a 2009

The molecular dynamics study of the RNA-binding domain of ADAR2 bound to dsRNA

PASULKA, Josef, Jaroslav KOČA and Richard ŠTEFL

Basic information

Original name

The molecular dynamics study of the RNA-binding domain of ADAR2 bound to dsRNA

Name in Czech

The molecular dynamics study of the RNA-binding domain of ADAR2 bound to dsRNA

Authors

PASULKA, Josef, Jaroslav KOČA and Richard ŠTEFL

Edition

7th Discussions in Structural Molecular Biology Nove Hrady, 12 - 14 March 2009, 2009

Other information

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

Keywords (in Czech)

molecular dynamics; RNA-binding motive; ADAR2; RNA recognition

Keywords in English

molecular dynamics; RNA-binding motive; ADAR2; RNA recognition
Changed: 10/4/2010 11:13, prof. RNDr. Jaroslav Koča, DrSc.

Abstract

V originále

Like RNA splicing, RNA editing alters the sequence of an RNA from that encoded in the DNA. Typically, a single RNA splicing reaction removes a large block of contiguous sequence, whereas each RNA editing reaction changes only one or two nucleotides. Therefore splicing is a cut-and-paste mechanism whereas editing is one of fine-tuning. RNA editing by adenosine deamination is catalyzed by members of an enzyme family known as adenosine deaminases that act on RNA (ADARs). ADARs are RNA editing enzymes that target double-stranded regions of nuclear-encoded RNA. 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. ADARs from all organisms have a common domain structure that includes variable numbers of double-stranded RNA (dsRNA) binding motifs (dsRBMs) followed by a highly conserved C-terminal catalytic domain. We focused on the N-terminal non-catalytic domain ADAR2, which recognizes the dsRNA with A-C mismatches. Using MD simulations, we study the role of mismatches and their flexibility for the formation of dsRBM-RNA complexes.

In Czech

Like RNA splicing, RNA editing alters the sequence of an RNA from that encoded in the DNA. Typically, a single RNA splicing reaction removes a large block of contiguous sequence, whereas each RNA editing reaction changes only one or two nucleotides. Therefore splicing is a cut-and-paste mechanism whereas editing is one of fine-tuning. RNA editing by adenosine deamination is catalyzed by members of an enzyme family known as adenosine deaminases that act on RNA (ADARs). ADARs are RNA editing enzymes that target double-stranded regions of nuclear-encoded RNA. 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. ADARs from all organisms have a common domain structure that includes variable numbers of double-stranded RNA (dsRNA) binding motifs (dsRBMs) followed by a highly conserved C-terminal catalytic domain. We focused on the N-terminal non-catalytic domain ADAR2, which recognizes the dsRNA with A-C mismatches. Using MD simulations, we study the role of mismatches and their flexibility for the formation of dsRBM-RNA complexes.

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
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