Počet záznamů: 1

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics

  1. 1.
    0347709 - BFU-R 2011 RIV US eng J - Článek v odborném periodiku
    Banáš, P. - Walter, N.G. - Šponer, Jiří - Otyepka, M.
    Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.
    Journal of Physical Chemistry B. Roč. 114, č. 26 (2010), s. 8701-8712 ISSN 1520-6106
    Grant CEP: GA MŠk(CZ) LC06030; GA ČR(CZ) GA203/09/1476; GA MŠk(CZ) GD203/09/H046; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) 1QS500040581
    Grant ostatní: GA MŠk(CZ) LC512
    Výzkumný záměr: CEZ:AV0Z50040507; CEZ:AV0Z50040702
    Klíčová slova: riboswitch * ribozyme * RNA structure * molecular dynamics simulations
    Kód oboru RIV: BO - Biofyzika
    Impakt faktor: 3.603, rok: 2010

    The glmS catalytic riboswitch is part of the 5’-untranslated region of mRNAs encoding glucosamine-6-phosphate (GlcN6P) synthetase (glmS) in numerous Gram-positive bacteria. Binding of the cofactor GlcN6P induces site-specific self-cleavage of the RNA. However, detailed reaction mechanism as well as protonation state of glmS reactive form remains still elusive. To probe the dominant protonation states of key active site residues, we carried out explicit solvent molecular dynamic simulations involving various protonation states of three crucial active site moieties observed in the available crystal structures: (i) guanine G40 (following the T. tengcongensis numbering), (ii) the GlcN6P amino/ammonium group, and (iii) the GlcN6P phosphate moiety.
    Trvalý link: http://hdl.handle.net/11104/0006029