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protein folds

Protein Science (1)

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Helix-bundle membrane protein fold templates
JAMES U. BOWIE
Journal:

Protein Science / Volume 8 / Issue 12 / December 1999

Published online by Cambridge University Press:

01 December 1999, pp. 2711-2719

Print publication:

December 1999
- Article
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In the fold recognition approach to structure prediction, a sequence is tested for compatibility with an already known fold. For membrane proteins, however, few folds have been determined experimentally. Here the feasibility of computing the vast majority of likely membrane protein folds is tested. The results indicate that conformation space can be effectively sampled for small numbers of helices. The vast majority of potential monomeric membrane protein structures can be represented by about 30-folds for three helices, but increases exponentially to about 1,500,000 folds for seven helices. The generated folds could serve as templates for fold recognition or as starting points for conformational searches that are well distributed throughout conformation space.