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 and 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, vol. 118, No 24, p. 6687-6701. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp5030685.

Basic information

• Original name: Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study
• Authors: PANECKA, Joanna (616 Poland), Marek HAVRILA (703 Slovakia, belonging to the institution), Kamila RÉBLOVÁ (203 Czech Republic, belonging to the institution), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Joanna TRYLSKA (616 Poland).
• Edition: Journal of Physical Chemistry B, WASHINGTON, American Chemical Society, 2014, 1520-6106.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10403 Physical chemistry
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 3.302
• RIV identification code: RIV/00216224:14740/14:00073917
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1021/jp5030685
• UT WoS: 000337784100037
• Keywords in English: NUCLEIC-ACIDS; DECODING SITE; CRYSTAL-STRUCTURE; ESCHERICHIA-COLI; RNA STRUCTURE; MINOR MOTIF; FORCE-FIELD; BASE-PAIRS; BINDING; SUBUNIT
• Tags: kontrola MP, MP, rivok
• Tags: International impact, Reviewed

Abstract

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.

Links

• ED1.1.00/02.0068, research and development project: Name: CEITEC - central european institute of technology
• GBP305/12/G034, research and development project: Name: Centrum biologie RNA