Mass spectrometry at the frontiers of molecular medicine

Lead Research Organisation: University of Oxford
Department Name: Oxford Chemistry

Abstract

Many of our vital cellular processes are controlled and carried out by proteins that come together to form large and dynamic machineries. As cornerstones of the proper functioning of the cell, unsurprisingly many of these protein assemblies play important roles in human health. These range from ensuring that other proteins are correctly folded and assembled; to being responsible for clearing and degrading toxic species; and allowing the correct movement of molecules and ions in and around the cell. As such many of these protein machineries are important drug targets, with the binding of these small molecules acting to stimulate or reduce their activity, and hence mitigate disease states. Obtaining a complete inventory and description of these machineries, in both healthy and disease states, therefore represents one of the continuing grand challenges of biology. The difficulty in studying the structure of these molecules is that they are often very dynamic, that is their composition and shape can change, particularly when they interact with other molecules or are subject to external stresses. Infact the nature, scale and frequency of these fluctuations themselves play a vital part in governing function. Here we propose to develop and apply mass spectrometry for the study of both the structure and dynamics of protein assemblies, and will tackle two of the most notoriously difficult classes of biomolecules: the molecular chaperones, involved in protecting proteins from unwanted interactions; and membrane complexes that regulate the transport of small molecules into and out of the cell. Mass spectrometry represents a particularly attractive approach as it is remarkably general in its applicability, and has a high resolution of separation in both space and time: in other words it is well suited to looking at mixtures of proteins, and to monitor the transitions they undergo. The output of this research will lead us towards a complete understanding of the sizes, shapes and movements of these cellular machineries, as well as a means for evaluating the effects of small molecules as potential therapeutic strategies.

Technical Summary

Much progress has been made in obtaining atomic images of the important machineries that govern protein folding, degradation and transport across the cell membrane. Complementary information is required however to probe the dynamic changes in organization and conformation that these protein assemblies undergo. We propose to develop and apply mass spectrometry based approaches to a range of biomolecules that are refractory to conventional structural approaches. We plan to develop our methodology to overcome two of the most challenging characteristics displayed by protein complexes: intrinsic heterogeneity; and association with membranes. The difficulties these pose is exemplified in two systems: the polydisperse small heat shock proteins chaperones that play a crucial role in maintaining protein homeostasis; and the membrane channels and transporters that play an active role in small molecule/drug transport. The small heat shock proteins are implicated in a range of protein deposition diseases, with specific variants directly linked to cataract, desmin-related cardiomyopathy and Charcot-Marie-Tooth disease. The membrane channels and transporters we will study have important implications in type II diabetes, and the oral bio-availability of drugs. Through the basic biomedical research programme outlined here we will probe the molecular properties of these assemblies with a particular focus on monitoring their oligomeric state, heterogeneity, dynamics and conformational changes; and the ways in which these are altered in response to small molecule binding. We plan to implement the results of these fundamental studies to gain insight into the mechanism of ligand binding and its effects on these dynamic properties. We anticipate that the outcomes of this research will be a new means of studying these intractable biomolecules that will be broadly applicable to studying the effects of small molecules in polydisperse and membrane associated assemblies with high impact for biomedical research.

Publications


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Ahnert SE (2015) Principles of assembly reveal a periodic table of protein complexes. in Science (New York, N.Y.)
Borysik AJ (2012) The 'sticky business' of cleaning gas-phase membrane proteins: a detergent oriented perspective. in Physical chemistry chemical physics : PCCP
Borysik AJ (2012) Formation and dissociation processes of gas-phase detergent micelles. in Langmuir : the ACS journal of surfaces and colloids
Ebong IO (2011) Heterogeneity and dynamics in the assembly of the heat shock protein 90 chaperone complexes. in Proceedings of the National Academy of Sciences of the United States of America
Hopper JT (2014) Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. in Angewandte Chemie (International ed. in English)
 
Description Blackett Review
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Blackett review
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description Programme Grant Renewal
Amount £1,700,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2016 
End 04/2021
 
Description University of Oxford Confidence in Concept Scheme
Amount £23,421 (GBP)
Organisation Medical Research Council (MRC) 
Department MRC Confidence in Concept Scheme
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 06/2014 
End 12/2014
 
Description University of Oxford MRC Confidence in Concept Funds
Amount £34,600 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 10/2013 
End 04/2014
 
Title UniDec 
Description Computer programme - deconvolutes mass spectra 
Type Of Material Improvements to research infrastructure 
Year Produced 2014 
Provided To Others? Yes  
Impact Considerable uptake - more than 50 downloads 
 
Title hybrid mass spec 
Description interfacing of mass spectrometry with EM an dAFM 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact considerable interest in this development 
 
Title massign 
Description a computer programme for analysing hetergoeneous mass spectra 
Type Of Material Data analysis technique 
Year Produced 2012 
Provided To Others? Yes  
Impact improved assignment of mass spectra 
 
Description Industry Visitor 
Organisation Amgen Inc
Country United States of America 
Sector Private 
PI Contribution Study of membrane proteins and ligand binding using approaches developed in laboratory.
Collaborator Contribution Contacts in industry
Impact Invitation to speak at Amgen
Start Year 2014
 
Description Joe Marsh 
Organisation Medical Research Council (MRC)
Department MRC Human Genetics Unit
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Public 
PI Contribution Mass spectrometry of protein complexes
Collaborator Contribution Data mining and modelling
Impact Publication: S. E. Ahnert, J. A. Marsh, H. Hernández, C. V. Robinson and S. A. Teichmann Principles of assembly reveal a periodic table of protein complexes. Science, 2015, 350(6266): aaa2245 Collaboration multi-disciplinary.
Start Year 2013
 
Description Liz Carpenter 
Organisation University of Oxford
Department Structural Genomics Consortium (SGC)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Not applicable
Collaborator Contribution Donation of proteins
Impact No outcomes yet.
Start Year 2016
 
Description MscL 
Organisation Caltech Division of Chemistry and Chemical Engineering
Department Biochemistry & Molecular Biophysics
Country United States of America 
Sector Academic/University 
PI Contribution study of MscL channel in the presence of different lipids
Collaborator Contribution proteins and plasmids
Impact Publication: E. Reading, T. A. Walton, I. Liko, M. T. Marty, A. Laganowsky, D. C. Rees and C. V. Robinson The effect of detergent, temperature and lipid on the oligomeric state of MscL constructs: Insights from mass spectrometry. Chem Biol , 2015, 22(5): 593-603 Work not multi-disciplinary
Start Year 2011
 
Description Roche 
Organisation Roche
Country Global 
Sector Private 
PI Contribution Hosting visitor to study membrane proteins and ligand binding using unique approaches developed in our laboratory
Collaborator Contribution Contacts in industry
Impact Invitation to visit F. Hoffmann-La Roche to give lecture and set up possible studentship.
Start Year 2014
 
Description Sarah Teichmann 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Mass spectrometry of protein complexes
Collaborator Contribution Data mining and modelling
Impact Publication: S. E. Ahnert, J. A. Marsh, H. Hernández, C. V. Robinson and S. A. Teichmann Principles of assembly reveal a periodic table of protein complexes. Science, 2015, 350(6266): aaa2245 Collaboration multi-disciplinary.
Start Year 2013
 
Description Simon Newstead 
Organisation Medical Sciences Division
Department Department of Biochemistry
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Not applicable
Collaborator Contribution Donation of proteins
Impact Mass spectra
Start Year 2016
 
Title A mass spectrometry methodology for drug discovery 
Description Mass spectrometry as a tool for drug discovery 
IP Reference WO2012172378 
Protection Patent application published
Year Protection Granted 2013
Licensed No
Impact Interest from industry
 
Description Amgen Lecture China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Amgen Lecture to audience of scientists and industry. Increased awareness in research and applications to medical research.
Year(s) Of Engagement Activity 2015
 
Description Anatrace 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Recipient of Anatrace Membrane Protein Award, Biophysical Society, Philadelphia, USA

Increase in applications to work in laboratory
Year(s) Of Engagement Activity 2013
 
Description Article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Article in MRC Network Magazine - results not known

Impacts not known - article
Year(s) Of Engagement Activity 2014
URL http://www.mrc.ac.uk/news-events/publications/network-autumn-2014
 
Description Cass 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact CASS Mass Spectrometry Conference, Boston USA. September 2013

Increase in collaboration requests
Year(s) Of Engagement Activity 2013
 
Description Dohme Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Charles E. Dohme Memorial Lecture, Distinguished Lecture Series, John Hopkins University, Baltimore, USA November 2013

Not yet known
Year(s) Of Engagement Activity 2013
 
Description Independent on Sunday 
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 Increased awareness in research evidenced by increased contact with office.
Year(s) Of Engagement Activity 2015
 
Description Life Scientific 
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 Interview on BBC Radio 4 The Life Scientific with Jim Al-Khalili - increased interest in research and career pathway evidenced by large number of people writing in after programme.
Year(s) Of Engagement Activity 2014
 
Description Oxford Alumni North America Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Raise awareness of research at Oxford
Year(s) Of Engagement Activity 2016
 
Description Public Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact Lecture initiated questions on working in STEM subjects

Considerable interest from talented students to pursue career in research, particularly Oxford
Year(s) Of Engagement Activity 2014
 
Description Royal Institution Discourse 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Royal Institution Friday evening Discourse - heightened awareness of research and its applications.
Year(s) Of Engagement Activity 2016