Elastic properties of ribosomal RNA building blocks: Molecular dynamics study

RÁZGA, Filip, Jaroslav KOČA and Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: Molecular dynamics study. In Strukturní biofyzika makromolekul II. první. Brno: Brno, 2007, p. 14-14.

Basic information

• Original name: Elastic properties of ribosomal RNA building blocks: Molecular dynamics study
• Name in Czech: Elastické vlastnosti stavebných blokov ribozomálnej RNA: Molekulovo dynamická štúdia
• Authors: RÁZGA, Filip, Jaroslav KOČA and Jiří ŠPONER.
• Edition: první. Brno, Strukturní biofyzika makromolekul II, p. 14-14, 1 pp. 2007.
• Publisher: Brno

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10403 Physical chemistry
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• Keywords in English: RNA flexibility; Molecular dynamics
• Tags: molecular dynamics, RNA flexibility

Abstract

Explicit solvent Molecular Dynamics was used to describe the intrinsic flexibility of 23S rRNA Kink-turn motifs (e.g. Kt-38, Kt-42, Kt-58) and 23S rRNA Helix 42-44 (i.e. GTPase associated center rRNA with adjacent Kt-42). We demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries. Additionally, the preferred low-energy motions of different rRNA motifs (e.g. 23S rRNA Kink-turn motifs, 23S rRNA Helix 42-44 (i.e. GTPase associated center rRNA), 23S rRNA Helix 90-92 (i.e. three-way-junction with A-loop), 23S Sarcin-ricin loop, 16S rRNA Helix 44 and 5S rRNA loop E) will be compared and discussed.

Abstract (in Czech)

Explicit solvent Molecular Dynamics was used to describe the intrinsic flexibility of 23S rRNA Kink-turn motifs (e.g. Kt-38, Kt-42, Kt-58) and 23S rRNA Helix 42-44 (i.e. GTPase associated center rRNA with adjacent Kt-42). We demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries. Additionally, the preferred low-energy motions of different rRNA motifs (e.g. 23S rRNA Kink-turn motifs, 23S rRNA Helix 42-44 (i.e. GTPase associated center rRNA), 23S rRNA Helix 90-92 (i.e. three-way-junction with A-loop), 23S Sarcin-ricin loop, 16S rRNA Helix 44 and 5S rRNA loop E) will be compared and discussed.