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The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry
A systematic classification of protein–protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1584320/ https://www.ncbi.nlm.nih.gov/pubmed/17009862 http://dx.doi.org/10.1371/journal.pcbi.0020124 |
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author | Kim, Wan Kyu Henschel, Andreas Winter, Christof Schroeder, Michael |
author_facet | Kim, Wan Kyu Henschel, Andreas Winter, Christof Schroeder, Michael |
author_sort | Kim, Wan Kyu |
collection | PubMed |
description | A systematic classification of protein–protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach of both sequential and structural features. The accuracy is evaluated on a hand-curated dataset of 416 interfaces. Our hybrid procedure achieves 83% precision and 95% recall, which improves the earlier sequence-based method by 5% on both terms. We classify virtually all domain interfaces of known structure, which results in nearly 6,000 distinct types of interfaces. In 40% of the cases, the interacting domain families associate in multiple orientations, suggesting that all the possible binding orientations need to be explored for modelling multidomain proteins and protein complexes. In general, hub proteins are shown to use distinct surface regions (multiple faces) for interactions with different partners. Our classification provides a convenient framework to query genuine gene fusion, which conserves binding orientation in both fused and separate forms. The result suggests that the binding orientations are not conserved in at least one-third of the gene fusion cases detected by a conventional sequence similarity search. We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. The taxonomic distribution of interface types suggests that ancient interfaces common to the three major kingdoms of life are enriched by symmetric homodimers. The classification results are online at http://www.scoppi.org. |
format | Text |
id | pubmed-1584320 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-15843202006-10-02 The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry Kim, Wan Kyu Henschel, Andreas Winter, Christof Schroeder, Michael PLoS Comput Biol Research Article A systematic classification of protein–protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach of both sequential and structural features. The accuracy is evaluated on a hand-curated dataset of 416 interfaces. Our hybrid procedure achieves 83% precision and 95% recall, which improves the earlier sequence-based method by 5% on both terms. We classify virtually all domain interfaces of known structure, which results in nearly 6,000 distinct types of interfaces. In 40% of the cases, the interacting domain families associate in multiple orientations, suggesting that all the possible binding orientations need to be explored for modelling multidomain proteins and protein complexes. In general, hub proteins are shown to use distinct surface regions (multiple faces) for interactions with different partners. Our classification provides a convenient framework to query genuine gene fusion, which conserves binding orientation in both fused and separate forms. The result suggests that the binding orientations are not conserved in at least one-third of the gene fusion cases detected by a conventional sequence similarity search. We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. The taxonomic distribution of interface types suggests that ancient interfaces common to the three major kingdoms of life are enriched by symmetric homodimers. The classification results are online at http://www.scoppi.org. Public Library of Science 2006-09 2006-09-29 /pmc/articles/PMC1584320/ /pubmed/17009862 http://dx.doi.org/10.1371/journal.pcbi.0020124 Text en © 2006 Kim et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Kim, Wan Kyu Henschel, Andreas Winter, Christof Schroeder, Michael The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry |
title | The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry |
title_full | The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry |
title_fullStr | The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry |
title_full_unstemmed | The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry |
title_short | The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry |
title_sort | many faces of protein–protein interactions: a compendium of interface geometry |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1584320/ https://www.ncbi.nlm.nih.gov/pubmed/17009862 http://dx.doi.org/10.1371/journal.pcbi.0020124 |
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