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

RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA a 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, s. 17-17.

Základní údaje

Originální název

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

Název česky

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

Autoři

RÁZGA, Filip (703 Slovensko), Martin ZACHARIAS (276 Německo), Kamila RÉBLOVÁ (203 Česká republika), Jaroslav KOČA (203 Česká republika) a Jiří ŠPONER (203 Česká republika, garant)

Vydání

prvé. Brno, Strukturní biofyzika makromolekul, od s. 17-17, 1 s. 2005

Nakladatel

Biofyzikálny ústav AVČR a MU v Brne

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Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10403 Physical chemistry

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14310/05:00014300

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Molecular Dynamics; RNA Kink Turn; Ribosome; RNA flexibility;

Štítky

molecular dynamics, Ribosome, RNA flexibility, RNA Kink Turn

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Anotace

V originále

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.

Česky

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.

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Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum