Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids

Junko Tanaka, Nobuhide Doi, Hideaki Takashima, Hiroshi Yanagawa

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)


Screening of functional proteins from a random-sequence library has been used to evolve novel proteins in the field of evolutionary protein engineering. However, random-sequence proteins consisting of the 20 natural amino acids tend to aggregate, and the occurrence rate of functional proteins in a random-sequence library is low. From the viewpoint of the origin of life, it has been proposed that primordial proteins consisted of a limited set of amino acids that could have been abundantly formed early during chemical evolution. We have previously found that members of a random-sequence protein library constructed with five primitive amino acids show high solubility (Doi et al., Protein Eng Des Sel 2005;18:279-284). Although such a library is expected to be appropriate for finding functional proteins, the functionality may be limited, because they have no positively charged amino acid. Here, we constructed three libraries of 120-amino acid, random-sequence proteins using alphabets of 5, 12, and 20 amino acids by preselection using mRNA display (to eliminate sequences containing stop codons and frameshifts) and characterized and compared the structural properties of random-sequence proteins arbitrarily chosen from these libraries. We found that random-sequence proteins constructed with the 12-member alphabet (including five primitive amino acids and positively charged amino acids) have higher solubility than those constructed with the 20-member alphabet, though other biophysical properties are very similar in the two libraries. Thus, a library of moderate complexity constructed from 12 amino acids may be a more appropriate resource for functional screening than one constructed from 20 amino acids. Published by Wiley-Blackwell.

Original languageEnglish
Pages (from-to)786-795
Number of pages10
JournalProtein Science
Issue number4
Publication statusPublished - 2010 Apr


  • In vitro selection
  • Primitive amino acids
  • Protein solubility
  • Random DNA library
  • Reduced alphabet
  • mRNA display

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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