title: RNA 3D structure prediction by using a coarse-grained model and experimental data.
abstract: 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 Å 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 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg(2+) 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.
authors: Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States.
authors: Zhen
authors: Z
authors: Xia
authors: David R
authors: DR
authors: Bell
authors: Yue
authors: Y
authors: Shi
authors: Pengyu
authors: P
authors: Ren
mesh_terms: D006860:Hydrogen Bonding; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry; D012342:RNA, Small Nuclear / Q000737:chemistry; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000737:chemistry; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D012341:RNA, Ribosomal, 5S; D012342:RNA, Small Nuclear; D017413:Ribonucleoprotein, U2 Small Nuclear; C405486:U6 small nuclear RNA; D012313:RNA