title: NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.
abstract: Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.
authors.affiliation: Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Gu
authors.affiliation: Department of Physics, Ohio State University , Columbus, Ohio 43210, United States.
authors.forename: Sun-Young
authors.initials: SY
authors.lastname: Park
authors.affiliation: NMRFAM, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Marco
authors.initials: M
authors.lastname: Tonelli
authors.affiliation: NMRFAM, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Cornilescu
authors.affiliation: Department of Molecular and Cell Biology, University of Texas , Dallas, Texas 75080, United States.
authors.forename: Tianbing
authors.initials: T
authors.lastname: Xia
authors.affiliation: Department of Physics, Ohio State University , Columbus, Ohio 43210, United States.
authors.forename: Dongping
authors.initials: D
authors.lastname: Zhong
authors.affiliation: Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Schroeder
mesh_terms: D017103:Bacillus Phages / Q000235:genetics*; D006860:Hydrogen Bonding; D007477:Ions / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008670:Metals / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D013050:Spectrometry, Fluorescence
chemical_list: D007477:Ions; D008670:Metals; D012367:RNA, Viral