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

Warning

This publication doesn't include Faculty of Medicine. It includes Central European Institute of Technology. Official publication website can be found on muni.cz.

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