Structural studies of phosphoinositide signalling and intracellular sorting
Lead Research Organisation:
MRC Laboratory of Molecular Biology
Abstract
Mammalian cells have a complex regulation that enables them to respond to growth factors, neurotransmitters and hormones. However, they also have cell-intrinsic responses to starvation and other environmental stresses. We are determining structures and dynamics of the cellular machines that integrate these cues to regulate cell responses. Lipid membranes partition organelles within cells and they help organise these responses. An important component of the work we do concerns how cellular machines interact with these membranes and how the shape and composition of the membranes determine the activity of these molecular machines. We are using the structures and dynamics of these machines to contribute to development of pharmaceuticals that may be useful in treating cancer, inflammation, diabetes and ageing.
Technical Summary
Eukaryotic cells have evolved a number of mechanisms to respond to environmental stress. These stress responses are tempered by growth factors and other signals from surrounding cells in multicellular organisms. Our research programme involves the mechanisms whereby these cellular signals are coupled to regulation of anabolic and catabolic processes in mammalian cells. Phosphoinositide 3-kinases (PI3Ks) modify lipid membranes and the modified phospholipids produced by the enzymes serve as second messengers and sorting signals in eukaryotic cells. The PI3Ks are essential for cell response to environmental cues, and play essential roles in innate and adaptive immune responses. Our most recent work is examining the roles of PI3Ks in immune response to cancers and in pathology characteristic of late-stage covid-19 infection. PI3Ks are part of a larger family of kinases known as the PI3K-related kinases (PIKKs). We study the structures, dynamics and functions of PI3Ks and PIKKs in cellular signalling, sorting, stress response and DNA damage repair. This includes almost all of the members of the PI3K family: class I PI3Ks activated by receptor tyrosine kinase and GPCRS, the primordial class III PI3K complex present in all eukaryotes, the golgi-associated PI4K, the PI3K related protein kinases (PIKKs) mTOR, ATM and ATR. Each of these PIKKs is a regulatory nexus, and our work produces variants in which specific regulatory inputs of the large enzyme complexes are ablated without affecting other activities. These modified complexes provide tools to decipher cellular regulation in ways that would not be possible with other approaches. We use X-ray crystallography, cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to marry structures with dynamics. In collaboration with our pharmaceutical partners, we are seeking to develop HDX-MS approaches to give better insight into conformational dynamics that could result in new therapeutic strategies. On-going efforts in the group concern the structural and dynamic basis of regulation of oncogenic PI3Ks, autophagic PI3K complexes, integration of amino acid and growth factor sensing in the PI3K pathway, and DNA damage repair.
Organisations
- MRC Laboratory of Molecular Biology, United Kingdom (Lead Research Organisation)
- University College London, United Kingdom (Collaboration)
- Intellikine, Inc. (Collaboration)
- Vertex Pharmaceuticals (Collaboration)
- Miltenyi Biotec GmBH (Collaboration)
- National Institute of Allergy and Infectious Diseases (NIAID) (Collaboration)
- Vlaams Instituut voor Biotechnologie (Collaboration)
- University of Liverpool, United Kingdom (Collaboration)
- University of Cambridge (Collaboration)
- University of Colorado Boulder (Collaboration)
- AstraZeneca plc (Collaboration)
- Novartis (Collaboration)
- Babraham Institute (Collaboration)
- Sanofi (Collaboration)
- University of Basel, Switzerland (Collaboration)
- Mount Sinai Hospital (Canada) (Collaboration)
- University of Virginia, United States (Collaboration)
- Eberhard Karls University Tuebingen, Germany (Collaboration)
- University of Oxford, United Kingdom (Collaboration)
- University of California, San Francisco, United States (Collaboration)
- Yeshiva University (Collaboration)
- Merck (Collaboration)
- Cornell University (Collaboration)
- Medical Research Council (Collaboration)
- University of Geneva, Switzerland (Collaboration)
- University of Leeds, United Kingdom (Collaboration)
- Whitehead Institute for Biomedical Research (Collaboration)
- Guy's Hospital (Collaboration)
- Pfizer Ltd (Collaboration)
- Texas A & M University, United States (Collaboration)
- Uni of Illinois at Urbana Champaign (Collaboration)
People |
ORCID iD |
| Roger Williams (Principal Investigator) |
Publications
Agromayor M
(2012)
The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain.
in Structure (London, England : 1993)
Anandapadamanaban M
(2019)
Prime Time for Dimeric Cytohesins: Surveying the Membrane with One Foot at a Time.
in Structure (London, England : 1993)
Anandapadamanaban M
(2019)
Architecture of human Rag GTPase heterodimers and their complex with mTORC1
in Science
Angulo I
(2013)
Phosphoinositide 3-kinase d gene mutation predisposes to respiratory infection and airway damage.
in Science (New York, N.Y.)
Apostolakis Apostolos
(2017)
High-frequency acoustoelectronic phenomena in miniband superlattices
Apsel B
(2008)
Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases.
in Nature chemical biology
Baretic D
(2019)
Structural insights into the critical DNA damage sensors DNA-PKcs, ATM and ATR.
in Progress in biophysics and molecular biology
Baretic D
(2017)
Structures of closed and open conformations of dimeric human ATM.
in Science advances
Baretic D
(2014)
The structural basis for mTOR function.
in Seminars in cell & developmental biology
Baretic D
(2014)
PIKKs--the solenoid nest where partners and kinases meet.
in Current opinion in structural biology
| Description | Chairman Scientific Advisory Board, PIQUR Therapeutics |
| Geographic Reach | Europe |
| Policy Influence Type | Participation in a advisory committee |
| Description | Diamond Light source peer review panel |
| Geographic Reach | National |
| Policy Influence Type | Participation in advisory committee |
| Description | Member of the MRC Molecular and Cellular Medicine Board |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Scientific advisory board for max planck society, dortmund |
| Geographic Reach | Asia |
| Policy Influence Type | Participation in advisory committee |
| Description | AstraZeneca-LMB Collaboration on HDX-MS Fragmentation |
| Amount | £300,000 (GBP) |
| Organisation | AstraZeneca |
| Sector | Private |
| Country | United Kingdom |
| Start | 04/2015 |
| End | 04/2018 |
| Description | AstraZeneca/LMB Blue-Skies Inniative. Structures of ATM and ATR complexes |
| Amount | £200,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2015 |
| End | 08/2017 |
| Description | BBSRC 2012 Responsive Mode Grant |
| Amount | £120,465 (GBP) |
| Funding ID | BB/K019155/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2013 |
| End | 04/2016 |
| Description | Boehringer Ingelheim Studentship (Howes) |
| Amount | € 58,800 (EUR) |
| Organisation | Boehringer Ingelheim |
| Sector | Private |
| Country | Germany |
| Start | 08/2019 |
| End | 07/2021 |
| Description | Cambridge Cancer Centre Studentship (Rotislavleva) |
| Amount | £80,000 (GBP) |
| Organisation | Cancer Research UK Cambridge Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2013 |
| End | 09/2016 |
| Description | Cancer Research UK Science Committee - Programme Award |
| Amount | £656,697 (GBP) |
| Funding ID | C14801/A21211 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2016 |
| End | 01/2021 |
| Description | EMBO Advanced Fellowship |
| Amount | £73,690 (GBP) |
| Funding ID | ALTF 603-2019 |
| Organisation | European Molecular Biology Organisation |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 02/2020 |
| End | 12/2021 |
| Description | EMBO Long Term Fellowship (Burke) |
| Amount | £60,000 (GBP) |
| Organisation | European Molecular Biology Organisation |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 01/2010 |
| End | 12/2011 |
| Description | EMBO Long Term Fellowship (Pobbati) |
| Amount | £48,000 (GBP) |
| Organisation | European Molecular Biology Organisation |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 09/2007 |
| End | 09/2009 |
| Description | EMBO Long Term Fellowship (Sachse) |
| Amount | £45,000 (GBP) |
| Organisation | European Molecular Biology Organisation |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 06/2008 |
| End | 03/2010 |
| Description | EMBO Long Term Fellowship (Vadas) |
| Amount | £7,500 (GBP) |
| Organisation | European Molecular Biology Organisation |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 09/2010 |
| End | 12/2010 |
| Description | FEBS long-term fellowship (Anandapadamanaban) |
| Amount | £29,010 (GBP) |
| Organisation | Federation of European Biochemical Societies (FEBS) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2017 |
| End | 01/2020 |
| Description | Intellikine Inc |
| Amount | £3,000 (GBP) |
| Organisation | Intellikine, Inc. |
| Sector | Private |
| Country | United States |
| Start | 09/2008 |
| End | 09/2009 |
| Description | LMB Cambridge Scholarship (Baretic) The Cambridge Trust |
| Amount | £95,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Laboratory of Molecular Biology (LMB) |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2010 |
| End | 09/2013 |
| Description | LMB Cambridge Scholarship (Zhang) The Cambridge Trust |
| Amount | £95,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Laboratory of Molecular Biology (LMB) |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2009 |
| End | 09/2012 |
| Description | MRC/AZ Cryo EM Structures and function studies of full length ATM & ATR: A molecular understanding of the regulation of DNA damage repair. |
| Amount | £296,249 (GBP) |
| Funding ID | BSF28 |
| Organisation | AstraZeneca |
| Sector | Private |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2020 |
| Description | MRC/AZ How do small-molecule activators of the PI3K superfamily work? |
| Amount | £200,000 (GBP) |
| Funding ID | BSF33 |
| Organisation | AstraZeneca |
| Sector | Private |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 08/2020 |
| Description | Marie Curie Intra European Fellowship (Vadas) |
| Amount | £124,296 (GBP) |
| Organisation | Marie Sklodowska-Curie Actions |
| Sector | Charity/Non Profit |
| Country | Global |
| Start | 01/2012 |
| End | 12/2012 |
| Description | Postdoc Fellowships for Research Abroad - Bioscience and Basic Biomedicine |
| Amount | kr 3,440,571 (DKK) |
| Funding ID | NNF18OC0030544 |
| Organisation | Novo Nordisk Foundation |
| Sector | Charity/Non Profit |
| Country | Denmark |
| Start | 11/2018 |
| End | 10/2022 |
| Description | Research Grant Intellikine |
| Amount | $50,000 (USD) |
| Organisation | Intellikine, Inc. |
| Sector | Private |
| Country | United States |
| Start | 12/2010 |
| End | 09/2013 |
| Description | Research Grant Serono |
| Amount | £281,240 (GBP) |
| Funding ID | LSF 24463-blsf8555 |
| Organisation | Merck |
| Department | Merck Serono |
| Sector | Private |
| Country | Germany |
| Start | 11/2005 |
| End | 10/2009 |
| Description | SNSF Fellowship (Vadas) |
| Amount | £38,000 (GBP) |
| Organisation | Swiss National Science Foundation |
| Sector | Public |
| Country | Switzerland |
| Start | 01/2011 |
| End | 12/2011 |
| Description | SNSF Postdoctoral Fellowship (Vadas) |
| Amount | £38,000 (GBP) |
| Organisation | Swiss National Science Foundation |
| Sector | Public |
| Country | Switzerland |
| Start | 09/2009 |
| End | 08/2010 |
| Description | St Catharines College JRF (Masson) |
| Amount | £75,000 (GBP) |
| Organisation | University of Cambridge |
| Department | St Catharine's College |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2015 |
| End | 09/2018 |
| Description | Wellcome Trust Programme Grant (Assembly and disassembly ESCRTs on membranes) |
| Amount | £561,453 (GBP) |
| Funding ID | 083639 |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2008 |
| End | 03/2013 |
| Title | PI3K crystallisation protocols |
| Description | We have developed detailed protocols for producing crystals of phosphoinositide 3-kinase gamma that can be used to determine the structures of complexes of the enzyme with small-molecule inhibitors. These include for expression in bacullovirus, purification, crystallisation, soaking crystals with compounds and crystal freezing protocols. We have communicated these protocols to various companies who have received materials from us. Without these protocols, it is difficult to produce high resolution structures. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2006 |
| Provided To Others? | Yes |
| Impact | The protocols and the reagents that we have provided (viruses, purified protein and bacmids). Have facilitated many drug discovery programmes aimed at specific PI 3-kinase inhibitors. |
| Title | baculovirus expression system for IA PI3Ks |
| Description | We developed a baculovirus expression system that has enabled us to express lare quantities of class IA phhosphoinositide 3-kinases. The system has enabled us to express all of the mammalian PI 3-kinases in a manner that is amenable to determining high-resolution structures of the complexes of the enzyme with isotype-specific inhibitors. The system is particularly well suited to inhibitors of p110delta, p110alpha and p110beta. The details of this system have only ben disclosed at this time to our industrial collaborators at Merck-Serono. We expect to make full public disclosure by the end of 2008. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2008 |
| Provided To Others? | Yes |
| Impact | This has allowed us to obtain the first structures of type IA PI 30kinases that are suitable for drug discovery programmes. |
| Title | co-expresson vectors for protein complexes |
| Description | We have developed a bacterial poly-cistronic expression system that we use to simultaneously express up to eight proteins. The system is used to express multi-subunit complexes with a variety of tags to facilitate X-ray crystallography, fluorescence spectroscopy and other biophysical techniques. The system involves a set of "shuttle" vectors as well as co-expression vectors. It has been been the basis for many of the structures that we have determined in the last five years, including the ESCRT complexes and catalytic/regulatory complexes for the PI 3-kinases. Work using these vectors has been published and the vectors have been provided to many researchers in the LMB and elsewhere. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2007 |
| Provided To Others? | Yes |
| Impact | Without these vectors, many complexes would have been impossible to obtain. It is common that components of biological complexes cannot be obtained in isolation. These vectors have enabled us to go from no measurable expression for isolated components to massive yields of complexes suitable for X-ray crystallography. |
| Description | Allosteric activation of mTORC1 |
| Organisation | Babraham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We will be examining the effects of structure-based mutants on the activation lifetime of mTORC1 in vitro |
| Collaborator Contribution | Nicholas Ktistakis at the Babraham Institute will be examining the effects of structure-based mutants on the activation lifetime of mTORC1 in vitro |
| Impact | None yet |
| Start Year | 2020 |
| Description | Bioinformatics of ESCRT complexes |
| Organisation | Miltenyi Biotec GmBH |
| Country | Germany |
| Sector | Private |
| PI Contribution | We have determined the structure of ESCRT-containing complexes |
| Collaborator Contribution | Kay Hoffman identified a novel ESCRT-I subunit |
| Impact | One publication, pubmed ID 22405001 |
| Start Year | 2012 |
| Description | Biological inhibitors of cancers |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have assisted in determining structures of complexes of intracellular antibodies with the small G-protein Ras |
| Collaborator Contribution | Prof. Rabbitts has explored the use of biological inhibitors such as intracellular antibodies for inhibiting cancers. |
| Impact | Publication 17568777 |
| Description | Chemistry of PI3K inhibiors |
| Organisation | University of California, San Francisco |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We determined the structures od a range of complexes of PI3Ks with isotype-selective inhibitors |
| Collaborator Contribution | Colleages in Kevan Shokat's group have provided a wide range of compounds that are inhibitors of PI3Ks. These have been central to our ongoing structural studies of these enzymes. |
| Impact | These collaborations have resulted in sev eral publications including: 16647110 18849971 |
| Description | Cryo-EM of ATM and ATR complexes |
| Organisation | Medical Research Council (MRC) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We are determining structures of ATM and ATR-containing complexes |
| Collaborator Contribution | Sjors is providing guidance for analysing cryo-EM data |
| Impact | No reportable outputs yet |
| Start Year | 2015 |
| Description | Cryo-EM structures and functional studies of full length ATM & ATR: A molecular understanding of the regulation of DNA damage repair |
| Organisation | AstraZeneca |
| Department | Research and Development AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are determining structures of the PI3K-related protein kinases ATM and ATR. |
| Collaborator Contribution | Through the AZ/LMB Blue Skies Innitiative, we have received funding for one postdoctoral researcher. AZ has also provided us large-scale cell cultures expressing the enzymes. |
| Impact | There have been no reportable outcomes yet |
| Start Year | 2015 |
| Description | Cryo-electron microscopy of a TOR complex |
| Organisation | Medical Research Council (MRC) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We have produced large quantities of pure complexes of the protein kinase TOR in a complex with LST8 |
| Collaborator Contribution | Dr. Vinothkumar has provided advice on cryo-EM, collected and analysed initial data sets and helped train members of my group |
| Impact | One publication in press |
| Start Year | 2015 |
| Description | Crystal structure of PI3K gamma |
| Organisation | Pfizer Ltd |
| Department | Warner-Lambert |
| Country | United States |
| Sector | Private |
| PI Contribution | We determined the first structure of a phosphoinositide 3-kinase. |
| Collaborator Contribution | We collaborated in developing approches to designing PI3K inhibitors |
| Impact | Protocols established in this collaboration resulted in a series of publications including pubmed ids: 10580505 11090628 11136978 16647110 18849971 |
| Description | Developing activators of lipid kinases |
| Organisation | AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We developed an assay to select for small molecules that would activate lipid kinases. We also will investigate the mechanism of activation using HDX-MS. |
| Collaborator Contribution | AstraZeneca carried out a large-scale screen of a compound library using our assays. Our collaborators at UCL will be involved in using these inhibitors in various biological contexts. |
| Impact | The collaboration has so far discovered a set of putative activators. |
| Start Year | 2015 |
| Description | Developing activators of lipid kinases |
| Organisation | University College London |
| Department | UCL Cancer Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We developed an assay to select for small molecules that would activate lipid kinases. We also will investigate the mechanism of activation using HDX-MS. |
| Collaborator Contribution | AstraZeneca carried out a large-scale screen of a compound library using our assays. Our collaborators at UCL will be involved in using these inhibitors in various biological contexts. |
| Impact | The collaboration has so far discovered a set of putative activators. |
| Start Year | 2015 |
| Description | Development of isotype-specific PI3K inhibitors |
| Organisation | University of California, San Francisco |
| Department | Helen Diller Family Comprehensive Cancer Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have provided structures of complexes of PI3Ks with inhibitors |
| Collaborator Contribution | Kevsn Shokat has provided isotype-spefic inhibitors |
| Impact | Seven publications, PUBMED IDS: 16647110, 18849971, 20081827, 20154668, 20339072, 24876499, 26756197 |
| Description | Establishment of a PI3K structure-based drug develpment programme |
| Organisation | Vertex Pharmaceuticals |
| Country | United States |
| Sector | Private |
| PI Contribution | We provided expression, purification and crystallisation protocols for PI3K gamma. We also provided plasmids and viruses for insect cell expression. |
| Impact | Vertex established a structural component of their drug discovery programme for PI3K |
| Description | Establishment of a structure-based PI3K drug discovery programme at Chiron |
| Organisation | Novartis |
| Department | Chiron Corp |
| Country | United States |
| Sector | Private |
| PI Contribution | We provided protocols for expression, purification and crystallisatiobn of PI3K gamma. We provided plasmids and viruses to facilitate expression. |
| Impact | Chron established a PI3K structure programme for developing their inhibitors. |
| Description | Establishment of a structure-based PI3K drug discovery programme at Sanofi-Aventis |
| Organisation | Sanofi |
| Department | Aventis |
| Country | France |
| Sector | Private |
| PI Contribution | We provided protocols for expression, purification and crystallisatiobn of PI3K gamma. We provided plasmids and viruses to facilitate expression. |
| Impact | Sanofi-Aventis established a PI3K structure programme for developing their inhibitors. |
| Description | HDX-MS studies of lipid transfer proteins |
| Organisation | Texas A&M University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have analysed PI transfer proteins using HDX-MS to determine how they interact with lipids and membranes |
| Collaborator Contribution | They have provided purified proteins |
| Impact | No reportable output yet |
| Start Year | 2015 |
| Description | HDX-MS to probe enzyme regulation and develop novel inhibitors of PI3Ks |
| Organisation | AstraZeneca |
| Department | Research and Development AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are using HDX-MS methods to develop inhibitors that prevent activation of PI3K complexes on membranes. In order to optimise this process, we are employing new MS fragmentation techniques. |
| Collaborator Contribution | We meet regularly with our partners to discuss HDX-MS data acquisition and processing. We have participated in training postdocs in our partner organisation. |
| Impact | There have not been any reportable outcomes yet |
| Start Year | 2015 |
| Description | Inhibition of oncogenic PI3Ks |
| Organisation | Albert Einstein College of Medicine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have determined the structures of class IA PI3Ks and used these structures to define mechanisms of oncogenesis by smatic mutations in these enzymes |
| Collaborator Contribution | Prof. Backer has provided valuable expertise and reagents for expressing and characterising PI3Ks |
| Impact | Publication 17626883 |
| Description | Mechanisms of PI3K-driven oncogenesis |
| Organisation | Albert Einstein College of Medicine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have analysed regulation of PI3K complexes using HDX-MS |
| Collaborator Contribution | Jonathan has examind the impact of input-ablated mutants on oncogenesis in vitro |
| Impact | Four publications, PUBMED IDs, 17626883, 23211529, 23328076, 24190998 |
| Start Year | 2011 |
| Description | Modelling flexibility in PI3Ks |
| Organisation | Intellikine, Inc. |
| Country | United States |
| Sector | Private |
| PI Contribution | We determined structures of complexes of isotype-specific inhibitors of PI3K delta with specific inhbitors developed by Intellikine. We also developed computational tools to model the flexibility of PI3Ks. |
| Collaborator Contribution | We have had ongoing discussions related to designing new PI3K inhibitors |
| Impact | We have published our structures and conclusions in Nature Chemical Biology. This is in press and due to be published in February, 2010. |
| Description | Nanobodies for structural studies |
| Organisation | Vlaams Instituut voor Biotechnologie |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | We have provided cross-linked PI3K-containing complexes for immunization |
| Collaborator Contribution | Jan Steyaert has provided nanobodies that bind to Vps34-containing complexes and complexes of a class IA PI3K |
| Impact | One publication, 26450213 |
| Start Year | 2012 |
| Description | PI3K delta activity in pathogenesis of APDS |
| Organisation | University of Cambridge |
| Department | Department of Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have characterised the activity and membrane interqactions of mutants of p110 delta associated with familial immune disorders |
| Collaborator Contribution | Alison has characterised the cells of APDS patients |
| Impact | One publication, pubmed id 24136356 |
| Start Year | 2012 |
| Description | Phosphoinositide recognition moduels |
| Organisation | University of Illinois |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have determined the structures of phosphoinositide-recognition modules such as PX domains |
| Collaborator Contribution | Prof. Cho has characterised the physics of interactions of recognition modules for lipid membranes. This has helped us understand our structures of these modules. |
| Impact | Publications: 17038310 17581820 1764168 |
| Description | Protein trafficking to lysosomes via ESCRT complexes |
| Organisation | Cornell University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have determined three-dimensional structures of a range of endosomal complexes involved in sorting membrane proteins into multivesicular bodies for degradation in lsosomes |
| Collaborator Contribution | We have published a series of papers with our structures and cellular sorting results from Scot Emr's groupDr. Urbe has been helped us decide important research directions that understanding lysosomal trafficking |
| Impact | Our structures have been the basis for several publications 16615893 17215868 17450176 |
| Description | Protein trafficking to lysosomes via ESCRT complexes |
| Organisation | University of Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have determined three-dimensional structures of a range of endosomal complexes involved in sorting membrane proteins into multivesicular bodies for degradation in lsosomes |
| Collaborator Contribution | We have published a series of papers with our structures and cellular sorting results from Scot Emr's groupDr. Urbe has been helped us decide important research directions that understanding lysosomal trafficking |
| Impact | Our structures have been the basis for several publications 16615893 17215868 17450176 |
| Description | Quantitative analysis of the effects of membrane curvatute on activity of Vps34 complexes |
| Organisation | University of Geneva |
| Department | Department of Biochemistry |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | We have provided purified Vps34 complexes and assayed them as a function of vesicle size and lipid composition |
| Collaborator Contribution | They have drawn lipid tubules to generate high-curvature structures on which to assay the Vps34 complexes |
| Impact | No reportable output yet |
| Start Year | 2015 |
| Description | Regulation of autophagy induction by the VPS34 complexes: structural and functional studies |
| Organisation | Babraham Institute |
| Department | Signalling |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have determined structures, in vitro activities, dynamics and membrane binding for several Vps34-containing complexes |
| Collaborator Contribution | Nicholas has assayed autophagy in mammalian cells |
| Impact | One publication, PUBMED ID 26450213 |
| Start Year | 2012 |
| Description | Regulation of autophagy induction by the Vps34 complex: structural and functional studies |
| Organisation | Babraham Institute |
| Department | Signalling |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We are collaborating on the structures of Vps34-containing complexes |
| Collaborator Contribution | Our work is primarily structural. The structures we are determining are being used as a framework for designing functional studies of these complexes by researchers in the Babraham Institute. |
| Impact | Several structures have been determined and publictions are in progress |
| Start Year | 2012 |
| Description | Regulation of class IB PI3Ks |
| Organisation | Eberhard Karls University of Tübingen |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | We have carried HDX-MS studies of class IB PI3Ks and determined their activities in vitro |
| Collaborator Contribution | They have provided lipidated Gbeta/gamma subunits expressed in SF9 cells |
| Impact | Three publications, PUBMED IDS: 3211529, 24190998 and 26173259 |
| Start Year | 2011 |
| Description | Role of ESCRTs in archaea |
| Organisation | University of Oxford |
| Department | Medical Sciences Division |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have determined the structures of complexes of ESCRT-replated proteins from archaeal cells |
| Collaborator Contribution | Prof. Bell has been essential in determining the roles of ESCRT-related proteins in archaeal cells |
| Impact | Publication 19008417 |
| Description | Single-molecule imaging of PI3K and PTEN activity on membranes |
| Organisation | University of Colorado Boulder |
| Department | Department of Chemistry and Biochemistry |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have provided large quantities of purified PI3K and PTEN |
| Collaborator Contribution | Joseph has characterised the activity, diffusion and lipid interactions using single-molecule spectrometry |
| Impact | Two publications |
| Start Year | 2012 |
| Description | Structural and functional studies of PI3Ks |
| Organisation | Babraham Institute |
| Department | Signalling |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have determined structures of PI3K-containing complexes and analysed their dynamics by HDX-MS. We have also characterised in vitro activitiies of these complexes |
| Collaborator Contribution | They have assayed PI3K complexes in cells and mice |
| Impact | Six publications, PUBMED IDS: 11090628 11136978 11684018 15581496 21362552 24136356 |
| Description | Structural and functional studies of PI3Ks |
| Organisation | University of Basel |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | We have carried out HDX-MS studies of p110gamma/p84 complexes |
| Collaborator Contribution | Matthis Wymann has determine the activity of PI3K gamma complexes in cells |
| Impact | publication 23824069 |
| Description | Structural studies of golgi-associated proteins |
| Organisation | Medical Research Council (MRC) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We have helped researchers in Sean Munro's lab to determine structures of golgi-associated proteins. |
| Collaborator Contribution | They have helped us with assays of intracellular protein sorting. |
| Impact | One publication, PUBMED ID 14580338, Another in review. |
| Description | Structural studies of the regulation of mtorc1 by Rag heterodimers |
| Organisation | Whitehead Institute for Biomedical Research |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We e determined crystal and cryo-EM structures of mTORC1 in a complex with a RagA/C heterodimer and crystal structures of RagA/C heterodimers |
| Collaborator Contribution | We have had several helpful discussions regarding strategies. Our collaborators have given valuable comments in the process of preparing a manuscript. |
| Impact | A manuscript is in preparation |
| Start Year | 2016 |
| Description | Structure and function of MITD1 |
| Organisation | Guy's Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | We have determined structures of MITD1 and associated proteins |
| Collaborator Contribution | Monica has determined the role of MITD1 in cells |
| Impact | Two publications, PUBMED ID 23045692 and 22405001 |
| Start Year | 2012 |
| Description | Structure and function of phosphoinositide kinases |
| Organisation | University of Cambridge |
| Department | Department of Pharmacology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have analysed the dynamics and membrane binding of phosphtidylinositol kinases, using HDX-MS |
| Collaborator Contribution | They have provided the ptoein complexes for analysis |
| Impact | Two publications: 15350214, 25495341 |
| Description | Structure-based drug discovery for PI3K delta inhibitors |
| Organisation | Merck |
| Department | Merck Serono |
| Country | Germany |
| Sector | Private |
| PI Contribution | We established protocols for expressing and purifying large quantities of phosphoinositide 3-kinase alpha and delta for structure-based drug discovery programmes. We crystallised and determned structures of a wide ranger of complexes of these enzymes with inhibitors designed by Serono and others. Using these structures, we established mechanisms that underpin one class of isotype-specific inhibitor. |
| Collaborator Contribution | We have extensive, ongoing discussions regarding important directions in designing PI3K inhbitors |
| Impact | We published our conclusions regarding isotype-specific inhibitors of PI3K delta in Nature Chemical Biology. This is currently in press and tentatively scheduled for publication in February, 2010. |
| Description | Structures of helical assemblies by electron microscopy |
| Organisation | University of Virginia (UVa) |
| Department | Health Sciences Centre |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We deterines the structure of ESCRT-III filaments by electron microscopy with the help of Prof. Egelman |
| Collaborator Contribution | Prof. Egelman provided expertise necessary to determine the structures of helical assemblies of ESCRT complexes |
| Impact | Publication 18786397 |
| Description | Structures of spindle-pole body complexes |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Laboratory of Molecular Biology (LMB) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have helped determine protein structures of complexes involved in spindle-pole bodies |
| Collaborator Contribution | They have provided crystals of purified protein complexes |
| Impact | We have published the structure and the invivo assembly of components of the spindle-pole body pubmed id: 16785321 |
| Description | Studies of phosphoinositide signalling using single molecule fluorescence methods on supported bilayers |
| Organisation | University of Colorado Boulder |
| Department | Department of Chemistry and Biochemistry |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have provided samples of various purified enzymes for studies of activity and difussion on membranes |
| Collaborator Contribution | Falke and his clleagues have used our material to characterise the molecular mechanisms whereby the activity of the enzymes is regulate on membranes |
| Impact | Two publications: PMID: 27933776 PMID: 27119641 |
| Start Year | 2012 |
| Description | The molecular basis of PI3Kgamma in autoimmune lymphoproliferative syndrome |
| Organisation | National Institute of Allergy and Infectious Diseases (NIAID) |
| Country | United States |
| Sector | Public |
| PI Contribution | We have assayed the PI3K activity of p110gamma mutants associated with familial autoimmune disease |
| Collaborator Contribution | Our partners have assayed the inluence of the p110gamma mutations in human cells |
| Impact | No reportable output yet |
| Start Year | 2015 |
| Description | The molecular basis of SHORT syndrome |
| Organisation | University of Cambridge |
| Department | Institute of Metabolic Science (IMS) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have provided p110alpha complexes and trained a Ph.D. student in work with mutants of the enzyme |
| Collaborator Contribution | The Ph.D. student has cloned SHORT syndrome mutants, expressed them and assayed their activity |
| Impact | No reprtable output yet |
| Start Year | 2014 |
| Description | The role of PTEN in Wnt signalling |
| Organisation | Mount Sinai Hospital (Canada) |
| Department | Samuel Lunenfeld Research Institute |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | We assayed in vitro activities of PTEN mutants |
| Collaborator Contribution | They characterised the role of PTEN in cilia formation |
| Impact | One publication, 26399523 |
| Start Year | 2014 |
| Description | The structure of PI3K alpha |
| Organisation | AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We expressed, purified and crystallised the core of the p110 alpha/p85 complex. We determined the structure of the adaptor-binding domain of p110 alpha in a complex with the iSH2 domain from p85 regulatory subunit. |
| Collaborator Contribution | Over the period of the collaboration, we have discussed directions important for development of PI3K inhibitors |
| Impact | This resulted in the publication f the structure and our conclusions in the journal Science. Pubmed id 17626883 |
| Description | structure and function of p110 beta/ p85 beta |
| Organisation | Babraham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have determined structures of the complexes of p110 beta with regulatory subunits |
| Collaborator Contribution | They have been involved in various aspects of our reserch programme, including mass spectrometry for assaying PI3Ks and mouse studies of structure guided mutations |
| Impact | publication 21362552 |
| Start Year | 2010 |
| Description | A public speech at the Cambridge Philosophical Society describing how small proteins interact with a ribosome |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Glenn Masson spoke to a general audience about how hydrogen/deuterium exchange mass spectrometry is altering the way we measure details of interactions between very large molecules. His talk "Flies dancing on the trunk of an elephant" described how the precise positions of a small protein could be detected on the surface of the giant complex that is a ribosome. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Big Biology Day 2108. Synthetic biology: Create a New Protein! |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Yohei Ohashi was a member of a team that visited Hills Road 6th Form to interest students in science. His focus was "Synthetic biology: Create a New Protein!" |
| Year(s) Of Engagement Activity | 2018 |
| Description | Biochemical Society Big Biology Day |
| 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 | Public/other audiences |
| Results and Impact | Two members of the group participated in a "Medicine Makers" event developed by the Biochemical Society and British Pharmacological Society. This was held in Cambridge at the at "Big Biology Day". |
| Year(s) Of Engagement Activity | 2016 |
| Description | Cambridge Science Festival 2018. Worms are cleverer than you think! |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Yohei Ohashi helped explain how C. elegans is used as a model research organism |
| Year(s) Of Engagement Activity | 2018 |
| Description | FindAPhD Fair - Cambridge |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Ksenia Rostislavleva, a Ph.D. student in the group, helped assemble a set of posters and a stand to advise undergratuates about careeres in research at the Laboratory of Molecular Biology |
| Year(s) Of Engagement Activity | 2015 |
| Description | Home in the Service of Science |
| 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 | Public/other audiences |
| Results and Impact | "Home in the Service of Science" is an art installation in the LMB. Olga Perisic in the group participated in a public event to open the installation for the general public. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Long Road 6th form |
| 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 | Schools |
| Results and Impact | About 10 sixth form students toured the lab, and we answered questions about research and medical careers |
| Year(s) Of Engagement Activity | 2014 |
| Description | Ridgefield Primary School Science Day |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Presentation for school children by Glenn Masson |
| Year(s) Of Engagement Activity | 2012 |
| Description | Royal Society annual 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 | Olga Perisic spent a day as a volunteer talking to visitors at a stand at the Royal Society annual exhibition called "Virus wars - antibodies strike back" which celebrated our immune system, research and 100 years of the MRC , Saturday 6th July 2013. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Science Festival, 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 | Glenn Masson helped man am LMB booth at the Science Festival |
| Year(s) Of Engagement Activity | 2015 |
| Description | See your cells |
| 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 | This was part of an event called the Big Biology Day. Yohei Ohashi participated in an event to show children the world that is visible with a high-power light microscope. The demonstration enabled children to see what their cheek cells look like, and let people use microscopes to other specimens such as insects. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Structural biology as a tool for finding new pharmaceutical agents |
| 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 | Schools |
| Results and Impact | The group of sixth form students who visited the institute learned about the mission of the LMB and some basic principles of strutural biology as applied to drug discovery. In addition, they took part in a discussion with several scientists on various aspects of a career as a scintist and practical information for applying to University, After the talk in 2013, the sixth form requested that we repeat this is 2014. |
| Year(s) Of Engagement Activity | 2013,2014 |
| Description | long road 6th form |
| 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 | Schools |
| Results and Impact | We hosted the visit of 10 top 6th form students to talk about careers in molecular biology with an emphasis on molecular medicine. The head of studies at the sixth form reported that students found the visit helpful and that they were interested in establishing a work experience program. |
| Year(s) Of Engagement Activity | 2013 |