Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins - Inria - Institut national de recherche en sciences et technologies du numérique
Journal Articles Nucleic Acids Research Year : 2016

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.

Dates and versions

hal-01505862 , version 1 (11-04-2017)

Identifiers

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