Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases

RÁZGA, Filip, Jaroslav KOČA, Jiří ŠPONER a Neocles B. LEONTIS. Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases. Biophysical Journal. USA: Biophysical Society, 2005, roč. 88, č. 5, s. 3466-3485. ISSN 0006-3495.

Základní údaje

• Originální název: Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases
• Název česky: Klbove pohyby RNA Kink-turnov: Uloha druheho A-minor motivu a nesparenych bazi
• Autoři: RÁZGA, Filip (703 Slovensko), Jaroslav KOČA (203 Česká republika), Jiří ŠPONER (203 Česká republika, garant) a Neocles B. LEONTIS (840 Spojené státy).
• Vydání: Biophysical Journal, USA, Biophysical Society, 2005, 0006-3495.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Spojené státy
• Utajení: není předmětem státního či obchodního tajemství
• Impakt faktor: Impact factor: 4.507
• Kód RIV: RIV/00216224:14310/05:00013730
• Organizační jednotka: Přírodovědecká fakulta
• UT WoS: 000228688800040
• Klíčová slova anglicky: Kink-turn; A-minor motif; RNA flexibility; Molecular Dynamics; Ribosome function
• Štítky: A-minor motif, Kink-turn, molecular dynamics, Ribosome function, 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 simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. 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. The simulated A-minor geometries fully agree with x-ray data. 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. We suggest that K-turns are flexible elements mediating large-scale ribosomal motions during the 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 simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. 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. The simulated A-minor geometries fully agree with x-ray data. 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. We suggest that K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

Návaznosti

• LN00A016, projekt VaV: Název: BIOMOLEKULÁRNÍ CENTRUM

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

• MSM0021622413, záměr: Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím