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A Novel Structural Motif and Structural Trees for Proteins Containing It

A. M. Kargatov and A. V. Efimov*

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; fax: (495) 632-7871; E-mail: efimov@protres.ru

* To whom correspondence should be addressed.

Received April 15, 2009
In the present study, a novel structural motif that can be represented as a combination of the known βαβ-unit and ψ-motif is described and analyzed. In theory, there are four possible combinations of the motifs since each of them can exist in two forms, left-handed and right-handed. For this study, we have selected 140 nonhomologous proteins in which 158 combinations of such types have been found. The combination of the right-handed ψ-motif and the right-handed βαβ-unit has been shown to occur most often (87 cases out of 158) and the combination of the left-handed βαβ-unit and the left-handed ψ-motif does not occur at all. Three novel structural trees in which the commonly occurring combinations are taken as the root structures have been constructed.
KEY WORDS: βαβ-unit, modeling, ψ-motif, protein folding, structural classification

DOI: 10.1134/S0006297910020161