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"Ribosomal proteins are essential components of the ribosome, working with ribosomal RNA (rRNA) to form the core machinery that translates mRNA into proteins. While rRNA carries out most catalytic steps, ribosomal proteins stabilize rRNA structure, guide ribosome assembly, and help correctly position mRNA and tRNA during translation. Because many ribosomal proteins are evolutionarily conserved, their structures provide useful models for understanding general mechanisms of RNA recognition.
In this project, we will carry out a statistical survey of the Protein Data Bank (PDB) to identify the structural and sequence features of ribosomal proteins across diverse organisms. Following data collection, we will use computational chemistry tools such as Amber 2020 to model and analyze ribosomal protein-nucleic acid interactions. These analyses will characterize common protein folds, conserved sequence motifs, and structural features associated with RNA binding. Key amino acids involved in hydrogen bonding, electrostatic contacts with the RNA backbone, and stacking interactions with nucleobases will be identified. Comparative structural analysis and conservation mapping will then be used to evaluate similarities and differences across ribosomal proteins from bacteria, archaea, and eukaryotes.
Findings of this project will identify shared principles that ribosomal proteins use to recognize and stabilize RNA, as well as lineage-specific adaptations that reflect differences in ribosome size and function. These results will provide an integrated view of the structural and functional roles of ribosomal proteins in translation and offer a foundation for understanding how mutations or chemical inhibitors may influence ribosome performance."
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