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Detecting internally symmetric protein structures

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 internall...

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Autores principales: Kim, Changhoon, Basner, Jodi, Lee, Byungkook
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894822/
https://www.ncbi.nlm.nih.gov/pubmed/20525292
http://dx.doi.org/10.1186/1471-2105-11-303
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author Kim, Changhoon
Basner, Jodi
Lee, Byungkook
author_facet Kim, Changhoon
Basner, Jodi
Lee, Byungkook
author_sort Kim, Changhoon
collection PubMed
description 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.
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spelling pubmed-28948222010-07-01 Detecting internally symmetric protein structures Kim, Changhoon Basner, Jodi Lee, Byungkook BMC Bioinformatics Research article 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. BioMed Central 2010-06-03 /pmc/articles/PMC2894822/ /pubmed/20525292 http://dx.doi.org/10.1186/1471-2105-11-303 Text en Copyright ©2010 Kim et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research article
Kim, Changhoon
Basner, Jodi
Lee, Byungkook
Detecting internally symmetric protein structures
title Detecting internally symmetric protein structures
title_full Detecting internally symmetric protein structures
title_fullStr Detecting internally symmetric protein structures
title_full_unstemmed Detecting internally symmetric protein structures
title_short Detecting internally symmetric protein structures
title_sort detecting internally symmetric protein structures
topic Research article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894822/
https://www.ncbi.nlm.nih.gov/pubmed/20525292
http://dx.doi.org/10.1186/1471-2105-11-303
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