Figure 14: Concept of RNA assisted protein folding.
The model comprises tRNA (upper part) and protein (lower part) folding cycles. During the tRNA cycle, the aminoacyl-tRNA (clover-leaf form, (a)) unfolds, interacts with its codon, and the previously attached tRNA (b) refolds to a configuration that brings the amino acid tail into close proximity with the codonanticodon site (c, d), loses the amino acid, refolds to its original cloverleaf configuration (e) and is recycled.
The protein folding cycle begins when the peptide synthetase forms peptide bonds between individual amino acids. Some “dedicated” amino acids remain attached to their codons, but most are displaced. The difference in length between the peptide and mRNA creates mRNA folds (f) and the interaction between complementary codons creates peptide folds (g), one after the other (h). The growing peptide-mRNA complex dissociates after “pairing” the last “dedicated” amino acid pair with its corresponding codon pair (i) and the mRNA is recycled. The numbers indicate the positions of the dedicated amino acids and their codons in a 25 amino acid-long peptide and its 75 nucleotide-long mRNA.
The inserted gray boxes depict the rules of the Proteomic Code [2]: colocating amino acids (α and β) and are encoded by codons (x and y) which are complementary to each other at the 1st and 3rd nucleotide positions; they form different complexes with each other (x/α, y/β, x/y/α/β, x/y, α/β).