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@article{1199998, author = {Panecka, Joanna and Havrila, Marek and Réblová, Kamila and Šponer, Jiří and Trylska, Joanna}, article_location = {WASHINGTON}, article_number = {24}, doi = {http://dx.doi.org/10.1021/jp5030685}, keywords = {NUCLEIC-ACIDS; DECODING SITE; CRYSTAL-STRUCTURE; ESCHERICHIA-COLI; RNA STRUCTURE; MINOR MOTIF; FORCE-FIELD; BASE-PAIRS; BINDING; SUBUNIT}, language = {eng}, issn = {1520-6106}, journal = {Journal of Physical Chemistry B}, title = {Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study}, url = {http://pubs.acs.org/doi/abs/10.1021/jp5030685}, volume = {118}, year = {2014} }
TY - JOUR ID - 1199998 AU - Panecka, Joanna - Havrila, Marek - Réblová, Kamila - Šponer, Jiří - Trylska, Joanna PY - 2014 TI - Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study JF - Journal of Physical Chemistry B VL - 118 IS - 24 SP - 6687-6701 EP - 6687-6701 PB - American Chemical Society SN - 15206106 KW - NUCLEIC-ACIDS KW - DECODING SITE KW - CRYSTAL-STRUCTURE KW - ESCHERICHIA-COLI KW - RNA STRUCTURE KW - MINOR MOTIF KW - FORCE-FIELD KW - BASE-PAIRS KW - BINDING KW - SUBUNIT UR - http://pubs.acs.org/doi/abs/10.1021/jp5030685 L2 - http://pubs.acs.org/doi/abs/10.1021/jp5030685 N2 - 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. ER -
PANECKA, Joanna, Marek HAVRILA, Kamila RÉBLOVÁ, Jiří ŠPONER a Joanna TRYLSKA. Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study. \textit{Journal of Physical Chemistry B}. WASHINGTON: American Chemical Society, 2014, roč.~118, č.~24, s.~6687-6701. ISSN~1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp5030685.
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