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Description
The protoribosome, carrying the peptidyl transferase center, represents an ancestral core of modern ribosomes. Fragments of several ribosomal proteins, so called rPeptides, extend toward the PTC and stabilize protoribosomal RNA (1).
In this work, we investigate the conformational stability of a protoribosome model from T. thermophilus upon replacement of lysine and arginine residues to their shorter prebiotic analogues, diaminobutyric acid (DAB) and diaminopropionic acid (DPR). We used all-atom molecular dynamics simulations with GROMACS. Our preliminary data show increased root mean squared deviation of two rPeptides, indicating looser binding, while other rPeptides and the RNA scaffold remained conformationally more stable. These results suggest that ancestral ribosomal proteins with electropositive residues with a shorter side chains may have reduced structural stabilization capacity. To deepen this understanding, future work will include additional prebiotically plausible amino acids, providing a more complete picture of protoribosome optimization and its role in the origin of life.
(1) Codispoti et al.: The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability, Nucl. Acids Res. 2024.
