RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance

RÁZGA, Filip, Jaroslav KOČA, Neocles B LEONTIS and Jiří ŠPONER. RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance. In Workshop on Modeling Interactions in Biomolecules II. prve. Praha: Praha, 2005, p. p37, 2 pp.

Basic information

• Original name: RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance
• Name in Czech: RNA K-turny-Flexibilne ribozomalne motivy: dynamika, hydratacia, konformacie a biologicky vyznam
• Authors: RÁZGA, Filip (703 Slovakia), Jaroslav KOČA (203 Czech Republic, guarantor), Neocles B LEONTIS (840 United States of America) and Jiří ŠPONER (203 Czech Republic).
• Edition: prve. Praha, Workshop on Modeling Interactions in Biomolecules II, p. p37, 2 pp. 2005.
• Publisher: Praha

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
• RIV identification code: RIV/00216224:14310/05:00013909
• Organization unit: Faculty of Science
• Keywords in English: RNA flexibility; Kink turn motif; A-minor motif; Molecular dynamics
• Tags: A-minor motif, Kink turn motif, molecular dynamics, RNA flexibility

Abstract

High-resolution x-ray structures of large and small ribosomal subunits revealed that rRNAs form intricate shapes and architectures, comprising single stranded loops, double stranded helices, and non-canonical regions compactly folded in specific rRNA segments known as RNA motifs. RNA motifs are biologically important structural segments necessary for correct functioning of ribosome. They are characterized by specific 3D architectures (consisting of canonical and non-canonical regions) which are in most cases very well conserved, and by their unique intrinsic properties. Kink-turns (Kt) are RNA motifs with sharp bend of phosphodiester backbone (~120) leading to "V" - shaped 3D architecture. They are composed of three distinct structural elements: canonical Watson-Crick helix (C-stem), internal loop (Kink) with nominally unpaired bases, and non-canonical helix (NC-stem). The Kink thus forms a tip of a "V" with C- and NC-stems attached as arms. The interaction between stems is mediated by A-minor interactions Explicit-solvent Molecular Dynamics (MD) simulations were carried out for selected isolated K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58), for K-turn of human U4 snRNA (Kt-U4) and for Kt-42 in complex with factor-binding site (i.g. GTPase-associated center). The MD simulations reveal hinge-like K-turn motions on the nanosecond time-scale and thus indicate that K-turns are dynamically flexible, and capable of regulating significant inter-segmental motions. Crucial role in K-turns dynamics is played by A-minor interaction. The presence of K-turns at key functional sites in the ribosome (A-site finger, factor-binding site, etc.), suggests that they confer flexibility to RNA protuberances that regulate the traversal of tRNAs from one binding site to another across the interface between the small and large subunit during protein synthesis cycle.

Abstract (in Czech)

High-resolution x-ray structures of large and small ribosomal subunits revealed that rRNAs form intricate shapes and architectures, comprising single stranded loops, double stranded helices, and non-canonical regions compactly folded in specific rRNA segments known as RNA motifs. RNA motifs are biologically important structural segments necessary for correct functioning of ribosome. They are characterized by specific 3D architectures (consisting of canonical and non-canonical regions) which are in most cases very well conserved, and by their unique intrinsic properties. Kink-turns (Kt) are RNA motifs with sharp bend of phosphodiester backbone (~120) leading to "V" - shaped 3D architecture. They are composed of three distinct structural elements: canonical Watson-Crick helix (C-stem), internal loop (Kink) with nominally unpaired bases, and non-canonical helix (NC-stem). The Kink thus forms a tip of a "V" with C- and NC-stems attached as arms. The interaction between stems is mediated by A-minor interactions Explicit-solvent Molecular Dynamics (MD) simulations were carried out for selected isolated K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58), for K-turn of human U4 snRNA (Kt-U4) and for Kt-42 in complex with factor-binding site (i.g. GTPase-associated center). The MD simulations reveal hinge-like K-turn motions on the nanosecond time-scale and thus indicate that K-turns are dynamically flexible, and capable of regulating significant inter-segmental motions. Crucial role in K-turns dynamics is played by A-minor interaction. The presence of K-turns at key functional sites in the ribosome (A-site finger, factor-binding site, etc.), suggests that they confer flexibility to RNA protuberances that regulate the traversal of tRNAs from one binding site to another across the interface between the small and large subunit during protein synthesis cycle.

Links

• LN00A016, research and development project: Name: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center