The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.

ABSTRACT: The kink-turn is a recurrent RNA structural motif that induces a sharp bend (kink) in the A-form RNA helix. It is defined by key structural features, including consecutive sheared AG base pairs, an A-minor interaction, and multiple base-sugar interactions. An accurate representation of these densely packed noncanonical interactions by molecular dynamics simulations poses a significant challenge for contemporary force fields (FFs). Here, we present extended simulations of the ribosomal kink-turn 7 (Kt-7) from H.m., the so-called "consensual" kink-turn, using a broad spectrum of pair-additive and polarizable RNA FFs. None of the tested FFs manage to flawlessly describe all of the structural features of the Kt-7 although several FFs provide rather acceptable results and should not caus

SUBMITTER: Lemmens T 

PROVIDER: S-EPMC12746442 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature