Abstract
We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering (SAXS) data to model low-resolution structures of particles having as many as 12 independent secondary structure elements. We assessed this model-building procedure by using both artificial data on a previously proposed benchmark and publicly available data. With the artificial data, SAXS-guided models show better similarity to native structures than ROSETTA decoys. The publicly available data showed that SAXS-guided models can be used to reinterpret RNA structures previously deposited in the Protein Data Bank. Our approach allows for fast and efficient building of de novo models of RNA using approximate secondary structures that can be readily obtained from existing bioinformatic approaches. We also offer a rigorous assessment of the resolving power of SAXS in the case of small RNA structures, along with a small multimetric benchmark of the proposed method.
Highlights
The number of functionally important RNAs of unknown structure is growing rapidly due to recent advances in transcript identification [1,2] and expression measurement [3].The processes for determining the structures of a few RNA families has developed to the point where the structures can be identified rapidly; the structures of RNAs from other families are famously difficult to solve even with state-of-art structure determination efforts [4,5]
First we propose a novel way to describe the informational complexity of an RNA structure at low resolution
Information fully describing RNA 3D structure may be captured by computing flexible torsion angles(nflex ) at high resolution [30], we use the number of junctions as the number of degrees of freedom to describe the complexity of the structure at low resolution. (Example decomposition of an RNA secondary structure into helices, loops, and junctions that form separate elements is shown on the Figure 1)
Summary
The number of functionally important RNAs of unknown structure is growing rapidly due to recent advances in transcript identification [1,2] and expression measurement [3].The processes for determining the structures of a few RNA families (ribosomal RNAs, tRNAs, and riboswitches) has developed to the point where the structures can be identified rapidly; the structures of RNAs from other families are famously difficult to solve even with state-of-art structure determination efforts [4,5]. The number of functionally important RNAs of unknown structure is growing rapidly due to recent advances in transcript identification [1,2] and expression measurement [3]. We propose a computational procedure that uses small-angle Xray solution scattering (SAXS) data to obtain low-resolution approximations of RNA structures. This process can be used as a diagnostic tool to help confirm predicted secondary structures with a higher degree of certainty than chemical footprinting approaches alone [10,11]
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