RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

0555925 - BFÚ 2023 RIV US eng J - Článek v odborném periodiku
Matoušková, E. - Drsata, T. - Pfeifferova, L. - Šponer, Jiří - Réblová, K. - Lankas, F.
RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.
Biophysical Journal. Roč. 121, č. 5 (2022), s. 705-714. ISSN 0006-3495. E-ISSN 1542-0086
Institucionální podpora: RVO:68081707
Klíčová slova: mechanical-properties * molecular-dynamics * sequence * motif * dna * visualization
Obor OECD: Biophysics
Impakt faktor: 3.4, rok: 2022
Způsob publikování: Omezený přístup
https://www.sciencedirect.com/science/article/abs/pii/S0006349522000753?via%3Dihub

Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.
Trvalý link: https://hdl.handle.net/11104/0339763