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: physics-events-pbp2011@forums.warwick.ac.uk
[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.
Programme
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 | |
Participants
Participation is by invitation only. Please contact physics-events-pbp2011@forums.warwick.ac.uk 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 http://www2.warwick.ac.uk/about/visiting/ for travel details and http://www2.warwick.ac.uk/about/visiting/maps/ 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 http://www2.warwick.ac.uk/about/visiting/ for travel details and http://www2.warwick.ac.uk/about/visiting/maps/ 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
Email: radcliffe@warwick.ac.uk
In case you are self-invited, please call the conference centre directly and arrange your stay.
Contact
Prof. Rudolf A Römer
Physics Department
University of Warwick
Coventry CV4 7AL
United Kingdom
e-mail: physics-events-pbp2011@forums.warwick.ac.uk
Phone: +44 (0)24 76574328
Fax: +44 (0)24 76150897
