Journal Article

Pressure pushes tRNALys3 into excited conformational states

Puglisi, Joseph D., Peters, Edgar V., Patel, Karishma S., Harish, Balasubramanian, Makhatadze, George, Royer, Catherine A., Koduru, Tejaswi, McCallum, Scott A., Gillilan, Richard E., Larsen, Kevin P., Wang, Jinqiu, Puglisi, Elisabetta V.

2023

Overview

Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNALys3, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine and guanosine U–A and G–C base pairs of tRNALys3. HP-SAXS profiles showed a change in shape, but no change in overall extension of the transfer RNA (tRNA) at HP. Configurations extracted from computational ensemble modeling of HP-SAXS profiles were consistent with the NMR results, exhibiting significant disruptions to the acceptor stem, the anticodon stem, and the D-stem regions at HP. We propose that initiation of reverse transcription of HIV RNA could make use of one or more of these excited states.

• Publisher: National Academy of Sciences
• Subject: Biological Sciences / Biophysics and Computational Biology / Computer applications / Excitation / HIV / Human immunodeficiency virus / Hydrostatic pressure / NMR / Nuclear magnetic resonance / Protons / Reverse transcription / Ribonucleic acid / RNA / Small angle X ray scattering / Structural analysis / Transcription initiation / tRNA / Uridine / X-ray scattering