title: Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics.
abstract: The difficulty of analyzing higher order RNA structure, especially for folding intermediates and for RNAs whose functions require domains that are conformationally flexible, emphasizes the need for new approaches for modeling RNA tertiary structure accurately. Here, we report a concise approach that makes use of facile RNA structure probing experiments that are then interpreted using a computational algorithm, carefully tailored to optimize both the resolution and refinement speed for the resulting structures, without requiring user intervention. The RNA secondary structure is first established using SHAPE chemistry. We then use a sequence-directed cleavage agent, which can be placed arbitrarily in many helical motifs, to obtain high quality inter-residue distances. We interpret this in-solution chemical information using a fast, coarse grained, discrete molecular dynamics engine in which each RNA nucleotide is represented by pseudoatoms for the phosphate, ribose, and nucleobase groups. By this approach, we refine base paired positions in yeast tRNA(Asp) to 4 A rmsd without any preexisting information or assumptions about secondary or tertiary structures. This blended experimental and computational approach has the potential to yield native-like models for the diverse universe of functionally important RNAs whose structures cannot be characterized by conventional structural methods.
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
authors.forename: Costin M
authors.initials: CM
authors.lastname: Gherghe
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Leonard
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Weeks
mesh_terms: D001483:Base Sequence; D004492:Edetic Acid / Q000031:analogs & derivatives / Q000737:chemistry; D005290:Ferric Compounds / Q000737:chemistry; D005296:Ferrous Compounds / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012349:RNA, Transfer, Asp / Q000737:chemistry / Q000235:genetics
chemical_list: D005290:Ferric Compounds; D005296:Ferrous Compounds; D012349:RNA, Transfer, Asp; C055526:Fe(II)-EDTA; D012313:RNA; D004492:Edetic Acid; C019179:Fe(III)-EDTA