The ionic atmosphere around A-RNA

Poisson-Boltzmann and molecular dynamics simulations

Serdal Kirmizialtin, Alexander R.J. Silalahi, Ron Elber, Marcia O. Fenley

    Research output: Contribution to journalArticle

    Abstract

    The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg 2+ distributions are still at significant variances for shorter distances.

    Original languageEnglish (US)
    Pages (from-to)829-838
    Number of pages10
    JournalBiophysical Journal
    Volume102
    Issue number4
    DOIs
    StatePublished - Feb 22 2012

    Fingerprint

    Molecular Dynamics Simulation
    Atmosphere
    RNA
    Ions
    Strontium
    Cations
    Sodium
    Research

    ASJC Scopus subject areas

    • Biophysics

    Cite this

    The ionic atmosphere around A-RNA : Poisson-Boltzmann and molecular dynamics simulations. / Kirmizialtin, Serdal; Silalahi, Alexander R.J.; Elber, Ron; Fenley, Marcia O.

    In: Biophysical Journal, Vol. 102, No. 4, 22.02.2012, p. 829-838.

    Research output: Contribution to journalArticle

    Kirmizialtin, Serdal ; Silalahi, Alexander R.J. ; Elber, Ron ; Fenley, Marcia O. / The ionic atmosphere around A-RNA : Poisson-Boltzmann and molecular dynamics simulations. In: Biophysical Journal. 2012 ; Vol. 102, No. 4. pp. 829-838.
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