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Structural dynamics of the box C/D RNA Kink-Turn and its complex with proteins: The role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations

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    0347728 - BFÚ 2011 RIV US eng J - Journal Article
    Špačková, Naďa - Réblová, Kamila - Šponer, Jiří
    Structural dynamics of the box C/D RNA Kink-Turn and its complex with proteins: The role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.
    Journal of Physical Chemistry B. Roč. 114, č. 32 (2010), s. 10581-10593. ISSN 1520-6106. E-ISSN 1520-5207
    R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476
    Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
    Keywords : RNA-protein complex * molecular dynamics * kink-turn
    Subject RIV: BO - Biophysics
    Impact factor: 3.603, year: 2010

    The study is focused on investigation of Box C/D RNA Kink-Turn with two proteins: native archaeal L7ae protein and human 15.5 kDa protein. The simulations reveal structural details of the studied molecules on nanosecond time scale, i.e. structural dynamics of essential tertiary interaction within kink-turn, reduced kink-turn flexibility upon protein binding, structurally important water molecules and ion binding sites.
    Permanent Link: http://hdl.handle.net/11104/0006032

     
     
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