Theoretical infrared spectroscopy of transfer RNA: Insight on ion effects

Transfer RNA (tRNA) plays a central role in the translation process of protein synthesis. It is established that cations such as Mg²⁺ help stabilize the secondary and tertiary structure of tRNA, but the ion effects are not fully understood at the molecular level. In this work, we focus on the yeast phenylalanine tRNA and combine molecular dynamics simulations and IR spectra modeling to elucidate the influence of the K⁺ and Mg²⁺ ions on its structure. Using the recently developed frequency and coupling maps, we calculate the IR spectra of the phenylalanine tRNA in the folded and unfolded states in aqueous solutions and show that the theoretical spectra are in good agreement with experiments. We further demonstrate how the K⁺ or Mg²⁺ ions alter the vibrational couplings and spectral features of the biomolecule, which results from changes in its secondary structure and hydrogen bonding conditions, and reveal that the Mg²⁺ ions induce partial unfolding of the tRNA. Our results demonstrate that the IR spectra modeling methods provide a useful tool to characterize the structure and dynamics of nucleic acids.