Computational exploration of mobile ion distributions around RNA duplex

Serdal Kirmizialtin, Ron Elber

    Research output: Contribution to journalArticle

    Abstract

    Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures of monovalent and divalent ions are considered explicitly. Studies of tightly bound and of diffusive (but bound) ions around 25 base pairs RNA are conducted in explicit solvent. Replica exchange simulations provide detailed equilibrium distributions with moderate computing resources (20 ns of simulation using 64 replicas). The simulations show distinct behavior of single and double charged cations. Binding of Mg2+ ion includes tight binding to specific sites while Na+ binds only diffusively. The tight binding of Mg2+ is with a solvation shell while Na+ can bind directly to RNA. Negative mobile ions can be found near the RNA but must be assisted by proximate and mobile cations. At distances larger than 16 Å from the RNA center, a model of RNA as charged rod in a continuum of ionic solution provides quantitative description of the ion density (the same as in atomically detailed simulation). At shorter distances, the structure of RNA (and ions) has a significant impact on the pair correlation functions. Predicted binding sites of Mg2+ at the RNA surface are in accord with structures from crystallography. Electric field relaxation is investigated. The relaxation due to solution rearrangements is completed in tens of picoseconds, while the contribution of RNA tumbling continues to a few nanoseconds.

    Original languageEnglish (US)
    Pages (from-to)8207-8220
    Number of pages14
    JournalJournal of Physical Chemistry B
    Volume114
    Issue number24
    DOIs
    StatePublished - Jun 24 2010

    Fingerprint

    ion distribution
    RNA
    Ions
    ions
    replicas
    simulation
    cations
    Cations
    Positive ions
    crystallography
    solvation
    Barreling
    resources
    rods
    Crystallography
    Solvation
    Binding sites
    continuums
    electric fields
    Binding Sites

    ASJC Scopus subject areas

    • Physical and Theoretical Chemistry
    • Materials Chemistry
    • Surfaces, Coatings and Films

    Cite this

    Computational exploration of mobile ion distributions around RNA duplex. / Kirmizialtin, Serdal; Elber, Ron.

    In: Journal of Physical Chemistry B, Vol. 114, No. 24, 24.06.2010, p. 8207-8220.

    Research output: Contribution to journalArticle

    Kirmizialtin, Serdal ; Elber, Ron. / Computational exploration of mobile ion distributions around RNA duplex. In: Journal of Physical Chemistry B. 2010 ; Vol. 114, No. 24. pp. 8207-8220.
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