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Open Access Research article

Detecting internally symmetric protein structures

Changhoon Kim12, Jodi Basner1 and Byungkook Lee1*

  • * Corresponding author: Byungkook Lee bk@nih.gov

Author Affiliations

1 Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bldg. 37, Room 5120, 37 Convent Dr MSC 4264, Bethesda MD 20892-4264 USA

2 Bioinformatics & Molecular Design Research Center, Yonsei Engineering Research Park, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea

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BMC Bioinformatics 2010, 11:303  doi:10.1186/1471-2105-11-303

Published: 3 June 2010

Abstract

Background

Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information.

Results

We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure.

Conclusions

SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe.