Elbow-like motions in Ribosomal Kink-turns: The role of the second A-minor motif and Nominally unpaired bases

RÁZGA, Filip, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Elbow-like motions in Ribosomal Kink-turns: The role of the second A-minor motif and Nominally unpaired bases. In Journal Of Biomolecular Structure and Dynamics. prve. New York, USA: Adenine Press, 2005, s. 800-801. ISBN 1533-0346.

Základní údaje

• Originální název: Elbow-like motions in Ribosomal Kink-turns: The role of the second A-minor motif and Nominally unpaired bases
• Název česky: Klbove pohyby Ribosomalnych Kink turnov: Uloha druhej A-minor interakcie a nesparenych nukleotidov
• Autoři: RÁZGA, Filip (703 Slovensko), Jaroslav KOČA (203 Česká republika), Neocles B. LEONTIS (840 Spojené státy) a Jiří ŠPONER (203 Česká republika, garant).
• Vydání: prve. New York, USA, Journal Of Biomolecular Structure and Dynamics, od s. 800-801, 2 s. 2005.
• Nakladatel: Adenine Press

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Stať ve sborníku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Spojené státy
• Utajení: není předmětem státního či obchodního tajemství
• Kód RIV: RIV/00216224:14310/05:00013831
• Organizační jednotka: Přírodovědecká fakulta
• ISBN: 1533-0346
• Klíčová slova anglicky: Kink-turn; RNA flexibility; A-minor; Ribosome dynamics
• Štítky: A-minor, Kink-turn, Ribosome dynamics, RNA flexibility

Anotace

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing "V"-shaped structures. Explicit-solvent Molecular Dynamics (MD) simulations were carried out for selected K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58) and for K-turn of human U4 snRNA (Kt-U4). 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. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. The presence of K-turns at key functional sites in the ribosome 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.

Anotace česky

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing "V"-shaped structures. Explicit-solvent Molecular Dynamics (MD) simulations were carried out for selected K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58) and for K-turn of human U4 snRNA (Kt-U4). 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. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. The presence of K-turns at key functional sites in the ribosome 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.

Návaznosti

• LN00A016, projekt VaV: Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum