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.

The cloverleaf model shows how the RNA strand base pairs with itself to form loops and stems, but does not accurately depict its structural motif.

The tertiary structure of a tRNA molecule shows how the stems and loops fold together.

The Cloverleaf Model

The structure of tRNA molecules is often represented by showing how stems and loops are formed by base pairing within a two-dimensional context—useful for depicting secondary structure, but unable to show three dimensional folding. Each tRNA molecule consists of five arms, and each, with the exception of the acceptor arm, contains both stems and loops. A stem is formed by self base-pairing along the RNA strand, and loops are formed from non-paired nucleotides. The 3′ terminus of the TRNA strand protrudes beyond the 5′ terminus by several nucleotides, but the 5′ terminus is base-paired. The appropriate amino acid is connected to the 3′ terminus by an amino acyl tRNA synthetase, an enzyme that uses the unique structural motif of each tRNA to consistently pair it with its designated amino acid. Moving from the 3′ terminus in the 5′ direction, the TΨC arm is encountered. It is so named because of the presence of the sequence 5′-TΨC-3′, where Ψ stands for the base pseudouracil, an isomer of uracil formed from post-transcriptional modification. Continuing in the 5′ direction, the variable loop is encountered. This portion of the tRNA family of molecules shows high size variation, from only a few nucleotides to well over a dozen. Next is the anticodon arm, which contains the anticodon itself. The anticodon recognizes its mRNA complement, and may contain a wobble base-pairing at the 5′ end residue of the anticodon. This wobble base-pairing often utilizes the abundant assortment of non-standard nucleotides. The final arm before the 5′ terminus is the D arm. It contains the D base, or dihydrouracil.

The Spacial tRNA Structural Motif

Base-pairing between arms stabilizes the structure of the tRNA molecule into a L-shape. The acceptor arm is positioned at one and of the L, and the anticodon at the other. The size and sequence of each arm influences the spacial structure of the tRNA, and allows enzymes responsible for maintaining function to recognize each tRNA.

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.

The PDB Format Defined

PDB is an acronym for Protein Data Bank. Although predominately a resource for protein files, it does include some nucleic acid files. Coordinate files following the PDB format are in plain text, and carry the ".pdb" extension. A PDB file itself contains a series of columns of data aligned to prescribed boundaries. A PDB file contains an expanse of information pertaining to the molecule in question. Among them are authorship of the file, method of data collection, primary sequence, secondary structural features, the location of hydrogen bonds and disulfide bridges, placement of hetero groups such as solvents, and most importantly the Cartesian space coordinate triples that code for individual atom placement.

Modifying a PDB File

Building a Physical Model