3D complex: a structural classification of protein complexes
Autor(a) principal: | |
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Data de Publicação: | 2006 |
Outros Autores: | , , |
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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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 |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799130571402641408 |