Three conformations of the tRNA and the recognition of the synthetase

In the previous symposium, it was pointed out that a complex of the anticodon bases and the discriminator base on the tRNA could recognize the corresponding protein amino acid by a key and lock relation. There are two possibilities to make this complex: (1) a set of two L shaped tRNAs in a head and tail conformation (2) the possibility for an U shaped structure of the tRNA. By using the HGS molecular model, the whole tRNAs were constructed and the above possibilities were checked. In both cases, the C4Ns were easily formed as expected. In the 2L case, the alpha helixes on the aminoacyl tRNA synthetase were found to fit the grooves on the two tRNAs beautifully. The C4N was formed just on the Rossmann fold of the synthetase. In the U case, since the uracyl at the 8th position at the D stem could have a covalent bonding to synthetase, the C4N is again formed over the Rossmann fold. After the amino acid charging, the tRNA could have an extended, T C exposed, structure. In concerning with this conformational change, the amino acid uptake through membrane by the specific uncharged tRNA can be a good evidence for the direct interaction between the amino acids and its cognate tRNAs, thus for the C4N.