Computational study of switching mechanism in add A-riboswitch.

Riboswitch can bind small molecules to regulate gene expression. Unlike other RNAs, riboswitch relies on its conformational switching for regulation. However, the understanding of the switching mechanism is still limited. Here, we focussed on the add A-riboswitch to illustrate the dynamical switching mechanism as an example. We performed molecular dynamics simulation, conservation and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding, whereas the switching base pairings are co-evolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design. Riboswitch can bind small molecules to regulate gene expression. However, the understanding of switching mechanism is very limited. We performed molecular dynamics simulation, conservation, and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding while the switching base pairings are coevolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design. [ABSTRACT FROM AUTHOR]