What is it about?

We investigated a small synthetic riboswitch that binds neomycin. We developed a method and tools to describe the association pathway of neomycin to the riboswitch at an atomistic level of detail. Two-dimensional molecular dynamics simulations elucidated the mechanism of functioning of this riboswitch.

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Why is it important?

The insight about the full association path of neomycin to the riboswitch and its mutants can help design synthetic riboswitches and ligands that control their dynamics and structure.


Our work shows how the crucial steps of the interaction of neomycin with the riboswitch can be optimized through mutations to enhance riboswitch regulatory effectiveness in cells. The results highlight key dynamic differences in neomycin binding for the experimentally reported mutants, unravelling the effects of mutations on the riboswitch activity that cannot be determined solely through experiments.

Joanna Trylska
University of Warsaw

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This page is a summary of: Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch, Proceedings of the National Academy of Sciences, April 2024, Proceedings of the National Academy of Sciences,
DOI: 10.1073/pnas.2317197121.
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