2005
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. LEONTISZákladní 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
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
Změněno: 3. 6. 2005 17:06, prof. RNDr. Jaroslav Koča, DrSc.
V originále
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.
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 |
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| MSM0021622413, záměr |
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