Work packages

Creation and characterisation of functional RRMs

Lead beneficiary: HMGU

Duration: Months 8–44

Involved ESRs: ESR3, ESR5, ESR6, ESR7, and ESR9

Objectives

1. Creating a complete and comprehensive database of available RRM information from the many available RRM data covering a broad range of behaviours

2. Enriching the RRM database with results from in silico methodologies

3. Computing binding energies based on RRM-RNA structures and models by molecular dynamics simulations

4. Determining the most suitable and critical positions for one or several RRMs for each ‘design cycle’

5. Creating RRMs certified to bind particular RNA fragments for synthetic biology and bio-analytics

6. Defining, understanding and predicting the determinants of RNA binding, with a particular focus on the interplay between the rigid elements and flexible loops of RRMs

7. Characterising the binding of single- and multi-domain model and newly computationally designed RRM with RNA at the atomic level.

8. Characterising the behaviour of RRM domains as influenced by RNA binding or small molecule binding

Representation and design of dynamic proteins

Lead beneficiary: CNRS

Duration: Months 8–44

Involved ESRs: ESR1, ESR2, ESR4, and ESR5

Objectives

1. Developing sequence-based methodology to characterize and generate RRM sequences, including their dynamics properties

2. Improving the protein structure representation for dynamic regions to connect this to the (biophysical) sequence space and existing protein design methodology

3. Improving RNA-RRM docking through fragment-based methods, with ssRNA conformational modelling included

4. Delivering computationally designed RRMs and related models of RRM-RNA complexes

5. Delivering an RRM protein design toolkit that covers sequence, biophysical space, and structure

Bio-analytics and synthetic biology

Lead beneficiary: CSIC

Duration: Months 8–44

Involved ESRs: ESR8, ESR9, and ESR10

Objectives

1. Developing synthetic circuits in bacteria based on post-transcriptional regulation

2. Measuring in vitro RRM-RNA interactions through RNA biochips

3. Designing novel RNA biochips that reflect the unique structure and sequence of RNA molecules

4. Understanding how RRMs can be allosterically modulated and determining the size and conformation of RRM-RNA complexes

5. Developing methods to monitor bacterial cell cultures to characterize the regulatory behaviour triggered by synthetic circuits

6. Developing analytical tools to characterize RNAs from intact (or lysed) cells

Training and education

Lead beneficiary: VUB

Duration: Months 8–44

Involved ESRs: All

Objectives

1. Offering tailored training on scientific and transferable skills

2. Providing ESRs with a cross-disciplinary (i.e. experimental and computational) background

3. Involving ESRs in both academic and industral environments, as well as in innovation and communication activities

Coordination and management

Lead beneficiary: VUB

Duration: Months 1–48

Objectives

1. Coordinating RNAct activities and events

2. Monitoring the progress of ESR projects

3. Organizing meetings

4. Reporting to the European Commission

5. Managing Intellectual Property Rights (IPR)

6. Managing finances and research data

Dissemination and communication

Lead beneficiary: VUB

Duration: Months 1–48+

Involved ESRs: All

Objectives

1. Disseminating research results to specialized stakeholders

2. Communicating research results and bringing the involved scientific disciplines closer to citizens

3. Organizing outreach activities

4. Publishing research results

5. Exploiting transferable results