Timetable of Tasks, Deliverables and Milestones for the first 18 months:

8.2 Planning and timetable - Gantt chart showing the timed plan for each workpackage, with deliverables and milestones

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
2.1 Protein production                                    
2.1.1 Develop  multi-high  throughput  expression  systems                                    
2.1.2 Develop cyanobacterial expression system for NMR                                    
2.1.3 Purification strategies for protein complexes                                    
2.1.4 Optimised  refolding  for  proteins in inclusion bodies                                    
D2.1.1 Co-expression in several system platforms                                    
D2.1.2 Protocols for refolding and co-refolding                                    
M2.1.1 Several expression systems for protein complexes                                    
M2.1.2 Protocol for optimised refolding                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE

 

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
WP2.2 Eukaryotic model systems                                    
2.2.1 Development of model stable system in Alvinella                                    
2.2.2 Limited set of Alvinella cDNAs available to partners                                    
2.2.3 Investigate stability of complexes from C. diabolis                                    
D2.2.1 Alvinella cDNA library made available                                    
D2.2.2 Limited  set  of  expression  vectors  made  available                                    
M2.2.1 Infrastructure  establishment  for  Alvinella  cDNA                                    
M2.2.2 Delivery of first expression vectors                                    
M2.2.3 Identification  of  targets for  analysis from C. diabolis                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE

 

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
WP2.3 Library methods                                    
2.3.1 Identify soluble domains for complex reconstitution                                    
2.3.2 Develop methods to minimize size and flexibility                                    
2.3.3 Implement point mutagenesis for protein solubilisation                                    
2.3.4 Screen synthetic binding proteins as complex stabilisers                                    
2.3.5 Develop  new HTP  screens  for  soluble protein  complexes                                    
D2.3.1 Implementation of random mutagenesis                                    
D2.3.2 Development of random library and screening methods                                    
M2.3.1 Protocols for the production of protein components                                    
M2.3.2 Publication on library methodologies for complexes                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE

 

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
WP2.4 Biophysical methods                                    
2.4.1 Comparative benchmarking of biophysical methods                                    
2.4.2 Screening for conformational stability of weak complexes                                    
2.4.3 Biophysical characterisation of complex formation                                    
2.4.4 In vivo complex characterisation                                    
2.4.5 Provide access to microfluidics crystallization platform                                    
2.4.6 Hybrid methods for the determination of structures                                    
D2.4.1 Delivery of stabilization screens                                    
D2.4.2 Established  protocols for  in vivo  complex characterisation                                    
D2.4.3 Systematic protocol for hybrid structure determination                                    
D2.4.4 Evaluation of biophysical methods                                    
M2.4.1 Proof-of-principle of limited proteolysis protocols                                    
M2.4.2 Benchmarking screen                                    
M2.4.3 Protocol for in vivo complex determination                                    
M2.4.4 An operating cryoEM protocol                                    
M2.4.5 Uptake of microfluidic crystallization technology                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE

 

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
WP2.5 X-ray technologies                                    
2.5.1 Development of precision sample positioning                                    
2.5.2 Development of software and hardware for HTP screens                                    
2.5.3 Provision of dehumidifier at a synchrotron beam-line                                    
D2.5.1 Micron-sized X-ray beam on a beam-line                                    
D2.5.2 First device minimising drift and vibration at the sample                                    
D2.5.3 Development of protocols for comparative crystal screens                                    
D2.5.4 Maintenance of unfrozen crystal in controlled environment                                    
M2.5.1 Strategic plan to solve drift and vibration problems                                    
M2.5.2 Control software; error <100nm at 1Hz feedback frequency                                    
M2.5.3 Interim report on comparative screening of complex crystals                                    
M2.5.4 Controlled delivery of <nanolitre drops on mounted crystals                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE

 

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
WP2.6 NMR technology                                    
2.6.1 NMR technology for protein-protein interface analysis                                    
2.6.2 Methods using paramagnetic ions for protein complexes                                    
2.6.3 Software development for protein-protein docking                                    
D2.6.1 NMR pulse sequences fro heteronuclear signal detection                                    
D2.6.2 Improved scoring functions for protein docking solutions                                    
D2.6.3 Bioinformatics tools for interface predictions                                    
D2.6.4 New HADDOCK version for flexible regions                                    
D2.6.5 NMR pulse sequences for paramagnetic constraints                                    
M2.6.1 NMR methodology for protein-protein interface mapping                                    
M2.6.2 Demonstration of improved software for protein docking                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE

 

Task Description 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
WP2.7 LIMS, data management and bioinformatics                                    
2.7.1 Extension of data model for protein complexes                                    
2.7.2 Integration of target selection tools                                    
2.7.3 Implementation of web service                                    
2.7.4 Analysis of multiple sequences using PipeAlign                                    
2.7.5 Extension of data model for complex bioinformatics data                                         
2.7.6 Development of LIMS compatible bioinformatics                                    
D2.7.1 Extended protein production data model for complexes                                    
D2.7.2 Integrated tools for target selection                                    
D2.7.3 Web services for LIMS                                    
D2.7.4 Extended data model for bioinformatics                                    
M2.7.1 Extended protein production data model                                    
M2.7.2 Functional web services for LIMS                                    
M2.7.3 Bioinformatics platform available to members                                    

  ACTIVITY PERIOD   TASK ACTIVITY   DELIVERABLES DUE   MILESTONE