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India-UK workshop on "Trends in protein biophysics: from in silico molecules to in vivo and vitro proteins"

Tuesday 17th – Thursday 19th May 2011

Department of Physics and MOAC research centre and DTC, University of Warwick

Organiser: R.A. Römer (Physics, Warwick), S. Vishveshwara (Molecular BioPhysics, IISc Bangalore)

Local organizers: R. Freedman, J.E. Jimenez, J. Heal, S.A. Wells

Conference email:

[Sponsored by funds from the Royal Society]


Background and Purpose

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, to 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, including X-ray or neutron crystal structure determination, at atomic resolution, of molecules caught in different conformational states; NMR structure determination, at atomic resolution, of an ensemble of structures existing in solution; FRET techniques which probe the distribution of distances between two or more probe molecules, tethered to a protein; also single-molecule FRET, IR spectroscopy, biochemical probes (cross-linking), mass spectrometry, etc.

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. The most detailed molecular dynamics methods typically require CPU-weeks or even months to probe motion on a timescale of nanoseconds, making it difficult to relate MD directly to biologically relevant functional motion on timescales of microseconds or slower. Other methods in use include elastic network modelling, rigidity analysis with simulation of flexible motion, coarse-grained MD (e.g. GO, FIRST, FRODA, 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 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. Often each of these techniques performs well under certain conditions and less well under other conditions. This is true both for the experimental as well as computational techniques. Still, 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 meso-scale models seems not only feasible, but quickly becomes a necessity. Turning this necessity into reality is what our workshop is about.



This is a nearly complete programme (130511).

Time Title Speaker
Tuesday, May 17th, 2011
09:00-10:00 Registration  
Morning Chair: Robert Freedman
10:00-10:45 Rapid simulation of protein functional motion Stephen A Wells
10:45-11:30 Probing allosteric communication through protein structure networks and essential dynamics Saraswathi Vishveshwara
11:30-12:00 Scientific Speed Dating all participants
12:00-14:00 Lunch Break  
Afternoon Chair: Stephen Wells
14:00-14:45 Nested Sampling and more David Wild
14:45-15:30 Genome scale Comparison of ligand binding sites in protein structures: Algorithms and application for drug discovery Nagasuma Chandra
15:30-16:00 Tea Break  
16:00-16:30 Simulating large amplitude protein motion using normal mode and rigidity analysis Emilio Jimenez
16:30-17:00 Protein Unfolding Under Force: Crack Propagation in a Network Gareth Shannon
17:00-18:00 Panel discussion: what does it mean to model a protein? Chandra, Cole, Dixon, Freedman, Harris, Vishweshwara
18:00 something to eat  
Wednesday, May 18th, 2011
Morning Chair: Rebecca Notmann
09:00-09:45 Applications of MD Simulations for exploring conformational flexibility and substrate specificity of enzymes from natural product biosynthetic pathways Debasish Mohanty
09:45-10:30 Structural and Dynamics Properties of Biopolymers in Solution: Insights from Molecular Dynamics Simulations and Fluorescence Spectroscopy Danilo Roccatano
10:30-11:15 Coffee Break  
11:15-12:00 Flexible peptide ligands in target recognition: Molecular dynamics simulations of GPCR peptide hormones and BH3 peptides Ramasubbu Sankararamakrishnan
12:00-14:00 Lunch Break  
13:30-14:00 Discussion of possible funding opportunities between India and the UK everyone interested
Afternoon Chair: Saraswathi Vishveshwara
14:00-14:45 Probing conformational changes by means of ion mobility mass spectrometry Konstantinos Thalassinos
14:45-15:30 Mapping protein flexibility through crystallographic refinement and Normal Mode Analysis Shekhar Mande
15:30-16:00 Tea Break  
16:00-16:45 Simulations and experiment support role of loop in liver alcohol dehydrogenase as a NAD+-activated switch for domain closure Steven Hayward
16:45-17:30 Modelling Conformational Transitions with FIRST/FRODA William Belfield
17:30-18:00 Poster session  
18:00 something to eat (BBQ, let's hope for a bit of sunshine)  
Thursday, May 19th, 2011
Morning Chair: Steven Hayward
09:00-09:45 Atomistic modelling of Biomolecules using Molecular Dynamics Sarah A Harris
09:45-10:30 Biomolecular Simulation with ONETEP Daniel Cole
10:30-11:15 Cofee Break  
11:15-12:00 Atomistic to Coarse-Grained Simulations of Biomolecules Rebecca Notmann
12:00-14:00 Lunch Break  
13:30-14:00 Discussion of possible funding opportunities between India and the UK everyone interested
Afternoon Chair: Konstantinos Thalassinos
14:00-14:45 Milestones in a protein’s lifetime: Atomistic simulation of force-induced unfolding Phil Williams
14:45-15:30 Structure-Dynamics of yeast protein disulfide isomerase PDI: insights from MD simulation Moitrayee Bhattacharyya
15:30-16:00 Tea Break and Farewell  



Participation is by invitation only. Please contact if you think this workshop is interesting. Normally, we would be happy to accept self-invitations, but will not be able to pay for any expenses in this case.

The symposium will start May 17th, 2011, at 09:30am at the University of Warwick. Note that the university is located at the outskirts of Coventry and not in Warwick. See for travel details and for maps of the central campus. In case you come by car, parking is available for delegates at car park 15.

This list of participants is accurate as of April 20th, 2011, 14:46 BST.

Name Affiliation Status
1 Robert Baldock Cambridge 17-19 May
2 Moitrayee Bhattacharyya IISC Bangalore 16-20 May
3 William Belfield Cambridge 17-19 May
4 Claudia Blindauer Warwick 17-19 May
5 Nikolas Burkoff Warwick 17-19 May
  Nagasuma Chandra IISc Bangalore 16-20 May
  Daniel Cole Cambridge 17-19 May
  Ann Dixon Warwick 17-19 May
  Robert B. Freedman Warwick 17-19 May
10 Sarah Anne Harris Leeds 17-19 May
  Steven Hayward Norwich 17-19 May
  Jack W. Heal Warwick 17-18 May
  J. Emilio Jimenez Warwick 17-19 May
  Greg Lever Cambridge 17-19 May
15 Shekhar Menda Hyderabad 16-20 May
  Debasish Mohanty New Delhi 16-20 May
  Rebecca Notman Warwick 18-19 May
  Mike Payne Cambridge 19 May
  Frank Pinski Cincinnati 17-19 May
20 Danilo Roccatano Bremen 17-19 May
  Rudolf A. Römer Warwick 17-19 May
  Sanakaramakrishnan IIT Kanpur 16-20 May
  Gareth Shannon Nottingham 17-19 May
  Konstantinos Thalassinos UCL/Birkbeck 17-19 May
25 Csilla Varnai Warwick 17-19 May
  Saraswathi Vishveshwara IISs Bangalore 16-20 May
  Stephen A. Wells Warwick 17-19 May
  David Wild Warwick 17-19 May
  Phil Williams Nottingham 17-19 May


Venue and Accommodation

Registration will be held in the Seminar Room of the MOAC research centre and DTC in Coventry House. All talks will be held in the Seminar Room of the said MOAC. This is building 14 of the Warwick central campus.

The workshop will start with the registration at the University of Warwick. Note that the university is located at the outskirts of Coventry and not in Warwick. See for travel details and for maps of the central campus. In case you come by car, parking is available for delegates at car park 15.

Accommodation for invited speakers shall be provided at

Radcliffe Training & Conference Centre
The University of Warwick
Gibbet Hill Road
Coventry, CV4 7AL UK
Tel: +44 (0) 24 7647 4711
Fax: +44 (0) 24 7669 4282

In case you are self-invited, please call the conference centre directly and arrange your stay.



Prof. Rudolf A Römer
Physics Department
University of Warwick
Coventry CV4 7AL
United Kingdom

Phone: +44 (0)24 76574328
Fax: +44 (0)24 76150897

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