Prebiotic protein design supports a halophile origin of foldable proteins

There are significant challenges in forming testable hypotheses regarding abiogenesis (i.e., the origin of life); for example, the original environment on the early Earth during the process of abiogenesis is a matter of debate [although it was significantly different from the current environment (Oparin, 1952; Hazen et al., 2008)]. Furthermore, the process of abiogenesis occurred over a time scale that is impractical to replicate as a laboratory experiment. More difficult still is the likelihood that current life forms are far removed from the earliest “living systems”—which may well have utilized entirely different initial energetic, biochemical, and “genetic” systems. Despite such difficulties, there are potentially testable hypotheses regarding the origin of important classes of biomolecules from abiotic processes. A key biomolecule that emerged in abiogenesis is the foldable polypeptide, which ultimately evolved to provide essentially all of the important biochemical and structural machinery in living systems. Each of the generally-acknowledged abiotic chemical processes present during abiogenesis, including atmospheric spark discharge, hydrothermal vent chemistry, as well as deep-space synthesis and delivery of organic material via comet and asteroid bombardment, can produce a subset of the 20 common α-amino acids [for a summary see Longo and Blaber (2012)]. Such prebiotic amino acids would have provided the raw material for the earliest polypeptides (i.e., “proteogenesis”); thus, the properties of such amino acids and polypeptides are of special interest. As with all things related to abiogenesis, the set of prebiotic amino acids available for proteogenesis has been a matter of debate; however, a compilation of broad and diverse analyses is arguably converging upon a consensus set of 10 prebiotic α-amino acids (Figure 1). The alphabet size and chemical properties of the prebiotic α-amino acids are critical parameters as regards the capability to form foldable polypeptides. The rules of protein folding are not fully understood; however, some essential requirements of amino acids to promote folding are known. The tertiary structure of folded proteins is an assemblage of common secondary structure elements—including α-helix, β-strand, and reverse-turns. Thus, a foldable set of amino acids includes representatives with a high propensity to form each of the common secondary structure elements. Additionally, soluble globular proteins typically fold so as to sequester hydrophobic side chains within the protein interior, and this forms a significant energetic contribution to the overall stability of the folded protein; thus, a foldable set of amino acids contains both hydrophobic and hydrophilic members. Finally, functional considerations require that among the amino acids is a representative that can act as a nucleophile, and thereby provide useful chemical activity to an otherwise benign structural scaffold. While folding requirements are demanding, it is clear that the extant set of 20 common α-amino acids is redundant in this regard. Thus, the question of the minimum α-amino acid alphabet necessary to enable protein foldability has also been investigated, with a proposed minimum alphabet size of 9–10 amino acids (Romero et al., 1999; Murphy et al., 2000). Thus, with regard to set size, the prebiotic α-amino acid alphabet is located on the very cusp of foldable potential—a precarious position indeed, as it would provide essentially no redundancy in the requirements for protein foldability. Viewed in these terms, the prebiotic set is remarkable in containing all necessary elements for foldability—including high-propensity amino acids for each of the basic types of protein secondary structure, hydrophobic and hydrophilic amino acids, as well as several nucleophilic amino acids [for a discussion of such properties see Longo and Blaber (2012)]. However, the characteristics of a protein comprised of the prebiotic set of α-amino acids present a stark deviation from the majority of extant proteins, since aromatic residues, key contributors to the critical hydrophobic effect that drives protein folding, are absent in the prebiotic alphabet. Furthermore, there are no basic amino acids in the prebiotic set (McDonald and Storrie-Lombardi, 2010), thus restricting protein design to exclusively acidic polypeptides—limiting the presence of salt bridge interactions and resulting in acidic pI. A number of successful studies of simplified protein design have been reported whereby foldable proteins have been constructed from a reduced α-amino acid alphabet, and relevance for proteogenesis have been described. However, such studies have focused exclusively upon achieving minimization of the alphabet size, without regard to the prebiotic relevance of the included amino acid alphabet.