Dynamics of metal binding and mutation in yybP–ykoY riboswitch of Lactococcus lactis

Riboswitch is a regulatory segment of messenger RNA (mRNA), which by binding to various cellular metabolites regulates the activity of mRNA via modulating transcription, translation, alternative splicing, and stability of the mRNA. yybP–ykoY riboswitch of Lactococcus lactis, which is present upstream of the yoaB gene, functions as a Mn(2+)-specific genetic ON-switch, and modulates expression of proteins which are significant for Mn(2+) homeostasis. The P1.1 switch helix of the aptamer domain of the riboswitch contains an intrinsic transcription terminator structure, which gets stabilized with Mn(2+) binding and causes disruption of terminator structure and allows the continuation of transcription. The current research work involved the evaluation of structural and dynamical properties of the yybP-ykoY riboswitch of L. lactis in its Mn(2+)-free, Mn(2+)-bound (wild-type), and Mn(2+)-bound mutant (A41U) states by applying molecular dynamics simulations. Based on the simulations, the effects of Mn(2+) absence and A41U mutation were evaluated on the structure and dynamics of the riboswitches followed by the computation of the free energy of metal binding in the wild-type and the mutant riboswitches. The simulation results provided insights into the properties of the riboswitch with the focus on the dynamics of the P1.1 switch helix, and the manganese binding site designated as M(B) site, as well as the relative stability of the wild-type and the mutant riboswitches, which helped to understand the structural and dynamical role of the metal ion involved in the function of Mn(2+)-sensing riboswitch.