Počet záznamů: 1
lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop
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SYSNO ASEP 0422258 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop Tvůrce(i) Havrila, Marek (BFU-R)
Réblová, K. (CZ)
Zirbel, C.L. (US)
Leontis, N. B. (US)Celkový počet autorů 4 Zdroj.dok. Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 117, č. 46 (2013), s. 14302-14319Poč.str. 18 s. Forma vydání Tištěná - P Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova 23S RIBOSOMAL-RNA ; PARTICLE MESH EWALD ; NUCLEIC-ACIDS Vědní obor RIV BO - Biofyzika CEP GBP305/12/G034 GA ČR - Grantová agentura ČR ED1.1.00/02.0068 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy Institucionální podpora BFU-R - RVO:68081707 CEZ AV0Z50040702 - BFU-R (2007-2013) UT WOS 000327557700013 DOI 10.1021/jp408530w Anotace The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base phosphate, and backbone backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Pracoviště Biofyzikální ústav Kontakt Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Rok sběru 2014
Počet záznamů: 1