RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function

RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA and Jiří ŠPONER. RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function. In Strukturní biofyzika makromolekul. prvé. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005, p. 17-17.

Basic information

• Original name: RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function
• Name in Czech: RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function
• Authors: RÁZGA, Filip (703 Slovakia), Martin ZACHARIAS (276 Germany), Kamila RÉBLOVÁ (203 Czech Republic), Jaroslav KOČA (203 Czech Republic) and Jiří ŠPONER (203 Czech Republic, guarantor).
• Edition: prvé. Brno, Strukturní biofyzika makromolekul, p. 17-17, 1 pp. 2005.
• Publisher: Biofyzikálny ústav AVČR a MU v Brne

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/00216224:14310/05:00014300
• Organization unit: Faculty of Science
• Keywords in English: Molecular Dynamics; RNA Kink Turn; Ribosome; RNA flexibility
• Tags: molecular dynamics, Ribosome, RNA flexibility, RNA Kink Turn

Abstract

Explicit-solvent Molecular Dynamics (MD) simulations were carried out for three K-turns (Kt) from 23S rRNA, i.e., Kt-38 located at the A-site finger base, Kt-42 located at the L7/L12 stalk base, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The presence of K-turns at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some K-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. MD simulations demonstrated that the K-turns can act as flexible molecular elbows. The angle between the helical arms is regulated by local variations of the second A-minor (type I) interaction, which mediates the contact between the helical stems, and by conformational change of the single base from the nominally unpaired region. Moreover, K-turns are associated with a unique network of long-residency and dynamical hydration sites that are intimately involved in modulating their conformational dynamics. Variability of A-minor interaction ranges from closed geometries to open ones stabilized by insertion of long-residency waters between the interacting bases. Implicit solvent conformational search confirms the flexibility of K-turns around their x-ray geometries and identifies a second separate low-energy region with more open structures that could correspond to K-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor-binding site shows that elbow-like motion fully propagates beyond the K-turn and could mediate large-scale adjustments of distant RNA regions.

Abstract (in Czech)

Explicit-solvent Molecular Dynamics (MD) simulations were carried out for three K-turns (Kt) from 23S rRNA, i.e., Kt-38 located at the A-site finger base, Kt-42 located at the L7/L12 stalk base, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The presence of K-turns at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some K-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. MD simulations demonstrated that the K-turns can act as flexible molecular elbows. The angle between the helical arms is regulated by local variations of the second A-minor (type I) interaction, which mediates the contact between the helical stems, and by conformational change of the single base from the nominally unpaired region. Moreover, K-turns are associated with a unique network of long-residency and dynamical hydration sites that are intimately involved in modulating their conformational dynamics. Variability of A-minor interaction ranges from closed geometries to open ones stabilized by insertion of long-residency waters between the interacting bases. Implicit solvent conformational search confirms the flexibility of K-turns around their x-ray geometries and identifies a second separate low-energy region with more open structures that could correspond to K-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor-binding site shows that elbow-like motion fully propagates beyond the K-turn and could mediate large-scale adjustments of distant RNA regions.

Links

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

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