Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study

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Authors	PANECKA Joanna HAVRILA Marek RÉBLOVÁ Kamila ŠPONER Jiří TRYLSKA Joanna
Year of publication	2014
Type	Article in Periodical
Magazine / Source	Journal of Physical Chemistry B
MU Faculty or unit	Central European Institute of Technology
Citation
Web	http://pubs.acs.org/doi/abs/10.1021/jp5030685
Doi	http://dx.doi.org/10.1021/jp5030685
Field	Physical chemistry and theoretical chemistry
Keywords	NUCLEIC-ACIDS; DECODING SITE; CRYSTAL-STRUCTURE; ESCHERICHIA-COLI; RNA STRUCTURE; MINOR MOTIF; FORCE-FIELD; BASE-PAIRS; BINDING; SUBUNIT
Description	The mRNA decoding site (A-site) in the small ribosomal subunit controls fidelity of the translation process. Here, using molecular dynamics simulations and bioinformatic analyses, we investigated the structural dynamics of the human mitochondrial A-site (native and A1490G mutant) and compared it with the dynamics of the bacterial A-site. We detected and characterized a specific RNA backbone configuration, S-turn2, which occurs in the human mitochondrial but not in the bacterial A-site. Mitochondrial and bacterial A-sites show different propensities to form S-turn2 that may be caused by different base-pairing patterns of the flanking nucleotides. Also, the S-tum2 structural stability observed in the simulations supports higher accuracy and lower speed of mRNA decoding in mitochondria in comparison with bacteria. In the mitochondrial A-site, we observed collective movement of stacked nucleotides A1408 center dot C1409 center dot C1410, which may explain the known differences in aminoglycoside antibiotic binding affinities toward the studied A-site variants.
Related projects:	CEITEC - Central European Institute of Technology Centrum biologie RNA