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Proteins. 2010 May 15;78(7):1618-30. doi: 10.1002/prot.22678.

Circular permuted proteins in the universe of protein folds.

Author information

1
Institute of Chemistry and Biochemistry, Freie Universit├Ąt Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany.

Abstract

Finding and identifying circular permuted protein pairs (CPP) is one of the harder tasks for structure alignment programs, because of the different location of the break in the polypeptide chain connectivity. The protein structure alignment tool GANGSTA+ was used to search for CPPs in a database of nearly 10,000 protein structures. It also allows determination of the statistical significance of the occurrence of circular permutations in the protein universe. The number of detected CPPs was found to be higher than expected, raising questions about the evolutionary processes leading to CPPs. The GANGSTA+ protein structure alignment tool is available online via the web server at http://gangsta.chemie.fu-berlin.de. On the same webpage the complete data base of similar protein structure pairs based on the ASTRAL40 set of protein domains is provided and one can select CPPs specifically.

PMID:
20112421
DOI:
10.1002/prot.22678
[Indexed for MEDLINE]

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