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

ABSTRACT: 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 high

SUBMITTER: Matouskova E 

PROVIDER: S-EPMC8943727 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature