Three-dimensional structure prediction of [GADS]-proteins as tentative primitive proteins

[GADV]-protein is a random peptide constructed from glycine (G), alanine (A), aspartic acid (D), and valine (V), whereas [GADS]-protein is constructed from G, A, D, and serine (S). Both [GADV]- and [GADS]-proteins are candidates of primitive proteins. In this study, the three-dimensional structure formation ability of [GADS]-proteins was compared with that of [GADV]-proteins. Based on the results of molecular dynamics simulations, the secondary structure formation ability and rigid structure formation ability of [GADS]-proteins were inferior to those of [GADV]-proteins. [GADV]- and [GADS]-proteins comprise limited types of amino acids and are candidates for primitive proteins. In this study, the abilities of forming "protein-like structures" for [GADV]- and [GADS]-proteins were evaluated using replica exchange molecular dynamics simulations. Although [GADS]-proteins exhibited higher solubilities than [GADV]-proteins, the rigid structure formation abilities of [GADS]-proteins were inferior to those of [GADV]-proteins.