Structure and Dynamics of RNA K-turn Motifs

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER a Neocles, B. LEONTIS. Structure and Dynamics of RNA K-turn Motifs. In RNA klub. vyd. Praha: Praha, 2003, s. 21-21.

Základní údaje

• Originální název: Structure and Dynamics of RNA K-turn Motifs
• Název česky: Struktura a dynamika RNA KInk-turn motivov
• Autoři: RÁZGA, Filip (703 Slovensko), Naděžda ŠPAČKOVÁ (203 Česká republika), Kamila RÉBLOVÁ (203 Česká republika), Jaroslav KOČA (203 Česká republika), Jiří ŠPONER (203 Česká republika, garant) a Neocles, B. LEONTIS (840 Spojené státy).
• Vydání: vyd. Praha, RNA klub, od s. 21-21, 1 s. 2003.
• Nakladatel: Praha

Další údaje

• Originální 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/00216224:14310/03:00009894
• Organizační jednotka: Přírodovědecká fakulta
• Klíčová slova anglicky: Molecular Dynamics; non-Watson-Crick basepairs; RNA flexibility
• Štítky: molecular dynamics, non-Watson-Crick basepairs, RNA flexibility

Anotace

Hinge-like RNA motifs occur at conserved positions in the 16S and 23S ribosomal RNAs, as revealed by x-ray crystallography of the 50S subunits of H. marismortui and D. radiodurans and the 30S subunit of T. thermophilus. The conformation of these asymmetric internal loops, called Kink-turns or K-turns, produces sharp, 120-degree bends in both phosphodiester backbones resulting in a V-shaped structure with an acute angle of ca.60 deg. between the RNA helices flanking the motif. In addition, some K-turns are specific binding sites for ribosomal proteins and others take part in RNA-RNA tertiary interactions. We have carried out a set of explicit-solvent Molecular Dynamics (MD) simulations for selected K-turn RNA motifs, including K-turn 38,K-turn 42 and K-turn 58 from the 23S ribosomal RNA of Haloarcula marismortui. The simulations reveal an unprecedented dynamical flexibility, suggesting that K-turn motifs may function as a very flexible internal loops linking rigid helix stems and thus capable of regulating significant inter-segmental motions. On a nano-second timescale, K-turns sample different isoenergetic conformational substates that are separated by virtually no free energy barriers and that are stabilized by specific long-residency hydration sites and monovalent counterions. The unique flexibility of K-turn RNA motifs contrasts sharply with the rigidity of other non-Watson-Crick RNA motifs, such as the 5S rRNA loop E and the sarcin-ricin motif. K-turn conformational changes may be modulated by protein-RNA or RNA-RNA interactions. Thus, K-turns can be utilized as hinges allowing flexible movements of selected parts of the ribosome during protein synthesis cycle.K-turns occur in the A-site finger domain, the factor-binding domain, and the L1-binding domain and even at the base of Domain VI includes the sarcin/ricin loop.

Anotace česky

Hinge-like RNA motifs occur at conserved positions in the 16S and 23S ribosomal RNAs, as revealed by x-ray crystallography of the 50S subunits of H. marismortui and D. radiodurans and the 30S subunit of T. thermophilus. The conformation of these asymmetric internal loops, called Kink-turns or K-turns, produces sharp, 120-degree bends in both phosphodiester backbones resulting in a V-shaped structure with an acute angle of ca.60 deg. between the RNA helices flanking the motif. In addition, some K-turns are specific binding sites for ribosomal proteins and others take part in RNA-RNA tertiary interactions. We have carried out a set of explicit-solvent Molecular Dynamics (MD) simulations for selected K-turn RNA motifs, including K-turn 38,K-turn 42 and K-turn 58 from the 23S ribosomal RNA of Haloarcula marismortui. The simulations reveal an unprecedented dynamical flexibility, suggesting that K-turn motifs may function as a very flexible internal loops linking rigid helix stems and thus capable of regulating significant inter-segmental motions. On a nano-second timescale, K-turns sample different isoenergetic conformational substates that are separated by virtually no free energy barriers and that are stabilized by specific long-residency hydration sites and monovalent counterions. The unique flexibility of K-turn RNA motifs contrasts sharply with the rigidity of other non-Watson-Crick RNA motifs, such as the 5S rRNA loop E and the sarcin-ricin motif. K-turn conformational changes may be modulated by protein-RNA or RNA-RNA interactions. Thus, K-turns can be utilized as hinges allowing flexible movements of selected parts of the ribosome during protein synthesis cycle.K-turns occur in the A-site finger domain, the factor-binding domain, and the L1-binding domain and even at the base of Domain VI includes the sarcin/ricin loop.

Návaznosti

• LN00A016, projekt VaV: Název: BIOMOLEKULÁRNÍ CENTRUM

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