Stabilization Mechanism\nof Initiator Transfer RNA\nin the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations

Proteins play a variety of roles in biological phenomena\nin cells.\nProteins are synthesized by the ribosome, which is a large molecular\ncomplex composed of proteins and nucleic acids. Among the many molecules\ninvolved in the process of protein synthesis, tRNA is one of the essential\nmolecules. In this study, coarse-grained molecular dynamics simulations\nwere performed to understand how the tRNA molecule is stabilized in\nthe ribosome, and the free energy along the dissociation path of the\ntRNA was calculated. We found that some ribosomal proteins, which\nare components of the ribosome, are involved in the stabilization\nof the tRNA. The positively charged amino acid residues in the C-terminal\nregion of the ribosomal proteins are particularly important for stabilization.\nThese findings contribute to our understanding of the molecular evolution\nof protein synthesis in terms of the ribosome, which is a universal\ncomponent of life.