Unveiling Putative Excited State and Transmission of Binding Information in the Fluoride Riboswitch

Riboswitches regulate downstream gene expression by binding to specific small molecules or ions with multiple mechanisms to transfer the binding information. In the case of the fluoride riboswitch, the transcription termination signal is conveyed through a transient excited state (ES). In this work, we performed conventional molecular dynamics (MD) simulations, totaling 180 μs, to obtain the ES structure and investigate the mechanism underlying information transmission in Mg²⁺/F^– binding within the fluoride riboswitch aptamer. The Mg²⁺/F^– binding pocket exhibits various conformations in its apo form. A series of ES structures were extracted from the MD trajectories of the apo form. The dynamics of the Mg²⁺/F^– binding pocket influenced key pair A40–U48 in ES structures. The pathway connecting the binding pocket to the pair involves interactions between the phosphate groups of U7 and G8 and the nucleobases of G8–C47–U48. Our work presents a structural ensemble of the ES and elucidates a pathway for transferring Mg²⁺/F^– binding information, thereby facilitating the understanding of how the holo-like apo state achieves transcriptional repression.