BBSRC David Phillips Research Fellowship an interdisciplinary perspective

Dr. Ed Tate, Department of Chemistry, ICL

• Context:• Current research• Career

• Fellowship Applications:• Personal perspective • Hints and Tips

• Research fellowship:• Advantages, challenges

Faculty of Medicine Fellowships DayJuly 2008

Research interests

1. Development & application of new technologies in chemical biology New chemical approaches for site-specific protein labelling Chemical tools for exploring post-translational modification of proteins Reactive probes for in vitro & in vivo enzyme activity profiling & imaging

2. Design and synthesis of small molecule inhibitors of: Protein-protein interactions: site-specific disruption of multi-protein complexes

• Martin Buck (CBC), Xiaodong Zhang (CBC), Tony Holder (NIMR) Protein-ligand interactions: transferase and protease inhibitors

• Neil Fairweather (CMMI), Miguel Seabra (NHLI), Debbie Smith (York)

Dr. Ed Tate, Department of ChemistryBBSRC David Phillips Research Fellow (since 2006)

e.tate@imperial.ac.uk; http://www3.imperial.ac.uk/people/e.tate/research

Chemical proteomics Applied organic chemistry of living systems Targets complex post-translational

phenomena: PTMs, enzyme activity in living systems, protein-protein interactions…

Proteomic complement of chemical genetics Protein labelling, imaging, biomarker

analysis…

What is chemical proteomics?

DNA RNA Protein

Transcription Translation

Post-translational modification

>300 types: Phosphorylation, glycosylation, lipidation, acetylation, proteolysis…

Origin

Post-translational Modifications

Phosphorylation

Signalling

Glycosylation

Immune system

Cell adhesion

Prenylation

Trafficking

Acylation

Membrane association

Acetylation

Transcriptional regulation

Proteolysis

Apoptotic cascade

Ubiquitination

Protein degradation

Site Dynamics

Function

Chemical Proteomics

Sulfenic acids

Redox response

Site-specific labelling of proteins

Metabolic tagging

Target proteins tagged at site of PTM

Protein bearing site-specific chemical feature

(active site, PTM)

Tagged PTM applied to

cells/animal

Proteins labelled site-specifically

- + ++

Drug mode-of-action studies

ID proteins and site of PTM

Live- and fixed-cell imaging

Bioorthogonal ligation chemistry

Chemical or enzymatic tagging

A platform for Chemical Myristomics

(‘Azido-myristic’ acid)

N3

HN

O

N3

HN

O

N3

HN

O

N3

S

O

CoA

N3

OH

O

N3

OH

O

N3

HN

O

N

NN

HN

O

Secondary Labels

Bioorthogonal ligation

Secondary Labels

MudPIT analysis

2D-DIGEOn-bead purification

Activity-based probesSurface layer formation in C. difficile

C. difficile Spore-forming anaerobe Most lethal hospital superbug Resistant to most antibiotics Lack of genetic tools

Excretes a crystalline S-layer Post-translational cleavage Unknown cysteine protease

O

HOOC

O

HN LysTyrGlu PEG3 Biotin

WarheadSpecificity

element

Linker

LabelFeed to C. difficile Affinity purify, ID

Chemical Technologies New chemical labelling

technologies New chemistries Extend to other PTMs ABPs for new enzyme activities

Discovery of new PTMs Pull out after metabolic labelling

Nucleotide tagging Protein-DNA interactions Transcriptional activation

Future perspectives

Biomedical Applications

+ Chemical genetics Drug screening Biomarker analysis

+ Synthetic biology Introducing new chemistries

+ Live cell & in vivo imaging Trafficking due to PTM Cell-surface display

+ Systems biology Dissect pathways Probes for protein-protein &

protein-membrane interactions

Career OverviewPhD and Postdoctoral Work

BSc in Chemistry (Durham)

1993-

1996

PhD in Organic Chemistry(Cambridge)

1996-

1999

1851 Research Fellowship(Ecole Polytechnique)

2000-

2001

Howard Trust Research Fellowship (Institut Pasteur)

2002-

2003

BBSRC-funded PDRA (ICL)

2004-

2006

New C-glycosidation reactionsTotal synthesis of natural products

Radical cyclisation chemistryTotal synthesis of natural products

Role of DNA helix stability & upstream sequences in transcriptional regulation

Protein/peptide synthesis and engineeringLibrary generation and screening techniques

Application StageSituation as of August 2005

Prior Applications: WT fellowship application in 2005 rejected – insufficient

biochemical track record Never been involved in writing a standard grant application!

Personal Situation: Current PDRA contract due to expire 1 month after expected

fellowship decision, no follow-on funding… Baby due 22nd November!

Research Track Record: Good chemical research track record No biochem research track record at time of application

Application StagePlan of Action

Applied for multiple fellowships EPSRC Advanced Research Fellowship (ARF) BBSRC David Phillips Fellowship Royal Society URF Wellcome Trust MRC

Novel proposal: chemical proteomics Topical and interdisciplinary Very limited literature precedent Minimal preliminary data, and no prior track record!

Plan B: other grant proposals Co-I on MRC Discipline-Hopping grant (related subject) ‘Researcher Co-I’ on BBSRC responsive mode grant (different subject)

Application StageMaking Multiple Applications

Address Remit Direct your proposal towards the funder’s remit

BBSRC: basic biology, complete independence (PI), 3-year postdoc MRC: medical emphasis, strong training/career development component Wellcome: technician for 5 years, previously had to have HoD as PI EPSRC: steer clear of biological outputs (stick to technology only) Royal Society: two FRS’s strongly supporting application, no support grant.

Remit is strictly based on the research outputs (‘deliverables’) of your

project (not the methodology and techniques applied)

Be flexible, rewrite application to take account of funding available, in

particular in justifying your costs

Advantages Spreads the risk of hitting a referee with strong negative bias Not always clear in advance of submission which funder is most

appropriate

Application StageWriting Applications

Writing the proposal Steep learning curve, very time-consuming (2-3 months) Sole PI, so responsible for all aspects of the proposal: financial,

planning, scientific Very good practice for later PI grant applications!

Costing the proposal Costing may feel rather abstract on the application, but you will

appreciate careful costing if you get the fellowship. Acquire a working knowledge of Full Economic Costing (fEC) The headline cost can be big: >£1 million for BBSRC DP Fellowship –

but 30%+ goes direct to Faculty under fEC… Request costs at the upper limit allowed if you can justify them for the

proposed work. You can usually move cash around later (within limits!)

Application StageGeneral Tips

Create a career narrative Justify your career choices (in hindsight) Highlight why you are ready to go independent

Fellowship proposals vs. grant proposals An original, cutting-edge idea can carry more weight than a strong

track record (esp. when compared to standard grants) You can get away with having (much) less preliminary data Interdisciplinary research may fare better in fellowship

applications than in standard grant applications.

Salary level Most funders don’t fix the level arbitrarily You don’t usually need to justify your own salary level

Some more things to think about… Scientific merit – external peer review (it is a grant proposal!) Address important questions – originality, fresh thinking Has to be feasible – you have to convince the referees that you

are capable of doing the work proposed, in the time available Show them that you have considered the riskier elements, and

propose contingency plans; don’t have the whole project dependent on a risky proposition

Mention preliminary data if you have it – I would say this is not absolutely essential, but you do need to be able to convince the referees that the riskier aspects could work

Know your competition in the scientific field – cite the key work of others in your background section

Cheaper proposals do not mean more chance of success; but high-cost proposals where costs are not justified will also not impress.

Application StageWriting Applications

Application StageStay or Go?

• Stay… Access to existing equipment and collaborations Minimal start-up time Can you achieve independence?

• In either case…• Ensure your expectations (support, space, teaching etc.) are understood

by host institute• Be prepared to justify choice of institute in the application and at interview• Be prepared for questions regarding future independence if you decide to

stay

• Or go? Start afresh on your own terms Will take time to get started• May help to get out of the ‘golden triangle’…

Interview StageSome suggestions

Presentation Practise in front of a diverse audience Keep it simple!

Interview BBSRC interview is very brief (20min), and (relatively) friendly. Interviews for other funders can be more intense… Be prepared for questions on: Past career choices How will a fellowship benefit you and your research? Minimal teaching, independence, opportunity to apply for

further grants during fellowship. How will you achieve independence? Where do you see yourself in 5 years, 10 years… Permanent position in academia, leader of a vibrant research

group

Award StageChallenges and Benefits

Benefits Minimal teaching load (vs. lectureship) = Time to set up collaborations, supervise research, write new grants… Support from BBSRC Once in post, be pro-active in applying for further funding:

From October: 14 (3 PDRAs, 9 PhD + 2 UG research students) Over £1 million in PI research income (+ £1 million fellowship)

Challenges Making the transition from PDRA to PI

Managing & applying for grants, recruitment Supervising a group on your own Dealing with internal departmental politics

You only have a few years to find a permanent position! Start looking after 1-2 years May entail a move to another institute Consider whether fellows have routinely been taken on permanently at the

host department/institute

Acknowledgements

JemimaGillianTamTook

PinarAlexLucy

Postgraduate Students (PhD and MRes)

Will Sasala

Postdoctoral Researchers

James Camille

Undergraduate Students