Unraveling the Structure-Spectrum Relationship of Yeast Phenylalanine Transfer RNA: Insights from Theoretical Modeling of Infrared Spectroscopy.

ABSTRACT: Yeast phenylalanine tRNA (tRNA^phe) is a paradigmatic model in structural biology. In this work, we combine molecular dynamics simulations and spectroscopy modeling to establish a direct link between its structure, conformational dynamics, and infrared (IR) spectra. Employing recently developed vibrational frequency maps and coupling models, we apply a mixed quantum/classical treatment of the line shape theory to simulate the IR spectra of tRNA^phe in the 1600-1800 cm^-1 region across its folded and unfolded conformations and under varying concentrations of Mg²⁺ ions. The predicted IR spectra of folded and unfolded tRNA^phe are in good agreement with experimental measurements, validating our theoretical framework. We then elucidate how the

SUBMITTER: Qian C 

PROVIDER: S-EPMC12013858 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature