title: 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.
authors.affiliation: Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic. Electronic address: nahalka@savba.sk.
authors.forename: Jozef
authors.initials: J
authors.lastname: Nahalka
mesh_terms: D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D005815:Genetic Code; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism*
chemical_list: D010455:Peptides; D011506:Proteins; D012343:RNA, Transfer; D000604:Amino Acyl-tRNA Synthetases
keywords: Aminoacyl transfer RNA synthetases; Bioinformatic analysis; Protein–RNA recognition; Release factor 1