Oct 6, 2015

3D RNA from evolutionary couplings

BioRxiv : the Preprint Server for Biology
Caleb WeinrebDebora S Marks

Abstract

Non-protein-coding RNAs are ubiquitous in cell physiology, with a diverse repertoire of known functions. In fact, the majority of the eukaryotic genome does not code for proteins, and thousands of conserved long non-protein-coding RNAs of currently unkown function have been identified. When available, knowledge of their 3D structure is very helpful in elucidating the function of these RNAs. However, despite some outstanding structure elucidation of RNAs using X-ray crystallography, NMR and cryoEM, learning RNA 3D structures remains low-throughput. RNA structure prediction in silico is a promising alternative approach and works well for double-helical stems, but full 3D structure determination requires tertiary contacts outside of secondary structures that are difficult to infer from sequence information. Here, based only on information from RNA multiple sequence alignments, we use a global statistical sequence probability model of co-variation in a pairs of nucleotide positions to detect 3D contacts, in analogy to recently developed breakthrough methods for computational protein folding. In blinded tests on 22 known RNA structures ranging in size from 65 to 1800 nucleotides, the predicted contacts matched physical nucleotide in...Continue Reading

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Mentioned in this Paper

Molecular Dynamics
Positioning Attribute
Size
Cellular Process
Genome
RNA, Untranslated
Three-dimensional
Riboswitch
AS 6
Determination Aspects

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