The Relevance of Peptides That Bind FeS Clusters, Phosphate Groups, Cations or Anions for Prebiotic Evolution

Abstract

The focus of this chapter is on the significance for evolution of three-dimensional peptide motifs made from main chain atoms of a few amino acid residues. The CONH group of every peptide bond is a polar group with the oxygen having substantial fractional negative charge and the hydrogen having significant partial positive charge. Appropriate conformations of polypeptides create binding sites for either anions or cations by bridging of the form NH–anion–HN or CO–cation–OC between non-adjacent CONH groups. These motifs are more common in proteins than is generally realized. About 8% of amino acid residues in native folded proteins belong to anion-binding motifs and another 8% belong to cation-binding motifs. Examination of native and synthetic polypeptides suggests these figures were even higher for peptides occurring during early evolution. The most common cation-binding motif is one named the niche, while the most common anion-binding motif is called the nest. Some nests bind single atoms and some bind groups like FeS clusters and phosphates. The P-loop, which is the commonest ATP/GTP-binding feature in proteins, as well as being one of the most ancient features of proteins in general, incorporates a phosphate-binding nest within its active site. If di- or triphosphates were the major sources of instant energy in the earliest forms of metabolism, phosphate-binding nests can be said to have retained the structure required for energy generation and thus be one of the most ancient molecular relics in existence.