it!
Year(s) Of Engagement Activity 2013
 
Description Participated in LMB open day with a lecture for the general public on cryoEM 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Gave lecture about cryoEM at the MRC Open Day.
Year(s) Of Engagement Activity 2017
URL https://www2.mrc-lmb.cam.ac.uk/news-and-events/public-engagement/open-day/
 
Description Participated in making film about cryo-EM at LMB 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Participated in filming of informational video about cryo-EM.
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=BtuAz12zXBs
 
Description Press coverage for paper on cryoEM structures of tau filaments from Alzheimers brain 
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 Media (as a channel to the public)
Results and Impact With input from us, MRC Head office made a press release about our paper no cryoEM structures of tau filaments from Alzheimers brains. This was subsequently reported on by many media: national and international newspapers, BBC radio 4, internet news sites, etc. Questions by reported were answered in approximately 10 telephone/email interviews.
Year(s) Of Engagement Activity 2017
URL https://www.mrc.ac.uk/news/browse/scientists-uncover-the-structure-of-tau-filaments-from-alzheimer-s...
 
Description Royal Society exhibit 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Poster Presentation
Geographic Reach Regional
Primary Audience Schools
Results and Impact Several hundred people visited our Virus Wars stand at the exhibit each day.

People gave very positive feedback. E.g. Amazingly elegant!" (Head of Science, Hertswood Academy); "Great display - great research - well explained. Glad to see some pure research!"

"Amazing - thank you so much! This is one of the very best exhibits here and the people were fantastic."
Year(s) Of Engagement Activity 2013
 
Description Talk at Alzheimer mini-symposium at Abcam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I gave a talk about our Alzheimer research at the Abcam company in Cambridge. Besides Abcam employees, there were also people from Alzheimer Research UK and a patient group present. The talk sparked a lively discussion with family members of Alzheimer patients, industry and people from academia, like myself.
Year(s) Of Engagement Activity 2019
 
Description Talk at Science Day of Queen Edith Primary School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Gave a talk about our science to primary school children (2 classes of 30 pupils)
Year(s) Of Engagement Activity 2017
 
Description Twitter feed about science 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact My twitter account has approximately 4.5 thousand followers. I use it to tweet mostly about science and science-related issues.
Year(s) Of Engagement Activity 2017,2018,2019,2020
URL https://twitter.com/SjorsScheres
 
Description press engagement after CTE tau filament structure in Nature 
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 Media (as a channel to the public)
Results and Impact We wrote an Insight on Research with the local news team and prepared an MRC-wide press release with the MRC head office. We also engaged with the press offices of the university of Leicester and the eBIC national EM facility at Diamond (at both places data for this project were acquired). Subsequently, we engaged with multiple reporters of the general press and of dedicated blogs liek Alzforum, some of which wrote about our work.
Year(s) Of Engagement Activity 2019
URL https://www.alzforum.org/news/research-news/traumatic-tau-filaments-cte-share-distinct-structure
 
Description press engagement after Pick's tau filament structure in Nature 
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 I engaged with the press (TechnologyNetworks and Alzforum) after our Nature paper about cryo-EM structures of tau filaments in Pick's disease came out.
Year(s) Of Engagement Activity 2018
URL https://www.technologynetworks.com/neuroscience/articles/scientists-explain-how-they-un-picked-picks...