Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 117, Issue 11, Pages 3135-3144Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp400751w
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Funding
- Robert A. Welch Foundation [F-1691]
- Tera-Grid/XSEDE [TG-MCB100057]
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RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen-bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 A of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model was able to characterize the complex tertiary structures of large size RNAs, such as SS ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg2+ cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.
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