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PEDS Advance Access published online on May 31, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi034
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org
Received March 18, 2005
Revised April 29, 2005
Accepted May 5, 2005

Article

High solubility of random-sequence proteins consisting of five kinds of primitive amino acids

Nobuhide Doi 1, Koichi Kakukawa 1, Yuko Oishi 1, and Hiroshi Yanagawa 1*

1 Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan

* To whom correspondence should be addressed.
Hiroshi Yanagawa, E-mail: hyana{at}bio.keio.ac.jp


  Abstract

Searching for functional proteins among random-sequence libraries is a major challenge of protein engineering; the difficulties include the poor solubility of many random-sequence proteins. A library in which most of the polypeptides are soluble and stable would therefore be of great benefit. Although modern proteins consist of 20 amino acids, it has been suggested that early proteins evolved from a reduced alphabet. Here, we have constructed a library of random-sequence proteins consisting of only five amino acids, Ala, Gly, Val, Asp and Glu, which are believed to have been the most abundant in the prebiotic environment. Expression and characterization of arbitrarily chosen proteins in the library indicated that five-alphabet random-sequence proteins have higher solubility than do 20-alphabet random-sequence proteins with a similar level of hydrophobicity. The results support the reduced-alphabet hypothesis of the primordial genetic code and should also be helpful in constructing optimized protein libraries for evolutionary protein engineering.

Keywords: genetic code; protein design; protein evolution; reduced amino acid alphabet; synthetic library.
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