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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F15%3A00080802" target="_blank" >RIV/00216224:14740/15:00080802 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/15:00446268
Result on the web
<a href="http://ac.els-cdn.com/S0300908415000565/1-s2.0-S0300908415000565-main.pdf?_tid=8897fe04-fd49-11e4-be13-00000aacb362&acdnat=1431945479_ccdf4009f334e3b29e3bd3a1b0fd95e8" target="_blank" >http://ac.els-cdn.com/S0300908415000565/1-s2.0-S0300908415000565-main.pdf?_tid=8897fe04-fd49-11e4-be13-00000aacb362&acdnat=1431945479_ccdf4009f334e3b29e3bd3a1b0fd95e8</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.biochi.2015.02.021" target="_blank" >10.1016/j.biochi.2015.02.021</a>

Result language
angličtina
Original language name
Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site
Original language description
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.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CE - Biochemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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