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Biology subjects

Cherepashuk, I.

Publications and source records attributed to Cherepashuk, I..

2 recordsLinked to original sources

Peptides at vesicle and mineral prebiotic interfaces

The origin of life likely involved a complex interplay between organic molecules and mineral surfaces, yet the molecular details of these interactions remain poorly understood. Over recent decades, considerable research has focused on the individual roles of key biomolecules - such as RNA, lipids, and proteins - in early abiogenesis. However, this reductionist view offers only a partial picture because the emergence of life likely involved networks of molecular interactions that collectively shaped early functional assemblies. In this study, we examine the ability of peptides - arguably one of the most abundant early polymers - to interact with mineral surfaces and lipid vesicles, prebiotic interfaces and compartments. Using peptide libraries constructed from either prebiotically plausible or contemporary amino acids, we demonstrate that while acidic residues drive peptide binding to mineral surfaces (such as fluorapatite, studied here), the inclusion of arginine - a basic residue that may have been accessible in specific prebiotic environments - synergistically enhances the mobilization of bioavailable phosphate from geological reservoirs. Furthermore, we observe a functional divergence in vesicle interactions: while prebiotic alphabets promote dynamic membrane behaviours such as budding, libraries with late canonical amino acids can help preserve vesicle integrity against salt-induced collapse. Our finding supports the view that interactions with peptides can elicit changes in both prebiotic minerals and vesicles, underscoring the importance of studying these systems collectively.

evolutionary biology↗

Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability

Whereas modern proteins rely on a quasi-universal repertoire of 20 canonical amino acids (AAs), numerous lines of evidence suggest that ancient proteins relied on a limited alphabet of 10 early AAs, and that the 10 late AAs were products of biosynthetic pathways. However, many non-proteinogenic AAs were also prebiotically available, which begs two fundamental questions: Why do we have the current modern amino acid alphabet, and Would proteins be able to fold into globular structures as well if different amino acids comprised the genetic code? Here, we experimentally evaluated the solubility and secondary structure propensities of several prebiotically relevant amino acids in the context of synthetic combinatorial 25-mer peptide libraries. The most prebiotically abundant linear aliphatic and basic residues were incorporated along with or in place of other early amino acids to explore these alternative sequence spaces. We show that foldability was a critical factor in the selection of the canonical alphabet. Unbranched aliphatic and short-chain basic amino acids were purged from the proteinogenic alphabet despite their high prebiotic abundance because they generate polypeptides that are over-solubilized and have low packing efficiency. Surprisingly, we find that the inclusion of a short-chain basic amino acid also decreases polypeptides secondary structure potential. Our results support the view that despite lacking basic residues, the early canonical alphabet was remarkably adaptive at supporting protein folding and explain why basic residues were only incorporated at a later stage of the alphabet evolution.

biophysics↗