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The European High Performance Computing Joint Undertaking (EuroHPC JU)

Cryo-EM ensemble refinement with molecular dynamics enables the structural characterisation of flexible RNAs

Awarded Resources (in node hours)
Leonardo Booster
System Partition
4 March 2024 - 3 March 2025
Allocation Period

RNA molecules span a great variety of biological functions, from genetic information storage to catalysis. This is possible thanks to the highly heterogeneous conformational ensembles that these molecules can adopt. The advent of the single particle cryo-electron microscopy (cryo-EM) technique enables to access large and highly flexible RNA macromolecules at near atomic-level resolution, thus allowing to fully assess their structural and functional features.

Still, given that standard refinement tools assume that all the collected images are associated to a single structure, the most mobile regions are very challenging to solve. The project aim is to tackle these problems by integration of molecular dynamics simulations and experimental density maps, using as a test case a group IIB intron ribozyme. This molecule is not only one of the first large RNA macromolecules resolved with cryo-EM but, in addition, displays biochemical inconsistencies (e.g., incorrect base pairing) in the deposited structure (PDB: 6ME0) that has been obtained with standard refinement approaches.

The integration will be done by combining metainference-based ensemble refinement, here used for the first time on an RNA system, and biochemically informed conformational restraints.