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RNA Structure Determination Using SAXS Data

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Department of Biochemistry and Molecular Biology, 929 East 57th Street, University of Chicago, Chicago, Illinois 60637, and Institute for Research in Immunology and Cancer and Department of Computer Science and Operations Research, University of Montreal, Montreal, Canada
* To whom correspondence should be addressed. E-mail: F.M., [email protected]; B.R., [email protected]
†University of Chicago.
‡University of Montreal.
Cite this: J. Phys. Chem. B 2010, 114, 31, 10039–10048
Publication Date (Web):July 21, 2010
https://doi.org/10.1021/jp1057308
Copyright © 2010 American Chemical Society
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Abstract

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Exploiting the experimental information from small-angle X-ray solution scattering (SAXS) in conjunction with structure prediction algorithms can be advantageous in the case of ribonucleic acids (RNA), where global restraints on the 3D fold are often lacking. Traditional usage of SAXS data often starts by attempting to reconstruct the molecular shape ab initio, which is subsequently used to assess the quality of a model. Here, an alternative strategy is explored whereby the models from a very large decoy set are directly sorted according to their fit to the SAXS data. For rapid computation of SAXS patterns, the method developed here makes use of a coarse-grained representation of RNA. It also accounts for the explicit treatment of the contribution to the scattering of water molecules and ions surrounding the RNA. The method, called Fast-SAXS-RNA, is first calibrated using a tRNA (tRNA-val) and then tested on the P4−P6 fragment of group I intron (P4−P6). Fast-SAXS-RNA is then used as a filter for decoy models generated by the MC-Fold and MC-Sym pipeline, a suite of RNA 3D all-atom structure algorithms that encode and exploit RNA 3D architectural principles. The ability of Fast-SAXS-RNA to discriminate native folds is tested against three widely used RNA molecules in molecular modeling benchmarks: the tRNA, the P4−P6, and a synthetic hairpin suspected to assemble into a homodimer. For each molecule, a large pool of decoys are generated, scored, and ranked using Fast-SAXS-RNA. The method is able to identify low-rmsd models among top ranking structures, for both tRNA and P4−P6. For the hairpin, the approach correctly identifies the dimeric state as the solution structure over the monomeric state and alternative secondary structures. The method offers a powerful strategy for recognizing native RNA conformations as well as multimeric assemblies and alternative secondary structures, thus enabling high-throughput RNA structure determination using SAXS data.

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List of parameters for the RNA dimer decoy sets. Figures showing SAXS scattering profiles, conformations of tRNA, P4−P6, and the RNA dimer, and Rg vs rmsd. This material is available free of charge via the Internet at http://pubs.acs.org/.

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