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Protein Engineering vol. 9 no. 8 pp. 657-662, 1996
© 1996 Oxford University Press

RESEARCH-ARTICLE

Predicting leucine zipper structures from sequence

Jonathan D. Hirst, Michal Vieth, Jeffrey Skolnick and Charles L. Brooks, III

Department of Molecular Biology, The Scripps Research Institute 10666 North Torrey Pines Road, La Jolla, CA 92037, USA

The leucine zipper structure is adopted by one family of the coiled coil proteins. Leucine zippers have a characteristic leucine repeat: Leu–X6–Leu–X6–Leu–X6–Leu (where X may be any residue). However, many sequences have the leucine repeat, but do not adopt the leucine zipper structure (we shall refer to these as non-zippers). We have found and analyzed residue pair patterns that allow one to identify correctly 90% of leucine zippers and 97% of non-zippers. Simpler analyses, based on the frequency of occurrence of residues at certain positions, specify, at most, 65% of zippers and 80–90% of non-zippers. Both short and long patterns contribute to the successful discrimination of leucine zippers from non-zippers. A number of these patterns involve hydrophobic residues that would be placed on the solvent-exposed surface of the helix, were the sequence to adopt a leucine zipper structure. Thus, an analysis of protein sequences has allowed us to improve discrimination between leucine zippers and non-zippers, and has provided some further insight into the physical factors influencing the leucine zipper structure.

Keywords: coiled coil/leucine zipper/protein sequence analysis/two residue pattems/TRESPASSER

Received December 6, 1995; revised April 11, 1996; accepted April 15, 1996.


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