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Novel protein folds and their nonsequential structural analogs

Department of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany

(RECEIVED March 20, 2008; FINAL REVISION May 1, 2008; ACCEPTED May 2, 2008)

Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison.

Keywords: nonsequential protein structure alignment; novel protein fold; protein fold space; protein structure/folding

Reprint requests to: Ernst-Walter Knapp, Department of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36A, 14195 Berlin, Germany; e-mail: knapp{at}chemie.fu-berlin.de; fax: 49-30-838-56921.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.035469.108.

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