Project

MSCA-ITN RNAct - Enabling proteins with RNA recognition motifs for synthetic biology and bio-analytics

Goal: RNAct is a EU-MSCA ITN project (grant agreement no. 813239) with as research aim the design of novel RNA recognition motif (RRM) proteins for exploitation in synthetic biology and bio-analytics. This is achieved through a design cycle that starts with computational approaches at the sequence and structure levels of proteins and RNA, in order to select amino acid positions and mutations for large-scale phage display experiments with RNA screening. Viable RRMs will be further investigated at the atomic level with integrative structural biology approaches,and will be applied in synthetic biology, to post-transcriptionally regulate fatty acid processing via RRMs, and in bio-analytics to detect RNA in-cell and design RNA biochips.

For further information, please visit http://www.rnact.eu .

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Project log

Wim Vranken
added an update
Resolving how proteins and RNA interact remains a key challenge in biology, as well as for understanding many diseases. In the RNAct MSCA-ITN final conference on 14-15 September 2022 in Valencia, Spain, we show the results of our project and focus on how proteins bind RNA, and how we can use that knowledge to tailor RNA binding proteins for synthetic biology and biosensor development. Protein-RNA interactions are essential - we invite you to participate in this conference to discuss how to further address this challenge. Registration is still open, and the keynote speakers are now finalised, see http://rnact.eu/FinalConference/.
 
Anna Kravchenko
added a research item
New strategy for optimizing docking parameters: application to single-stranded RNA-protein docking Abstract Docking is the computational prediction of the 3D structure of a molecular complex. A fragment-based approach [1] can tackle highly flexible ligands, like single-stranded RNA bound to a protein, by splitting the ligand into overlapping fragments. These fragments are docked separately onto the protein, then the resulting poses are assembled back into the full ligand. For successful docking, at least one correct pose per fragment must be generated. This is performed by energy minimization from random positions, with a differentiable energy function [2] depending on pairwise atom-atom distances. Its parameters must be optimized on complexes with experimentally known 3D structures. We propose a histogram-based optimization approach, where the energy function is converted into the observed frequencies of each atom-atom distance in real structures. Those are then adjusted by the ratio in correct/incorrect docking poses, and transformed back into new docking parameters, iteratively. After convergence, this procedure generates equal distributions of atom-atom distances in correct and incorrect poses, which are thus undistinguishable by atom-atom distances criteria. The number of correct poses will then have been completely optimized by atom-atom distances. Those pos Acknowledgments This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 813239.
Roswitha Dolcemascolo
added an update
We are glad to share the recent publication from our ESRs Jose Gavaldá-García and Joel Roca along with Wim Vranken aiming to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches.
 
Roswitha Dolcemascolo
added an update
We are glad to share the recent publication from our ESRs Jose Gavaldá-García and Joel Roca along with Wim Vranken focusing on protein sequence-based predictions for 27 SARS-CoV-2 proteins. All results can be found at: http://sars2.bio2byte.be/
 
Joel Roca
added an update
We are glad to announce the first version of the InteR3M, database for Interactions of RNA and RNA Recognition Motif. The database has been implemented by Hrishikesh Balaji Dhondge allowing very different queries and becoming a keypoint for the RNAct project.
 
Aitor Sánchez-Ferrero
added a project goal
RNAct is a EU-MSCA ITN project (grant agreement no. 813239) with as research aim the design of novel RNA recognition motif (RRM) proteins for exploitation in synthetic biology and bio-analytics. This is achieved through a design cycle that starts with computational approaches at the sequence and structure levels of proteins and RNA, in order to select amino acid positions and mutations for large-scale phage display experiments with RNA screening. Viable RRMs will be further investigated at the atomic level with integrative structural biology approaches,and will be applied in synthetic biology, to post-transcriptionally regulate fatty acid processing via RRMs, and in bio-analytics to detect RNA in-cell and design RNA biochips.
For further information, please visit http://www.rnact.eu .