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Description
The ribosome is a macromolecular complex that catalyzes all protein synthesis. It is composed of ribosomal RNA and proteins, which contribute to both its shape and function. The catalytic center of the ribosome, the peptidyl transferase, is where peptide bond formation occurs, and ribosomal proteins were gradually incorporated into this core during evolution. Whether the proteins associated with the catalytic center needed to adapt, or naturally adopted specific conformations based on their native states regardless of ribosomal interactions, is still not fully understood. We used molecular dynamics simulations of short ribosomal-protein fragments close to the catalytic center in water. Dihedral angles were compared with experimental data. The dihedral angles of peptides in water closely resemble the ones experimentally obtained and are near the global energy minima found in the modern ribosome. This may hint that the conformational pre-arrangement could contribute to the selection pressure. As a negative control, we are conducting simulations with randomized amino acid sequences containing the same amino acid composition as the original fragments. The results may give some insight into how proteins and RNA came to work together in the ribosome.
