Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

Abstract Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction b...

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Autores principales:	Farideh Halakou, Emel Sen Kilic, Engin Cukuroglu, Ozlem Keskin, Attila Gursoy
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/949dd284a74d474493635e53aa861100
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spelling	oai:doaj.org-article:949dd284a74d474493635e53aa8611002021-12-02T16:08:01ZEnriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins10.1038/s41598-017-07351-02045-2322https://doaj.org/article/949dd284a74d474493635e53aa8611002017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07351-0https://doaj.org/toc/2045-2322Abstract Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies.Farideh HalakouEmel Sen KilicEngin CukurogluOzlem KeskinAttila GursoyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Farideh Halakou Emel Sen Kilic Engin Cukuroglu Ozlem Keskin Attila Gursoy Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
description	Abstract Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies.
format	article
author	Farideh Halakou Emel Sen Kilic Engin Cukuroglu Ozlem Keskin Attila Gursoy
author_facet	Farideh Halakou Emel Sen Kilic Engin Cukuroglu Ozlem Keskin Attila Gursoy
author_sort	Farideh Halakou
title	Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
title_short	Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
title_full	Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
title_fullStr	Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
title_full_unstemmed	Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
title_sort	enriching traditional protein-protein interaction networks with alternative conformations of proteins
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/949dd284a74d474493635e53aa861100
work_keys_str_mv	AT faridehhalakou enrichingtraditionalproteinproteininteractionnetworkswithalternativeconformationsofproteins AT emelsenkilic enrichingtraditionalproteinproteininteractionnetworkswithalternativeconformationsofproteins AT engincukuroglu enrichingtraditionalproteinproteininteractionnetworkswithalternativeconformationsofproteins AT ozlemkeskin enrichingtraditionalproteinproteininteractionnetworkswithalternativeconformationsofproteins AT attilagursoy enrichingtraditionalproteinproteininteractionnetworkswithalternativeconformationsofproteins
_version_	1718384672240566272

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

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