Evidence map›Paper›PMID 27631837›Full record

ArticleThe journal of physical chemistry letters2016

NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.

Xiaobo Gu, Sun-Young Park, Marco Tonelli, Gabriel Cornilescu, Tianbing Xia, Dongping Zhong, Susan J Schroeder

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The journal of physical chemistry letters, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Xiaobo GuDepartment of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.
Sun-Young ParkDepartment of Physics, Ohio State University , Columbus, Ohio 43210, United States.
Marco TonelliNMRFAM, University of Wisconsin , Madison, Wisconsin 53706, United States.
Gabriel CornilescuNMRFAM, University of Wisconsin , Madison, Wisconsin 53706, United States.
Tianbing XiaDepartment of Molecular and Cell Biology, University of Texas , Dallas, Texas 75080, United States.
Dongping ZhongDepartment of Physics, Ohio State University , Columbus, Ohio 43210, United States.
Susan J SchroederDepartment of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.

Funding

TR&D 3: TECHNOLOGY DEVELOPMENT FOR NMR STUDIES OF SMALL MOLECULES (METABOLOMICS, NATURAL PRODUCTS, METABOLITE-PROTEIN INTERACTIONS) pp.537-585 P41GM103399 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI BUTCHER, SAMUEL E · 2012 to 2019
$9.4M
Integrated state-of-the-art LC-MS/NMR system for the University of WisconsinS10RR025062 · NCRR · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 2008 to 2008
$1.7M
Dynamics and Mechanism of Water-Protein InteractionsR01GM095997 · NIGMS · OHIO STATE UNIVERSITY · PI ZHONG, DONGPING · 2011 to 2014
$1.1M
Upgrade of the NMRFAM 750 MHz NMR SpectrometerS10RR029220 · NCRR · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 2010 to 2010
$766k
NMR Spectrometer System Optimized for Direct 13C or 15N DetectionS10RR023438 · NCRR · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 2008 to 2008
$500k
CONSOLE UPGRADES FOR NMR FACILITYS10RR008438 · NCRR · UNIVERSITY OF WISCONSIN MADISON · PI MARKLEY, JOHN L · 1993 to 1993
–
WIDE-BORE 9.4 TESLA NMR SPECTROMETER FOR UW-MADISONS10RR002781 · NCRR · UNIVERSITY OF WISCONSIN MADISON · PI MARKLEY, JOHN L · 1986 to 1986
–
NCRR NIH HHS S10 RR002781NCRR NIH HHS S10 RR008438NCRR NIH HHS S10 RR023438NCRR NIH HHS S10 RR025062NCRR NIH HHS S10 RR029220NIGMS NIH HHS P41 GM103399NIGMS NIH HHS R01 GM095997
6 · The paper itself

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.

Indexed as

Bacillus PhagesHydrogen BondingIonsMagnetic Resonance SpectroscopyMetalsNucleic Acid ConformationRNA, ViralSpectrometry, FluorescenceIonsMetalsRNA, Viral

Identifiers

PMID27631837
PMCPMC5762182

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.