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@article{1299542,
author = {Panecka, Joanna and Šponer, Jiří and Trylska, Joanna},
article_location = {Paris},
article_number = {May},
doi = {http://dx.doi.org/10.1016/j.biochi.2015.02.021},
keywords = {Aminoglycoside antibiotics; Bacterial A-site; Human cytoplasmic A-site; Molecular dynamics simulations; Ribosomal RNA},
language = {eng},
issn = {0300-9084},
journal = {Biochimie},
title = {Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site},
url = {http://ac.els-cdn.com/S0300908415000565/1-s2.0-S0300908415000565-main.pdf?_tid=8897fe04-fd49-11e4-be13-00000aacb362&acdnat=1431945479_ccdf4009f334e3b29e3bd3a1b0fd95e8},
volume = {112},
year = {2015}
}
TY - JOUR
ID - 1299542
AU - Panecka, Joanna - Šponer, Jiří - Trylska, Joanna
PY - 2015
TI - Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site
JF - Biochimie
VL - 112
IS - May
SP - 96-110
EP - 96-110
PB - Elsevier France- editions Scientifiques Medicales Elsevier
SN - 03009084
KW - Aminoglycoside antibiotics
KW - Bacterial A-site
KW - Human cytoplasmic A-site
KW - Molecular dynamics simulations
KW - Ribosomal RNA
UR - http://ac.els-cdn.com/S0300908415000565/1-s2.0-S0300908415000565-main.pdf?_tid=8897fe04-fd49-11e4-be13-00000aacb362&acdnat=1431945479_ccdf4009f334e3b29e3bd3a1b0fd95e8
L2 - http://ac.els-cdn.com/S0300908415000565/1-s2.0-S0300908415000565-main.pdf?_tid=8897fe04-fd49-11e4-be13-00000aacb362&acdnat=1431945479_ccdf4009f334e3b29e3bd3a1b0fd95e8
N2 - The aminoacyl-tRNA binding site (A-site) is located in helix 44 of small ribosomal subunit. The mobile adenines 1492 and 1493 (Escherichia coli numbering), forming the A-site bulge, act as a functional switch that ensures mRNA decoding accuracy. Structural data on the oligonucleotide models mimicking the ribosomal A-site with sequences corresponding to bacterial and human cytoplasmic sites confirm that this RNA motif forms also without the ribosome context. We performed all-atom molecular dynamics simulations of these crystallographic A-site models to compare their conformational properties. We found that the human A-site bulge is more internally flexible than the bacterial one and has different base pairing preferences, which result in the overall different shapes of these bulges and cation density distributions. Also, in the human A-site model we observed repetitive destacking of A1492, while A1493 was more stably paired than in the bacterial variant. Based on the dynamics of the A-sites we suggest why aminoglycoside antibiotics, which target the bacterial A-site, have lower binding affinities and anti-translational activities toward the human variant. © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléeculaire (SFBBM). All rights reserved.
ER -
PANECKA, Joanna, Jiří ŠPONER a Joanna TRYLSKA. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. \textit{Biochimie}. Paris: Elsevier France- editions Scientifiques Medicales Elsevier, 2015, roč.~112, May, s.~96-110. ISSN~0300-9084. Dostupné z: https://dx.doi.org/10.1016/j.biochi.2015.02.021.
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