Structure, mechanisms, regulation and assembly of ATP synthase

Lead Research Organisation: University of Cambridge

Abstract

Biological life depends on a source of energy. That energy comes from sunlight. It is harvested by photosynthesis in green plants, and provides the high energy components in the foods that we eat. We harvest that energy in our bodies by "burning" (oxidising) the high energy components, releasing cellular energy in a controlled way to generate the fuel of life, in the form of the molecule known as adenosine triphosphate (or ATP for short). The key steps in this process take place in the mitochondria inside the cells that make up our tissues. The mitochondria are biological "power stations" full of millions of tiny molecular turbines, the ATP synthases, that rotate rather like man-made turbines churning out the cellular fuel in massive quantities, which is then delivered to all parts of our bodies to provide the energy to make them function. We understand in great detail many aspects of how these molecular turbines work, but as yet not how the rotary action is generated. Part of this project is about providing that crucial missing information. Bacteria have similar turbines that differ is some respects from the human turbines. We want to understand these differences better, so that we can devise drugs to kill pathogenic bacteria, such as the one that causes tuberculosis, by stopping their turbines without influencing the human ones. Associated with the human turbines, but not part of the ATP making machinery, is a channel that becomes opened, for example during a heart attack, letting out the contents of the mitochondria in an uncontrolled way leading to the death of the cell. We want to understand how this pore works, so that we can help design other drugs to control the pore.

Technical Summary

The F-ATP synthases in eubacteria and mitochondria are rotary machines with many common features. We will build on past achievements to extend fundamental knowledge about them and provide a basis for putting that knowledge to practical use. The mechanism of their catalytic domains is well understood, but how rotation is generated from the transmembrane proton-motive force is less clear. We will provide a molecular explanation of the generation of rotation. We intend to exploit mechanistic differences between human and bacterial enzymes to develop new drugs. One difference concerns their mechanisms of regulation. The mitochondrial enzyme is regulated by the inhibitor protein, IF1; in vitro, it inhibits ATP hydrolysis and not ATP synthesis, but its in vivo role is unclear, except that it inhibits the hydrolase activity of assembly intermediates. It may also inhibit in vivo ATP synthesis by a mechanism that we will investigate possible involving other unidentified proteins. Different regulatory mechanisms operate in eubacteria; for example in Mycobacteria, the enzyme can only make ATP and not hydrolyze it, but we do not yet know how hydrolysis is prevented. Eubacterial and mitochondrial enzymes differ also in their subunit compositions. They have a common core set to allow them to make ATP, but the mammalian mitochondrial enzymes have a "supernumerary" set of seven membrane proteins, each with a single predicted transmembrane alpha-helix. Six of them participate in the formation of a non-specific pore, called the mitochondrial permeability transition pore (PTP) which opens in response to high concentrations of Ca2+ inside mitochondria and leads to cell death, linked to many human diseases. Therefore, we will characterize the structure and properties of the PTP, and develop it as another drug target. As part of a wider collaboration we will study how the human ATP synthase is assembled.

Publications

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Boreikaite V (2019) Extrinsic conditions influence the self-association and structure of IF, the regulatory protein of mitochondrial ATP synthase. in Proceedings of the National Academy of Sciences of the United States of America

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Carroll J (2019) Persistence of the permeability transition pore in human mitochondria devoid of an assembled ATP synthase. in Proceedings of the National Academy of Sciences of the United States of America

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Duncan AL (2016) Cardiolipin binds selectively but transiently to conserved lysine residues in the rotor of metazoan ATP synthases. in Proceedings of the National Academy of Sciences of the United States of America

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Ferguson SA (2016) Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum. in Proceedings of the National Academy of Sciences of the United States of America

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He J (2018) Assembly of the membrane domain of ATP synthase in human mitochondria. in Proceedings of the National Academy of Sciences of the United States of America

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He J (2017) Persistence of the mitochondrial permeability transition in the absence of subunit c of human ATP synthase. in Proceedings of the National Academy of Sciences of the United States of America

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He J (2017) Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase. in Proceedings of the National Academy of Sciences of the United States of America

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He J (2020) Assembly of the peripheral stalk of ATP synthase in human mitochondria. in Proceedings of the National Academy of Sciences of the United States of America

 
Description Crystallography of F-ATPases 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Academic/University 
PI Contribution purification and crystallization of F-ATPases; X-ray crystallographic studies of F-ATPases
Collaborator Contribution MRC: Access to data, equipment and facilities. Otago: Provision of scientific materials. Parasitology: Provision of scientific materials.
Impact 16754973; 16728506; 16791136; 16929099; 17082766; 17350959; 17698806; 17895376; 19233840
 
Description Crystallography of F-ATPases 
Organisation University of Otago
Country New Zealand 
Sector Academic/University 
PI Contribution purification and crystallization of F-ATPases; X-ray crystallographic studies of F-ATPases
Collaborator Contribution MRC: Access to data, equipment and facilities. Otago: Provision of scientific materials. Parasitology: Provision of scientific materials.
Impact 16754973; 16728506; 16791136; 16929099; 17082766; 17350959; 17698806; 17895376; 19233840
 
Description Crystallography of F-ATPases 
Organisation University of South Bohemia
Department Institute of Parasitology
Country Czech Republic 
Sector Academic/University 
PI Contribution purification and crystallization of F-ATPases; X-ray crystallographic studies of F-ATPases
Collaborator Contribution MRC: Access to data, equipment and facilities. Otago: Provision of scientific materials. Parasitology: Provision of scientific materials.
Impact 16754973; 16728506; 16791136; 16929099; 17082766; 17350959; 17698806; 17895376; 19233840
 
Description cryoEM of ATP synthases 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of scientific materials and expertise
Collaborator Contribution Provision of expertise and access to equipment
Impact 27791192
Start Year 2014
 
Description BCA/CCP4 Crystallography Summer School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The BCA/CCP4 Crystallography Summer School at the Diamond Science and Technology Centre, Harwell, Oxford, U. K.
Year(s) Of Engagement Activity 2016
 
Description Big Biology Day, Cambridge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Members of the MRC MBU participated in the Big Biology Day 2017 at Hills Road Sixth Form College. Scientists explained the Unit's research with hands-on activities. These included experiments using Drosophila melanogaster - with fluorescent markings and temperature sensitivity, our "Find the mutant fly" game, colouring books and posters.
Year(s) Of Engagement Activity 2017,2018
 
Description Class to Part III students in Biochemistry, University of Cambridge. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Class to Part III students in Biochemistry, University of Cambridge.
Year(s) Of Engagement Activity 2018
 
Description Dissemination of scientific achievements via the internet 
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 Dissemination of scientific achievements via the Unit's website and social media sites.
Year(s) Of Engagement Activity 2015,2016
URL http://www.mrc-mbu.cam.ac.uk/people/john-walker
 
Description Dissemination of scientific achievements via the internet 
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 Dissemination of scientific achievements and publications to the general public, scientists and others via the Unit's website, Twitter and Facebook.

https://www.facebook.com/mrc-mbu
Twitter - @MRC_MBU
http://www.mrc-mbu.cam.ac.uk/people/john-walker
http://www.mrc-mbu.cam.ac.uk
Year(s) Of Engagement Activity 2015,2016
URL http://www.mrc-mbu.cam.ac.uk/people/john-walker
 
Description Dissemination of scientific achievements via the internet 
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 Dissemination of scientific achievements and publications to the general public, scientists and others via the Unit's website, Twitter and Facebook.

https://www.facebook.com/mrc-mbu
Twitter - @MRC_MBU
http://www.mrc-mbu.cam.ac.uk/people/john-walker
http://www.mrc-mbu.cam.ac.uk
Year(s) Of Engagement Activity 2015,2016,2017,2018
URL http://www.mrc-mbu.cam.ac.uk/people/john-walker
 
Description Dortmund University, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact International Student Symposium, Dortmund University, Dortmund, Germany.
Year(s) Of Engagement Activity 2016
 
Description EBEC 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact "Structure and Mechanism of ATP Synthase", at the European Bioenergetics Conference 2016, Riva del Garda, Italy.
Year(s) Of Engagement Activity 2016
 
Description GAP Summit 2016 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Professor Sir John Walker talks at the GAPSummit 2016. During the three days of the GapSummit the Leaders of Tomorrow will learn from and challenge current leaders in the bioeconomy through a programme which is dedicated to addressing 7 gaps in biotechnology:

Research and Innovation Gap
Funding Gap
Future Health Gap
Future Resources Gap
People Gap
Bioethics Gap
Public Perception and Education Gap
Year(s) Of Engagement Activity 2016
 
Description GAP Summit 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Keynote Speaker at the Gap Summit, an International Biotechnology Conference, Cambridge, U. K.
Year(s) Of Engagement Activity 2016
 
Description Girton Brownies 
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Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Showcase of MBU science including: fruit flies under microscope (phenotypes), fruit flies in water bath (behaviour at different temperatures).
Smilies in feedback jar: 21; frownies in feedback jar: 3
Year(s) Of Engagement Activity 2018
 
Description Hills Road Sixth Form College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk to Sixth Form Science students
Year(s) Of Engagement Activity 2016
 
Description Imperial College Chemical Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Lecture for the Imperial College Chemical Society, London, U.K.
Year(s) Of Engagement Activity 2017
 
Description KITT University, India 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact John Walker addressed 4612 students and staff at a degree ceremony
Year(s) Of Engagement Activity 2015
URL http://kiit.ac.in/11thconvocation/index.html
 
Description Klosters, Switzerland 
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Geographic Reach International
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Results and Impact 50th Winterseminar, Klosters. Switzerland
Year(s) Of Engagement Activity 2016
 
Description Landmark Lecture Series, Biochemistry, Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Landmark Lecture Series, Department of Biochemistry, Cambridge, U. K. - undergraduate biochemistry students.
Year(s) Of Engagement Activity 2016,2017
 
Description Lecture: Discovering ATP synthase at The Biology Society, St John's College, Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Gave a lecture to undergraduates on "Discovering ATP synthase" at The Biology Society, St John's College, Cambridge
Year(s) Of Engagement Activity 2018
 
Description Lecture: Structure, mechanism and regulation of ATP synthase. Gordon Research Conference on Bioenergetics, Proctor Academy, New Hampshire, U. S. A. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Lecture: Structure, mechanism and regulation of ATP synthase. Gordon Research Conference on Bioenergetics, Proctor Academy, New Hampshire, U. S. A.
Year(s) Of Engagement Activity 2017
 
Description Lecture: The ATP synthase in cellular life and death. 67th Lindau Nobel Laureate Meeting, Lindau, Germany. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Lecture: The ATP synthase in cellular life and death. 67th Lindau Nobel Laureate Meeting, Lindau, Germany.
Year(s) Of Engagement Activity 2017
 
Description Lecture: The Future of Scientific Research, Sir William Dunn School of Pathology, University of Oxford. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Lecture: The Future of Scientific Research to graduate students at Sir William Dunn School of Pathology, University of Oxford.
Year(s) Of Engagement Activity 2017
 
Description Lecture: The Mitochondrial Respiratory Chain from 1978-2017: A Triumph for Biochemistry and Biophysics. Italian Biochemical Society, Catania, Sicily. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Lecture: The Mitochondrial Respiratory Chain from 1978-2017: A Triumph for Biochemistry and Biophysics. Italian Biochemical Society, Catania, Sicily.
Year(s) Of Engagement Activity 2017
 
Description Lecture: The role of ATP synthase in cellular life and death. Scientific Symposium: Proteins, the Molecular Machines of Life, Department of Sciences, Roma Tre University, Rome, Italy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Lecture: The role of ATP synthase in cellular life and death. Scientific Symposium: Proteins, the Molecular Machines of Life, Department of Sciences, Roma Tre University, Rome, Italy
Year(s) Of Engagement Activity 2017
 
Description Lecture: Understanding the membrane domain of ATP synthase. Bunty Bioenergetics Meeting, Imperial College, London. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Lecture: Understanding the membrane domain of ATP synthase. Bunty Bioenergetics Meeting, Imperial College, London.
Year(s) Of Engagement Activity 2017
 
Description Lecture: Where does biological energy come from?, Scuola Superiore di Catania, Sicily 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
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Results and Impact Lecture: Where does biological energy come from?, Scuola Superiore di Catania, Sicily
Year(s) Of Engagement Activity 2017
 
Description NTU, Singapore 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
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Results and Impact 4th International Workshop on Solar Energy Sustainability,
NTU, Singapore.
Year(s) Of Engagement Activity 2016
 
Description School of Biochemstry, Bristol 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Lecture at the School of Biochemistry, Bristol University, Bristol, U. K.
Year(s) Of Engagement Activity 2016
 
Description Sixth Form Students from Lancashire 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
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Results and Impact Outreach Event for Sixth Form Pupils from Lancashire, The Divinity School, St John's College, Cambridge, U. K.
Year(s) Of Engagement Activity 2016
 
Description Speech and demonstration of oxygen evolution during photosynthesis, St Mary's Junior School, Hackney, London. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Speech and demonstration of oxygen evolution during photosynthesis, St Mary's Junior School, Hackney, London. Feedback (Teachers and Friends Association): We wanted to write and thank you and the team from the MRC for the wonderful science workshops you provided the children with last week. The feedback has been fantastic, with the children clearly feeling inspired to learn more about science through their enjoyment of the experiments and activities you provided. One of our Year 3 girls reported back, in no uncertain terms, that she has decided she will be attending the University of Cambridge when she is older!
Year(s) Of Engagement Activity 2018
URL http://st-marys.hackney.sch.uk/2018/science-week-january-2018
 
Description The Amgen Lecture: The Mitochondrial Respiratory Chain from 1978-2017: A Triumph for Biochemistry and Biophysics. 4th ShanghaiTech-SIAIS Bioforum, Shanghai, China. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Amgen Lecture: The Mitochondrial Respiratory Chain from 1978-2017: A Triumph for Biochemistry and Biophysics. 4th ShanghaiTech-SIAIS Bioforum, Shanghai, China.
Year(s) Of Engagement Activity 2017
 
Description The Leys School, Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
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Results and Impact Lecture for the The Leys School, Cambridge, U. K.
Year(s) Of Engagement Activity 2017
 
Description The Ruysch Lecture, Amsterdam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The Ruysch Lecture, E C Slater Memorial Symposium, University of Amsterdam, The Netherlands
Year(s) Of Engagement Activity 2016
 
Description University of Cambridge Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Our event was entitled, 'Fnidnig the msitkaes ni DNA that casue mitochondrial diseases'.
Visitors had the opportunity to learn all about mitochondrial diseases and took part in a range of activities, including fiendish genetic diagnosis puzzles, growing protein crystals and using scientific software to analyse a mitochondrial protein.

During the course of the day we welcomed in excess of 300 visitors, including young and teenage children, members of the local community and scientists from the region. We know we had this many visitors because we had 300 colouring books at the start and none left at the end of the day! They met with scientists of the Unit, who explained their work and gave insights into what it is like to work and study at the MRC MBU. For further feedback please see review document.
Year(s) Of Engagement Activity 2016
 
Description University of Helsinki 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Public lecture on 12 November in the Conference "Science for a Better World" on the occasion of the 375th anniversary of the University of Helsinki. Lecture: "How to Create World Class Research and Innovations".
Year(s) Of Engagement Activity 2015
 
Description University of Leeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Professor Sir John Walker FRS delivered a public lecture at a two-day symposium celebrating the life and work of Leeds Professor of Biochemistry and founding member of the Astbury Centre, Professor Steve Baldwin. Professor Walker also met approximately 50 A-level students from Yorkshire, who attended an afternoon event where they learned about the work going on at Leeds through poster displays, laboratory tours and scientific demonstrations.
Year(s) Of Engagement Activity 2015
 
Description University of Leeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Professor Sir John Walker FRS delivered a public lecture at a two-day symposium celebrating the life and work of Leeds Professor of Biochemistry and founding member of the Astbury Centre, Professor Steve Baldwin.

Approximately 50 A-level students from Yorkshire attended an afternoon event, where they learned about the work going on at Leeds through poster displays, laboratory tours and scientific demonstrations.
Year(s) Of Engagement Activity 2015
 
Description Videos for website 
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Part Of Official Scheme? No
Geographic Reach International
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Results and Impact Participation in video filming for MBU website (Cambridge TV)
Year(s) Of Engagement Activity 2016
 
Description Work Experience (Year 10) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Visit by three Year 10 students (age 15) to the Unit for a week's work experience/shadowing each in various research groups/environments, chaperoned throughout by individual members of the Unit. Presentation by the visitors at the end of their week.
Year(s) Of Engagement Activity 2016