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IAS 11/12 No:


Please refer to the Guidance Notesfor this programme before completing this application form. If in doubt about the suitability of this programme for your project, please check before filing an application with the IAS Director, Hilary Marland at Questions about allowable costs, the application form or the selection process should be directed to The deadline for receipt of application forms is 12 noon Wednesday 1 June 2011.

Part 1 Cover Sheet

Name and Title of Principal Investigator (PI):

Rudolf A Roemer, Prof

Department/Unit, Telephone and Email of PI:

Status of PI:

 Permanent Academic Other (please specify)

Name and Title of 1stCo-Investigator (CI):

David Wild, Prof
Department/Unit, Telephone and Email of 1st CI:
System Biology

Status of 1st CI:

 Permanent Academic Other (please specify)

Name and Title of 2ndCo-Investigator, if any:

Vilmos Fulop, Prof

Department/Unit and Email of 2nd CI:

Life Sciences

Status of 2nd CI:

 Permanent Academic Contract Research Staff (state end of contract period)
 Other (please specify)

Name and Title of 3rdCo-Investigator, if any:

Ann Dixon, Associate Prof.

Department/Unit and Email of 3rd CI:


Status of 3rd CI:

 Permanent Academic Contract Research Staff (state end of contract period)
 Other (please specify)

Descriptive Title of Project (25 words maximum):

Protein Biology and Biophysics Network (PBBPNet)

Previous applications made for this project, or a version thereof:

- Royal Society (UK) and Department of Science and Technology (India) funded India-UK workshop on "Trends in protein biophysics: from in silico molecules to in vivo and vitro proteins", 17-19 May 2011

Total amount of funding requested from the IAS:


Proposed Dates:

Start Date

1stAugust 2011

End Date

20thJuly 2011

Signature of Principal Investigator

Date Tuesday, 13 September 2011

Part 2 PROJECT DESCRIPTION and methodology statement (500 words maximum)

This proposal asks support for the formation of a “Protein Biology and Biophysics” network at Warwick to bring together a critical mass of researchers who are currently distributed among 5 departments.

The function of biomolecules (proteins) is determined by their structures, and the capacity for flexible motion that is intrinsic to those structures. Dynamic events span across different layers of hierarchy in biological organization – from electronic distribution at one end of the spectrum to population dynamics at the other end. They also happen at multiple time scales - from picoseconds for small conformational changes in protein molecules, milliseconds in protein-ligand binding, to seconds to achieve biochemical homeostasis, and days to years for larger phenotypic changes. Ultimately, mechanistic insights of the various dynamic events are crucial for understanding biological function.

Protein mobility can now be experimentally investigated by a number of means which probe a very wide range of timescales and resolutions. These include high resolution methods such as X-ray and neutron diffraction, high field nuclear magnetic resonance spectroscopy, and mass spectrometry where atomic level resolution of mass and structures can be obtained for single molecules caught in different conformational states or an averaged ensemble of molecules over longer timescales. Lower resolution methods such as FRET, IR spectroscopy, and biochemical probes (cross-linking) can also provide valuable information. A similarly wide range of timescales and resolutions can be probed in silico, with in general a trade-off between the level of detail in a simulation and the timescale or amplitude of motion that can be probed at a given computational expense – ranging from CPU-weeks or even months (for MD) to minutes for elastic network modelling, rigidity analysis, etc. Simulations have become the approach of choice to predict structures of biomolecules and their assemblies, dynamics, energetics, molecular recognition, biochemical reactivity. In recent years they have also been increasingly explored to study the dynamics of biochemical pathways and larger cellular networks.

This surge of new computational and experimental advancements in the field of structural biology has brought new tools for scientists to inquire into the nature of protein structure and their dynamics. At this point in time the techniques start to overlap significantly in their respective ranges of validity and a combined approach across different ranges, from the atomistic, to the molecular and on to coarse-grained and the meso-scale seems not only feasible, but quickly becomes a necessity. Here in Warwick, we have the critical mass of researchers and relevant expertise in nearly all techniques. Hence turning this necessity into reality at Warwick is what our network is about.

The goal of our proposal is therefore to establish a Warwick-internal network of researchers from Life Sciences, Systems Biology, Chemistry and Physics in which we combine our different methods and strengths in protein biology and biophysics. In addition, we recently participated in a UK-India workshop on “Trends in Protein Biophysics”, May 17-19 2011. This was instrumental in forming a core set of people interested in driving the network forward with the clear aim of also establishing long term, funded research collaborations with our Indian colleagues(see a list of participants).

Research groups participating in the proposed network in addition to the PI/CIs are those of C Blindauer (C), T Bretschneider (SB), S Brown (P), R Cross (MS), R Freedman (LS), R Notman (CSC/C), P O’Connor (C), T Pinheiro (LS), C Robinson (LS), A Rodger (MOAC/C), J Scrivens (LS), C Smith (LS), M Turner (P), S Wells (P). In total, this amounts to about 50 PGR students, PDRA and academics at Warwick.

Part 3 outputs statement (200 words maximum), including proposed funding applications

In order to drive this project forward, we intend to

(i) establish a series of monthly research get-togethers (at least 2 hours with 2-3 30 minute presentations and themed discussion panels) among the 5 involved departments,
(ii) hold two all-hands workshops (Sep 2011, Mar 20) and
(iii) form leadership teams tasked with writing the main parts of 3 international and 1 national network grant proposals.

Outputs (i) and (ii) are necessary during the award to forge and solidify the group of Warwick researchers indentified in the recent workshop and to include the members of their respective research groups. It will also be particularly useful for PG and PDRA training. Output (iii) is the intermediate goal of the network and already at the RS India-UK conference, we identified (a) International Networks – Leverhulme Trust, (b) India Partnering Awards – BBSRC, (c) Initial Training Networks – Marie Curie (FP7) as possible funding routes for the collaboration with India and (d) Network grants – EPSRC for a UK-only network. We intend to explore funding options for all 4 of these and write at least two such applications. This will then seamlessly lead to further outputs after the award, including additionally of course research outputs such as joint publications.
PART 4 BUDGET. Indicate clearly below the amounts requested for the 2011-12 financial year. Travel and subsistence costs must be in accordance with University Financial Regulations ( All invoices, receipts, etc must be returned/posted by the end of July 2012. Funds cannot be rolled over into 2012-13. Itemise both the source and amount of any additional income (department/research centre/other). It is expected that any overspend will be covered by the department concerned.
Research assistance (see Guidance Notes):

Travel and subsistence:

£500 for 5 key non-Warwick UK speakers to attend the all-hands workshops
Meeting accommodation:

£800=£80*5*2 for accommodation of 5 non-Warwick UK speakers

£2650= 11*30*£5+2*50*£10=£1650+£1000 for 11 monthly meetings and 2 all-hands meetings
Other (itemise):

Total Cost of Project:

Source and Amount of Additional Income:



I support the bid; I agree that any overspend will be covered by my department; I agree to provide necessary facilities; I confirm that the project would not entail a significant increase in use of any University services and that any health and safety and ethical requirements would be covered.

Name ..………………………………………………. Department …………………> ………………..

Signed ……..……………………………………….. Date ……………………………> ………………

I approve the costing of this proposal (DEPARTMENTAL ADMINISTRATOR)

Name ..……………………………………………….

Signed ……………………………………………… Date ……………………………………d ………

N.B. Please ensure that the proposal conforms to the criteria set out in the Guidance notes. The Chair of Department’s declaration and submission also confirms that if the proposal is successful any departmental resources specified in the application will be provided in support of the project. Budgetary evidence of such provision will be required for successful applications in the end of award report.

Please submit this form to: withIncub11 [+PI’s Surname and Department] as the subject of the email. Applications should be submitted electronicallyas EITHERi)a signed PDF, ORii)a Microsoft Word document anda signed copy posted in the internal mail to: Institute of Advanced Study, Millburn House.

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