Joanna Trylska

University of Warsaw, Centre of New Technologies, Warsaw, Poland - Research

Molecular dynamics in multi-dimensional space reveals how mutations reshape neomycin binding to the riboswitch

Abstract

Riboswitches are structured RNA elements that regulate gene expression upon ligand binding and represent promising targets for antimicrobial strategies. The N1 riboswitch, engineered to selectively recognize neomycin—an aminoglycoside antibiotic—serves as a model for RNA–small molecule recognition. Using all-atom molecular dynamics simulations in multi-dimensional space combined with enhanced sampling techniques, we characterized the complete association pathway of neomycin to the riboswitch and elucidated how single-point mutations alter this process. Our studies revealed that the riboswitch recognizes neomycin through a conformational selection mechanism, where mutations alter RNA flexibility and reshape the conformational ensemble available for binding. The subsequent induced fit arises from the interactions of neomycin with the RNA backbone, causing backbone rearrangement. Crucially, mutations shift the RNA– neomycin distance at which each step occurs. This approach uncovered that mutations do not merely weaken binding affinity but alter the association pathway, modifying intermediate states and transition barriers. These findings provide an atomistic-level understanding of how sequence variations modulate RNA–ligand recognition.

References

[1] Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska, Molecular dynamics in multi-dimensional space explains how mutations affect the association path of neomycin to a riboswitch, Proc. Natl. Acad. Sci., 121 (15) e2317197121, 2024, doi: 10.1073/pnas.2317197121 [2] Piotr Chyży, Marta Kulik, Suyong Re, Yuji Sugita, Joanna Trylska, Mutations of N1 riboswitch affect its dynamics and recognition by neomycin through conformational selection, Front. Mol. Biosciences, 8:633130, 2021, doi: 10.3389/fmolb.2021.633130