Protein–RNA recognition: Cracking the code

Abstract

In early papers, the intent was to find a simple protein–RNA/DNA recognition code. Many people expected a one-to-one correspondence between amino acids and nucleic bases, similar to the code that specifies how one DNA base pairs with another. Despite the lack of such a code, which was evident in the first crystal structures, researchers were indeed unwilling to give up on the idea. Despite the intense interest, a simple one-to-one correspondence has not materialised. The work presented here revisits this theme, and reports a general trend in which four elementary amino acids – G, A, V, and D – have a specific selectivity for four basic nucleotides – g, c, u, and a. During the evolution, as amino acid alphabets increased, new amino acids substituted G, A, V, D amino acids in way to keep hydropathic similarity and the selectivity to minimise errors in established RNA–protein interactions, 1-letter code was created. Additionally, the first nucleotide in codons is used for a 2-letter code. Protein–RNA recognition, visualised by these two code principles, uses a rotation of sensing and anti-sensing sequences in architecture of recognising peptides.