Skip to Main content Skip to Navigation

Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

Abstract : Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein-RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA-RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins.
Complete list of metadatas

https://hal.archives-ouvertes.fr/hal-01505862
Contributor : Isaure Chauvot de Beauchene <>
Submitted on : Tuesday, April 11, 2017 - 7:24:14 PM
Last modification on : Thursday, December 14, 2017 - 2:12:02 PM

Links full text

Identifiers

Citation

Isaure Chauvot de Beauchêne, Sjoerd de Vries, Martin Zacharias. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins. Nucleic Acids Research, Oxford University Press, 2016, ⟨10.1093/nar/gkw328⟩. ⟨hal-01505862⟩

Share

Metrics

Record views

124