Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds

Abstract

Background There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding. Results Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure to assess how well the prebiotic amino acid set preserves fold information against all other possible ten-amino acid sets. An extensive virtual mutagenesis procedure revealed that the prebiotic set excellently preserves sequence-dependent information regarding both backbone conformation and tertiary contact matrix of proteins. We observed that information retention is fold-class dependent: the prebiotic set sufficiently encodes the structure space of α/β and α + β folds, and to a lesser extent, of all-α and all-β folds. The prebiotic set appeared insufficient to encode the small proteins. Assessing how well the prebiotic set discriminates native vs. incorrect sequence-structure matches, we found that α/β and α + β folds exhibit more pronounced energy gaps with the prebiotic set than with nearly all alternatives. Conclusions The prebiotic set optimally encodes local backbone structures that appear in the folded environment and near-optimally encodes the tertiary contact matrix of extant proteins. The fold-class-specific patterns observed from our structural analysis confirm the postulated timeline of fold appearance in proteogenesis derived from proteomic sequence analyses. Polypeptides arising in a prebiotic environment will likely form α/β and α + β-like folds if any at all. We infer that the progressive expansion of the alphabet allowed the increased conformational stability and functional specificity of later folds, including all-α, all-β, and small proteins. Our results suggest that prebiotic sequences are amenable to mutations that significantly lower native conformational energies and increase discrimination amidst incorrect folds. This property may have assisted the genesis of functional proto-enzymes prior to the expansion of the full amino acid alphabet.

In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations

“…The structural and functional properties of early proteins are still debated. While previous studies have pointed out that acidic proteins can be soluble and sustain secondary structure information, it has generally been unclear how those proteins can form compact architectures and/or interact with the highly acidic nucleic acids (Doi et al 2011;Tanaka et al 2011;Longo et al 2013;Shibue et al 2018;Newton et al 2019;Solis 2019). A recent study by the Tawfik group suggested that polyamines and divalent cations may have played an important role in promoting the folding of such early proteins (Despotović et al 2020).…”

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase

“…Even though different reduced sets (of 7–13) of the amino acid alphabet have been shown or predicted to be sufficient for protein folding and catalysis, to our knowledge, none of the experimental studies recovered enzyme activity in complete absence of aromatics 13–18 . Computational inquiry indicates that the aromatics are the strongest structure promoters among the 20 amino acid alphabet 19 .…”

Enzyme catalysis prior to aromatic residues: reverse engineering of a dephosphoCoA kinase

“…Even though different reduced sets (of 7-13) of the amino acid alphabet have been shown or predicted to be sufficient for protein folding and catalysis, to our knowledge, none of the experimental studies recovered enzyme activity in complete absence of aromatics (13)(14)(15)(16)(17)(18). Computational inquiry indicates that the aromatics are the strongest structure promoters among the 20 amino acid alphabet (19).…”