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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...

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Detalles Bibliográficos
Autores principales: Tsuji, Toshiyuki, Yoda, Takao, Shirai, Tsuyoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
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.
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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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