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Alignment of protein structures in the presence of domain motions

BACKGROUND: Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter...

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Autores principales: Mosca, Roberto, Brannetti, Barbara, Schneider, Thomas R
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2535786/
https://www.ncbi.nlm.nih.gov/pubmed/18727838
http://dx.doi.org/10.1186/1471-2105-9-352
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author Mosca, Roberto
Brannetti, Barbara
Schneider, Thomas R
author_facet Mosca, Roberto
Brannetti, Barbara
Schneider, Thomas R
author_sort Mosca, Roberto
collection PubMed
description BACKGROUND: Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used. RESULTS: We introduce a new method called RAPIDO (Rapid Alignment of Proteins in terms of Domains) for the three-dimensional alignment of protein structures in the presence of conformational changes. The flexible aligner is coupled to a genetic algorithm for the identification of structurally conserved regions. RAPIDO is capable of aligning protein structures in the presence of large conformational changes. Structurally conserved regions are reliably detected even if they are discontinuous in sequence but continuous in space and can be used for superpositions revealing subtle differences. CONCLUSION: RAPIDO is more sensitive than other flexible aligners when applied to cases of closely homologues proteins undergoing large conformational changes. When applied to a set of kinase structures it is able to detect similarities that are missed by other alignment algorithms. The algorithm is sufficiently fast to be applied to the comparison of large sets of protein structures.
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spelling pubmed-25357862008-09-15 Alignment of protein structures in the presence of domain motions Mosca, Roberto Brannetti, Barbara Schneider, Thomas R BMC Bioinformatics Methodology Article BACKGROUND: Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used. RESULTS: We introduce a new method called RAPIDO (Rapid Alignment of Proteins in terms of Domains) for the three-dimensional alignment of protein structures in the presence of conformational changes. The flexible aligner is coupled to a genetic algorithm for the identification of structurally conserved regions. RAPIDO is capable of aligning protein structures in the presence of large conformational changes. Structurally conserved regions are reliably detected even if they are discontinuous in sequence but continuous in space and can be used for superpositions revealing subtle differences. CONCLUSION: RAPIDO is more sensitive than other flexible aligners when applied to cases of closely homologues proteins undergoing large conformational changes. When applied to a set of kinase structures it is able to detect similarities that are missed by other alignment algorithms. The algorithm is sufficiently fast to be applied to the comparison of large sets of protein structures. BioMed Central 2008-08-27 /pmc/articles/PMC2535786/ /pubmed/18727838 http://dx.doi.org/10.1186/1471-2105-9-352 Text en Copyright © 2008 Mosca 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 Methodology Article
Mosca, Roberto
Brannetti, Barbara
Schneider, Thomas R
Alignment of protein structures in the presence of domain motions
title Alignment of protein structures in the presence of domain motions
title_full Alignment of protein structures in the presence of domain motions
title_fullStr Alignment of protein structures in the presence of domain motions
title_full_unstemmed Alignment of protein structures in the presence of domain motions
title_short Alignment of protein structures in the presence of domain motions
title_sort alignment of protein structures in the presence of domain motions
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2535786/
https://www.ncbi.nlm.nih.gov/pubmed/18727838
http://dx.doi.org/10.1186/1471-2105-9-352
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