Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code

The nucleotide frequencies in the second codon positions of genes are remar kably different for the coding regions that correspond to different seconda ry structures in the encoded proteins, namely, helix, beta -strand and aper iodic structures. Indeed, hydrophobic and hydrophilic amino acids are encod ed by codons having U or A, respectively, in their second position. Moreove r, the beta -strand structure is strongly hydrophobic, while aperiodic stru ctures contain more hydrophilic amino acids. The relationship between nucle otide frequencies and protein secondary structures is associated not only w ith the physico-chemical properties of these structures but also with the o rganisation of the genetic code. In fact, this organisation seems to have e volved so as to preserve the secondary structures of proteins by preventing deleterious amino acid substitutions that could modify the physico-chemica l properties required for an optimal structure. (C) 2000 Elsevier Science B .V. All rights reserved.