Conformational dynamics of bacterial and human cytoplasmic
models of the ribosomal A-site

J 2015

Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

PANECKA, Joanna; Jiří ŠPONER a Joanna TRYLSKA

Základní údaje

Originální název

Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

Autoři

PANECKA, Joanna; Jiří ŠPONER a Joanna TRYLSKA

Vydání

Biochimie, Paris, Elsevier France- editions Scientifiques Medicales Elsevier, 2015, 0300-9084

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Francie

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.017

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/15:00080802

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

Aminoglycoside antibiotics; Bacterial A-site; Human cytoplasmic A-site; Molecular dynamics simulations; Ribosomal RNA

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 4. 2016 15:59, Mgr. Eva Špillingová

Anotace

V originále

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GBP305/12/G034, projekt VaV

Název: Centrum biologie RNA

Citovat

PANECKA, Joanna; Jiří ŠPONER a Joanna TRYLSKA. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Biochimie. Paris: Elsevier France- editions Scientifiques Medicales Elsevier, 2015, roč. 112, May, s. 96-110. ISSN 0300-9084. Dostupné z: https://doi.org/10.1016/j.biochi.2015.02.021.

@article{1299542,
   author = {Panecka, Joanna and Šponer, Jiří and Trylska, Joanna},
   article_location = {Paris},
   article_number = {May},
   doi = {https://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://doi.org/10.1016/j.biochi.2015.02.021.

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