title: Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.
abstract: A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned (13)C/(15)N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions.
authors.affiliation: Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Stelzer
authors.forename: Aaron T
authors.initials: AT
authors.lastname: Frank
authors.forename: Maximillian H
authors.initials: MH
authors.lastname: Bailor
authors.forename: Ioan
authors.initials: I
authors.lastname: Andricioaei
authors.forename: Hashim M
authors.initials: HM
authors.lastname: Al-Hashimi
mesh_terms: D001483:Base Sequence; D002247:Carbon Isotopes / Q000737:chemistry; D015497:HIV-1 / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009038:Motion; D009587:Nitrogen Isotopes / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D012367:RNA, Viral; D012313:RNA
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