Relationships between alpha and beta secondary structures and amino-acid pseudosymmetrical arrangements

A total of 51 polypeptides of known amino acid sequence and secondary structure have been screened for the presence of symmetrical arrangements of amino acids. Similarity between amino acids was derived by using a genetic test (minimum mutation distance) or a structural test (relative frequencies of amino acids substitutions in families of related proteins). It is shown that the frequency of proteins displaying symmetrical arrangements of amino acids is slightly higher than predicted by chance. In contrast, when the analysis is restricted to protein subregions displaying identical types of secondary structure, the frequency of proteins in which the alpha and beta subregions exhibit symmetrical arrangements of amino acids is significantly higher than predicted by chance. On the other hand, it is observed that more discriminatory results are always obtained when the structural test is used as a criterion for amino acid similarity. These data suggest that symmetrical arrangements of amino acids could result from structural constraints imposed either by the alpha or beta secondary structures. It is postulated that the regular alternation in hydrophobicity which is generally observed in the amino acid sub-sequences displaying alpha or beta secondary structures may be responsible for the occurrence of symmetrical arrangements of amino acids.