Diffusion of transfer ribonucleic acid depends on its position inside a ribosome
Diffusion of transfer ribonucleic acid depends on its position inside a ribosome lead image
As the sole protein producers in cells, ribosomes are responsible for many biological processes. In a new paper, Yang et al. present studies of the diffusive behavior of transfer ribonucleic acid (tRNA) molecules inside ribosomes to better understand principles of large-scale biological dynamics.
The researchers focused their calculations on the diffusion of tRNA molecules in the ribosome during a conformational stage that follows the initial association between the two. This process, known as accommodation, allows the ribosome a final opportunity to determine whether to accept or reject the incoming tRNA molecule.
“Understanding diffusion helps us characterize the energy landscape of accommodation, a conformational motion that governs accuracy of gene expression,” said author Paul Whitford.
The authors found the diffusion coefficient of the tRNA strongly depends on the position of the tRNA molecule. Specifically, during the accommodation process when the tRNA enters the ribosome, the diffusion coefficient decreases by an order of magnitude. This decrease in diffusion rate indicates an increased energetic roughness in the interaction between the tRNA and ribosome.
To estimate the diffusion coefficient at various points in the accommodation process, the researchers conducted a set of all-atom explicit-solvent molecular dynamics simulations. They calculated the diffusion in three ways and found the results were consistent with one another.
A major goal of ribosome studies is to understand the key molecular properties that govern biological dynamics, and this work will enable future studies to make precise comparisons between theory and experiment. “There are roughly 10 large-scale conformational rearrangements that are associated with tRNA binding and release from the ribosome,” Whitford said. “This work also provides a blueprint for how to characterize any number of conformational motions in the ribosome.”
Source: “Diffusion of tRNA inside the ribosome is position-dependent,” by Huan Yang, Prasad Bandarkar, Ransom Horne, Vitor B. Leite, Jorge Chahine, and Paul C. Whitford, The Journal of Chemical Physics (2019). The article can be accessed at https://doi.org/10.1063/1.5113814 .
