3D complex: a structural classification of protein complexes

Detalhes bibliográficos
Autor(a) principal: Levy, E.D.
Data de Publicação: 2006
Outros Autores: Pereira-Leal, J.B., Chothia, C., Teichmann, S.A.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.7/60
Resumo: Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes
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spelling 3D complex: a structural classification of protein complexesModels, ChemicalModels, MolecularMolecular Sequence DataMultiprotein Complexes/ultrastructureMultiprotein Complexes/chemistryProtein Interaction Mapping/methodsSequence Analysis, Protein/methodsAmino Acid SequenceMost of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexesARCALevy, E.D.Pereira-Leal, J.B.Chothia, C.Teichmann, S.A.2009-10-17T11:48:21Z2006-112006-11-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.7/60engLevy, E.D., Pereira-Leal, J.B., Chothia, C., Teichmann, S.A. (2006). "3D complex: a structural classification of protein complexes.". PLoS computational biology. 2(11):e1551553-7358info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-11-29T14:34:36Zoai:arca.igc.gulbenkian.pt:10400.7/60Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T16:11:33.417427Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv 3D complex: a structural classification of protein complexes
title 3D complex: a structural classification of protein complexes
spellingShingle 3D complex: a structural classification of protein complexes
Levy, E.D.
Models, Chemical
Models, Molecular
Molecular Sequence Data
Multiprotein Complexes/ultrastructure
Multiprotein Complexes/chemistry
Protein Interaction Mapping/methods
Sequence Analysis, Protein/methods
Amino Acid Sequence
title_short 3D complex: a structural classification of protein complexes
title_full 3D complex: a structural classification of protein complexes
title_fullStr 3D complex: a structural classification of protein complexes
title_full_unstemmed 3D complex: a structural classification of protein complexes
title_sort 3D complex: a structural classification of protein complexes
author Levy, E.D.
author_facet Levy, E.D.
Pereira-Leal, J.B.
Chothia, C.
Teichmann, S.A.
author_role author
author2 Pereira-Leal, J.B.
Chothia, C.
Teichmann, S.A.
author2_role author
author
author
dc.contributor.none.fl_str_mv ARCA
dc.contributor.author.fl_str_mv Levy, E.D.
Pereira-Leal, J.B.
Chothia, C.
Teichmann, S.A.
dc.subject.por.fl_str_mv Models, Chemical
Models, Molecular
Molecular Sequence Data
Multiprotein Complexes/ultrastructure
Multiprotein Complexes/chemistry
Protein Interaction Mapping/methods
Sequence Analysis, Protein/methods
Amino Acid Sequence
topic Models, Chemical
Models, Molecular
Molecular Sequence Data
Multiprotein Complexes/ultrastructure
Multiprotein Complexes/chemistry
Protein Interaction Mapping/methods
Sequence Analysis, Protein/methods
Amino Acid Sequence
description Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes
publishDate 2006
dc.date.none.fl_str_mv 2006-11
2006-11-01T00:00:00Z
2009-10-17T11:48:21Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.7/60
url http://hdl.handle.net/10400.7/60
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Levy, E.D., Pereira-Leal, J.B., Chothia, C., Teichmann, S.A. (2006). "3D complex: a structural classification of protein complexes.". PLoS computational biology. 2(11):e155
1553-7358
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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