Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking

Abstract

RNA-protein complexes underlie numerous cellular processes including translation, splicing, and posttranscriptional regulation of gene expression. The structures of these complexes are crucial to their functions but often elude high-resolution structure determination. Computational methods are needed that can integrate low-resolution data for RNA-protein complexes while modeling de novo the large conformational changes of RNA components upon complex formation. To address this challenge, we describe a Rosetta method called RNP-denovo to simultaneously fold and dock RNA to a protein surface. On a benchmark set of structurally diverse RNA-protein complexes that are not solvable with prior strategies, this fold-and-dock method consistently sampled native-like structures with better than nucleotide resolution. We revisited three past blind modeling challenges in which previous methods gave poor results:human telomerase, an RNA methyltransferase with a ribosomal RNA domain, and the spliceosome. When coupled with the same sparse FRET, cross-linking, and functional data used in previous work, RNP-denovo gave models with significantly improved accuracy. These results open a route to computationally modeling global folds of RNA-protein complexes from low-resolution data.

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

“…During this stage, the proteins are treated as rigid bodies. Each conformation is scored with the low-resolution RNA-protein potential in Rosetta [54], augmented by the “elec_dens_fast” score term, which scores the agreement between the map and model [55].…”

Macromolecular modeling and design in Rosetta: recent methods and frameworks

“…The fragment assembly protocol also supports modeling RNA-protein complexes through simultaneous folding and docking 143 . RNA-protein interactions are handled via additional knowledge-based score terms that supplement the low-resolution RNA scorefunction.…”

Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals

“…To further reveal the mechanisms responsible for the sequence-and structureselective recognition and methylation of mRNA substrates, we sought to use Rosetta comparative modelling [26], reporter assay and RNP-denovo [27] to model NSUN6-RNA complex structures in multiple species and identify residues responsible for NSUN6-RNA interaction.…”

“…CC-BY-NC-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted October 4, 2020. ; https://doi.org/10.1101/2020.10.03.324707 doi: bioRxiv preprint 8 comparative modelling [26], reporter assay and RNP-denovo [27] to model NSUN6-RNA complex structures in multiple species and identify residues responsible for NSUN6-RNA interaction.…”