Circular permuted proteins in the universe of protein folds

Proteins
Tobias Schmidt-GoennerErnst Walter Knapp

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.

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Citations

Dec 2, 2011·Bioinformatics·Ryotaro Koike, Motonori Ota
May 13, 2010·Nucleic Acids Research·Aysam Guerler, Ernst-Walter Knapp
Feb 10, 2012·Nucleic Acids Research·Manan M MehtaJonathan J Silberg
Apr 13, 2012·PLoS Computational Biology·Spencer Bliven, Andreas Prlić
Sep 25, 2016·Biochimie·Bruno Lopes de SousaBenildo Sousa Cavada
Aug 13, 2021·Molecular Biology and Evolution·Claudia Alvarez-CarreñoLoren Dean Williams

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