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Protein Engineering, Vol. 15, No. 5, 353-358, May 2002
© 2002 Oxford University Press

Occurrence, conformational features and amino acid propensities for the {pi}-helix

M.N. Fodje and S. Al-Karadaghi,1

Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, University of Lund, Box 124, SE-221 00 Lund, Sweden

The most abundant helix type in proteins is the {alpha}-helix, accounting for about 31% of amino acid secondary structure states, while the 310-helix accounts for about 4%. The {pi}-helix appears to be extremely rare and is considered to be unstable. Existing secondary structure definition methods find very few within the Protein Data Bank. Using an improved {pi}-helix definition algorithm to search a non-redundant subset of high-resolution and well-refined protein structures, we found that almost every tenth protein contained a {pi}-helix. This enabled us to show for the first time that the {pi}-helix has structural parameters that are different from the hypothesized model values. It also has distinctive amino acid preferences and it is conserved within functionally related proteins. Features that may contribute to the stability of the {pi}-helical structure have also been identified. In addition to hydrogen bonds, several other factors contribute to the stability of {pi}-helices. The {pi}-helix may have some functional advantages over other helical structures. Thus, we describe cases where the side chains of functionally important residues at every fourth position within a {pi}-helix could be aligned and brought close together in a way that would not be allowed by any other helix type.


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