Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality

Abstract

Primitive proteins are likely to have been constructed from non-enzymatically generated amino acids, due to the weak enzymatic activities of primitive biomolecules such as ribozymes. On the other hand, almost all present proteins are constructed only from l-amino acids. Therefore, there must have been a mechanism early in the origins of life that selected for one of the optical isomers of amino acids. In this study, we used molecular dynamics simulations to predict the three-dimensional structures of the putative primitive proteins constructed only from glycine, alanine, aspartic acid, and valine ([GADV]-peptides). The [GADV]-peptides were generated computationally at random from l-amino acids (l-[GADV]-peptides) and from both l- and d-amino acids (dl-[GADV]-peptides). The results indicate that the tendency of secondary structure formation for l-[GADV]-peptides was larger than that for dl-[GADV]-peptides, and l-[GADV]-peptides were more rigid than dl-[GADV]-peptides. These results suggest that the proteins with rigid structure motifs were more prone to have been generated in a primordial soup that included only l-amino acids than a the soup including racemic amino acids. The tendency of the rigid structure motif formation may have played a role in selecting for the homochirality that dominates life on Earth today.