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Published online before print March 7, 2006, 10.1110/ps.051971106
Protein Science (2006), 15:753-760. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Repeat protein architectures predicted by a continuum representation of fold space

Andrew C. Hausrath1 and Alain Goriely2

1 Department of Biochemistry and Molecular Biophysics
2 Program in Applied Mathematics and Department of Mathematics, University of Arizona, Tucson, Arizona 85721, USA

(RECEIVED November 13, 2005; FINAL REVISION January 9, 2006; ACCEPTED January 12, 2006)

It is an open question whether nature has utilized all possible protein folds. For a simple protein architecture, the helical repeats, we report a method to address this question based on a mapping between the set of repetitive curves and a space of parameters specifying the curve. The exploration of the parameter space for a particular architecture enables a systematic exploration of the fold space for that protein architecture. In a planar subspace of the parameter space of helical repeats we have identified points corresponding to both naturally occurring folds and potential folds not observed so far.

Keywords: protein fold space; repeat proteins; fold evolution; polyhelix


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