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Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics
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SYSNO ASEP 0347709 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics Author(s) Banáš, P. (CZ)
Walter, N.G. (US)
Šponer, Jiří (BFU-R) RID, ORCID
Otyepka, M. (CZ)Number of authors 4 Source Title Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 114, č. 26 (2010), s. 8701-8712Number of pages 12 s. Language eng - English Country US - United States Keywords riboswitch ; ribozyme ; RNA structure ; molecular dynamics simulations Subject RIV BO - Biophysics R&D Projects LC06030 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GA203/09/1476 GA ČR - Czech Science Foundation (CSF) GD203/09/H046 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) IAA400040802 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) 1QS500040581 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) CEZ AV0Z50040507 - BFU-R (2005-2011) AV0Z50040702 - BFU-R (2007-2013) UT WOS 000279282600015 DOI 10.1021/jp9109699 Annotation 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. Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2011
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