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Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine‐I Riboswitch

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2024

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Karakurt, Mehmet Can
Stephan, Theresa

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Macromolecular Rapid Communications. Wiley. 2024, 45(24), 2400606. ISSN 1022-1336. eISSN 1521-3927. Verfügbar unter: doi: 10.1002/marc.202400606

Zusammenfassung

Riboswitches are structured ribonucleic acid (RNA) segments that act as specific sensors for small molecules in bacterial metabolism. Due to the flexible nature of these highly charged macromolecules, molecular dynamics simulations are instrumental to investigating the mechanistic details of their regulatory function. In the present study, the guanidine‐I riboswitch serves as an example of how atomistic simulations can shed light on the effect of ions on the structure and dynamics of RNA and on ligand binding. Relying on two orthologous crystal structures from different bacterial species, it is demonstrated how the ion setup crucially determines whether the simulation yields meaningful insights into the conformational stability of the RNA, functionally relevant residues and RNA‐ligand interactions. The ion setup in this context includes diffuse ions in solution and bound ions associated directly with the RNA, in particular a triad of 2 Mg 2+ ions and a K + ion in close proximity to the guanidinium binding site. A detailed investigation of the binding pocket reveals that the K + from the ion triad plays a decisive role in stabilizing the ligand binding by stabilizing important localized interactions, which in turn contribute to the overall shape of the folded state of the RNA.

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540 Chemie

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ISO 690FRANKE, Leon, Christoph GLOBISCH, Mehmet Can KARAKURT, Theresa STEPHAN, Christine PETER, 2024. Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine‐I Riboswitch. In: Macromolecular Rapid Communications. Wiley. 2024, 45(24), 2400606. ISSN 1022-1336. eISSN 1521-3927. Verfügbar unter: doi: 10.1002/marc.202400606
BibTex
@article{Franke2024-12Atomi-70757,
  year={2024},
  doi={10.1002/marc.202400606},
  title={Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine‐I Riboswitch},
  number={24},
  volume={45},
  issn={1022-1336},
  journal={Macromolecular Rapid Communications},
  author={Franke, Leon and Globisch, Christoph and Karakurt, Mehmet Can and Stephan, Theresa and Peter, Christine},
  note={Article Number: 2400606}
}
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