Frameshift Suppressor tRNA Physical Modeling

tRNA Structure

All tRNAs, whether they contain a 3- or 5-base anticodon, conform to a general structure. They feature a series of loops and stems folded into a tertiary L-shape, with the amino acid acceptor arm opposite the anticodon. The structure of tRNA molecules is important because their unique structural motifs are recognized by the ribosome and enzymatic pathways, and allow tRNAs to carry out their life-sustaining function.

Using the PDB Format to Design a Frameshift Suppressor tRNA

The PDB format is a standard file type used in molecular modeling and known structures to code for the Cartesian space coordinate triple for each atom within the molecule. It also includes portions describing which atoms combine to form nucleotides or amino acids, the locations of hydrogen bonds, and other information pertaining to the structure of molecules. A PDB file coding for a theorized model of a 5-base anticodon was made by modifying the anticodon loop of the existing PDB file 1EHZ—yeast phenylalanine tRNA. This particular tRNA was one of the first to undergo extensive study, and remains a model molecule among the countless tRNA molecules within the diverse variety of life.

Building a Physical Model