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Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling
Many biological molecules are assembled into supramolecules that are essential to perform complicated functions in the cell. However, experimental information about the structures of supramolecules is not sufficient at this point. We developed a method of predicting and modeling the structures of su...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4637837/ https://www.ncbi.nlm.nih.gov/pubmed/26549015 http://dx.doi.org/10.1038/srep16341 |
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author | Tsuji, Toshiyuki Yoda, Takao Shirai, Tsuyoshi |
author_facet | Tsuji, Toshiyuki Yoda, Takao Shirai, Tsuyoshi |
author_sort | Tsuji, Toshiyuki |
collection | PubMed |
description | Many biological molecules are assembled into supramolecules that are essential to perform complicated functions in the cell. However, experimental information about the structures of supramolecules is not sufficient at this point. We developed a method of predicting and modeling the structures of supramolecules in a biological network by combining structural data of the Protein Data Bank (PDB) and interaction data in IntAct databases. Templates for binary complexes in IntAct were extracted from PDB. Modeling was attempted by assembling binary complexes with superposed shared subunits. A total of 3,197 models were constructed, and 1,306 (41% of the total) contained at least one subunit absent from experimental structures. The models also suggested 970 (25% of the total) experimentally undetected subunit interfaces, and 41 human disease-related amino acid variants were mapped onto these model-suggested interfaces. The models demonstrated that protein-protein interaction network modeling is useful to fill the information gap between biological networks and structures. |
format | Online Article Text |
id | pubmed-4637837 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-46378372015-11-30 Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling Tsuji, Toshiyuki Yoda, Takao Shirai, Tsuyoshi Sci Rep Article Many biological molecules are assembled into supramolecules that are essential to perform complicated functions in the cell. However, experimental information about the structures of supramolecules is not sufficient at this point. We developed a method of predicting and modeling the structures of supramolecules in a biological network by combining structural data of the Protein Data Bank (PDB) and interaction data in IntAct databases. Templates for binary complexes in IntAct were extracted from PDB. Modeling was attempted by assembling binary complexes with superposed shared subunits. A total of 3,197 models were constructed, and 1,306 (41% of the total) contained at least one subunit absent from experimental structures. The models also suggested 970 (25% of the total) experimentally undetected subunit interfaces, and 41 human disease-related amino acid variants were mapped onto these model-suggested interfaces. The models demonstrated that protein-protein interaction network modeling is useful to fill the information gap between biological networks and structures. Nature Publishing Group 2015-11-09 /pmc/articles/PMC4637837/ /pubmed/26549015 http://dx.doi.org/10.1038/srep16341 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Tsuji, Toshiyuki Yoda, Takao Shirai, Tsuyoshi Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling |
title | Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling |
title_full | Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling |
title_fullStr | Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling |
title_full_unstemmed | Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling |
title_short | Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling |
title_sort | deciphering supramolecular structures with protein-protein interaction network modeling |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4637837/ https://www.ncbi.nlm.nih.gov/pubmed/26549015 http://dx.doi.org/10.1038/srep16341 |
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