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Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.

Longo LM, Lee J, Blaber M
Proc Natl Acad Sci U S A 110 2135-9 (2013)
Related entries: 3q7w, 3q7y, 4d8h

Cited: 45 times
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Abstract

A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.

Articles - 3q7x mentioned but not cited (1)

  1. Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Longo LM, Lee J, Blaber M. Proc. Natl. Acad. Sci. U.S.A. 110 2135-2139 (2013)


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  15. In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions. Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P, Hlouchová K. Mol Biol Evol 39 msac032 (2022)
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  19. Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet. Zhao F, Akanuma S. J Mol Evol 91 10-23 (2023)
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  26. Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains. Seal M, Weil-Ktorza O, Despotović D, Tawfik DS, Levy Y, Metanis N, Longo LM, Goldfarb D. J Am Chem Soc 144 14150-14160 (2022)
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  28. Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. Longo LM, Despotović D, Weil-Ktorza O, Walker MJ, Jabłońska J, Fridmann-Sirkis Y, Varani G, Metanis N, Tawfik DS. Proc Natl Acad Sci U S A 117 15731-15739 (2020)
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