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

J 2014

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

PANECKA, Joanna, Marek HAVRILA, Kamila RÉBLOVÁ, Jiří ŠPONER, Joanna TRYLSKA et. al.

Základní údaje

Originální název

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

Autoři

PANECKA, Joanna (616 Polsko), Marek HAVRILA (703 Slovensko, domácí), Kamila RÉBLOVÁ (203 Česká republika, domácí), Jiří ŠPONER (203 Česká republika, garant, domácí) a Joanna TRYLSKA (616 Polsko)

Vydání

Journal of Physical Chemistry B, WASHINGTON, American Chemical Society, 2014, 1520-6106

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.302

Kód RIV

RIV/00216224:14740/14:00073917

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/jp5030685

UT WoS

000337784100037

Klíčová slova anglicky

NUCLEIC-ACIDS; DECODING SITE; CRYSTAL-STRUCTURE; ESCHERICHIA-COLI; RNA STRUCTURE; MINOR MOTIF; FORCE-FIELD; BASE-PAIRS; BINDING; SUBUNIT

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 1. 10. 2014 11:12, Martina Prášilová

Anotace

V originále

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.

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, 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. 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.

@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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