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

George Wanes1,2, Udayan Mohanty3, Paul C Whitford1,2,4

  • 1Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115.

Proceedings of the National Academy of Sciences of the United States of America
|April 7, 2026
PubMed
Summary

Transient ion interactions, like magnesium (Mg2+), influence RNA structure and dynamics. Our model shows how Mg2+ concentration shifts ribosome energetics, favoring specific conformations and reducing molecular kinetics.

Keywords:
RNAconformational transitionelongationionssimulation

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Ion binding is known to stabilize RNA structure.
  • The role of transient ionic interactions in conformational changes is poorly understood.

Purpose of the Study:

  • To develop a theoretical model for simulating ion effects on RNA.
  • To investigate how ions influence large-scale biomolecular dynamics, specifically ribosome intersubunit rotation.

Main Methods:

  • Developed a structure-based
  • SMOG
  • model with explicit electrostatics and ions (K+, Cl-, Mg2+).
  • Simulated the yeast ribosome to quantify ion-dependent energy landscapes.
  • Analyzed concentration-dependent ionic environments, including chelated and diffuse ions.

Main Results:

  • The model accurately describes ion concentrations and environments in RNA systems.
  • Simulations revealed that increased magnesium chloride ([MgCl2]) concentration shifts ribosome energetics to favor the unrotated state.
  • Higher [MgCl2] increased the free-energy barrier, reducing kinetics and correlating with ion-mediated intersubunit interactions.

Conclusions:

  • Transient ionic interactions, particularly Mg2+, play a crucial role in regulating large-scale biomolecular dynamics.
  • This study provides a physical mechanism for how ions modulate conformational rearrangements in complex biological molecules like the ribosome.