Fifth amino acid for primitive protein

Abstract

Although present proteins are constructed from about 20 amino acids, primitive proteins were frequently considered that they were composed by only limited number of amino acids. Generally, Glu, Ala, Asp, and Val were presumed to be the components of primitive proteins. In this study, Glu were added to the tentative primitive proteins as the “fifth” amino acid, and the protein structures were evaluated. Glu, Ala, Asp, Val, and Glu were randomly sequenced, and the three-dimensional structures of random peptides were predicted by using molecular dynamics simulations. The results suggest that the tentative primitive proteins including Glu can form secondary structures more frequently than those without Glu. In addition, the structural rigidity of the random peptide for the peptide including Glu was larger than those for the peptide without Glu. Thus, “protein-like” peptides can be obtained by only five types of amino acids, Gly, Ala, Asp, Val, and Glu, which can existed on the primitive Earth.