Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops

0394830 - BFÚ 2014 RIV US eng J - Článek v odborném periodiku
Krepl, Miroslav - Réblová, K. - Koča, J. - Šponer, Jiří
Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops.
Journal of Physical Chemistry B. Roč. 117, č. 18 (2013), s. 5540-5555. ISSN 1520-6106. E-ISSN 1520-5207
Grant CEP: GA ČR(CZ) GBP305/12/G034
Grant ostatní: GA MŠk(CZ) ED1.1.00/02.0068
Program: ED
Institucionální podpora: RVO:68081707
Klíčová slova: PARTICLE MESH EWALD * ION-BINDING SITES * A-MINOR MOTIF
Kód oboru RIV: BO - Biofyzika
Impakt faktor: 3.377, rok: 2013

The L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop, and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 mu s of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has an unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. Our analysis suggests that the anti orientation might be a mis-refinement, although even the anti interaction would be compatible with the sequence pattern and observed tertiary interaction.
Trvalý link: http://hdl.handle.net/11104/0223003