Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.

ABSTRACT: While it is known that ions are required for folding of RNA, little is known about how transient/probabilistic ionic interactions facilitate biologically-relevant conformational rearrangements. To address this, we developed a theoretical model that employs all-atom resolution, with a simplified representation of biomolecular energetics, explicit electrostatics and ions (K ⁺ , Cl ^- , Mg ²⁺ ). For well-studied RNA systems (58-mer and Ade riboswitch), the model accurately describes the concentration-dependent ionic environment, including (bidentate) chelated and hydrated (diffuse/outer-shell) ions. With this foundation, we applied the model to simulate the yeast ribosome and quantified the ion-dependent energy landscape of intersubunit rotation. These calculat

SUBMITTER: Wanes G 

PROVIDER: S-EPMC12363776 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature