The computational view inside the dynamical behavior of the RNA-binding motive

PASULKA, Josef, Jaroslav KOČA and Richard ŠTEFL. The computational view inside the dynamical behavior of the RNA-binding motive. In 8th Discussions in Structural Molecular Biology, Nove Hrady, March 18 - 20, 2010. 2010. ISSN 1211-5894.

Basic information

• Original name: The computational view inside the dynamical behavior of the RNA-binding motive
• Name in Czech: The computational view inside the dynamical behavior of the RNA-binding motive
• Authors: PASULKA, Josef, Jaroslav KOČA and Richard ŠTEFL.
• Edition: 8th Discussions in Structural Molecular Biology, Nove Hrady, March 18 - 20, 2010, 2010.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: Genetics and molecular biology
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• ISSN: 1211-5894
• Keywords (in Czech): molecular dynamics; RNA-binding motive; ADAR2; RNA recognition
• Keywords in English: molecular dynamics; RNA-binding motive; ADAR2; RNA recognition

Abstract

The members of an enzyme family known as ADARs (adenosine deaminases that act on RNA) play a crucial role in the RNA editing process in all organisms. ADARs target double-stranded regions of nuclear-encoded RNA (dsRNA). ADARs are also interesting in regard to the remarkable double-stranded structures of their substrates and how enzyme specificity is achieved with little regard to sequence. We focus on the N-terminal non-catalytic domain ADAR2, which recognizes the dsRNA with A-C mismatches. Molecular dynamics (MD) techniques are capable of providing detailed insight into the motions that occur during molecular recognition and how motional properties change upon binding. MD and NMR techniques synergistically reinforce each other when applied to the same system. Our goal in this work is to explain the role of mismatches and their flexibility for the ADAR2-dsRNA complex.

Abstract (in Czech)

The members of an enzyme family known as ADARs (adenosine deaminases that act on RNA) play a crucial role in the RNA editing process in all organisms. ADARs target double-stranded regions of nuclear-encoded RNA (dsRNA). ADARs are also interesting in regard to the remarkable double-stranded structures of their substrates and how enzyme specificity is achieved with little regard to sequence. We focus on the N-terminal non-catalytic domain ADAR2, which recognizes the dsRNA with A-C mismatches. Molecular dynamics (MD) techniques are capable of providing detailed insight into the motions that occur during molecular recognition and how motional properties change upon binding. MD and NMR techniques synergistically reinforce each other when applied to the same system. Our goal in this work is to explain the role of mismatches and their flexibility for the ADAR2-dsRNA complex.

Links

• GA204/08/1212, research and development project: Name: Strukturní studium interakcí mezi proteiny a RNA účastnící se v mechanismu kontroly kvality RNA

Investor: Czech Science Foundation, Structural studies of protein-RNA complexes involved in RNA quality control

• GD301/09/H004, research and development project: Name: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny

Investor: Czech Science Foundation

• IAA401630903, research and development project: Name: Strukturní podstata mechanismu ukončení transkripce nepolyadenylovaných transkriptů

Investor: Academy of Sciences of the Czech Republic, Structural basis for transcription termination of nonpolyadenylated transcripts

• LA08008, research and development project: Name: Strukturní studium interakcí mezi bíkovinami a poškozenou RNA.

Investor: Ministry of Education, Youth and Sports of the CR, Structural studies of protein-RNA complexes involved in RNA quality control

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment