Protein Engineering vol. 16 no. 12 pp. 897-904, 2003
© 2003 Oxford University Press
A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells?
1Serono Reproductive Biology Institute, One Technology Place, Rockland, MA 02370, 2Department of Biology, MIT, Mass Avenue, Cambridge, MA 02139 and 3BMERC, Boston University, 36 Cummington Street, Boston, MA 02215, USA
4 To whom correspondence should be addressed. e-mail: Jadwiga.Bienkowska{at}serono.com
The question of protein homology versus analogy arises when proteins share a common function or a common structural fold without any statistically significant amino acid sequence similarity. Even though two or more proteins do not have similar sequences but share a common fold and the same or closely related function, they are assumed to be homologs, descendant from a common ancestor. The problem of homolog identification is compounded in the case of proteins of 100 or less amino acids. This is due to a limited number of basic single domain folds and to a likelihood of identifying by chance sequence similarity. The latter arises from two conditions: first, any search of the currently very large protein database is likely to identify short regions of chance match; secondly, a direct sequence comparison among a small set of short proteins sharing a similar fold can detect many similar patterns of hydrophobicity even if proteins do not descend from a common ancestor. In an effort to identify distant homologs of the many ubiquitin proteins, we have developed a combined structure and sequence similarity approach that attempts to overcome the above limitations of homolog identification. This approach results in the identification of 90 probable ubiquitin-related proteins, including examples from the two prokaryotic domains of life, Archaea and Bacteria.
Received December 1, 2002; revised October 22, 2003; accepted October 24, 2003
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