Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks

Abstract Protein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	David O. Holland, Benjamin H. Shapiro, Pei Xue, Margaret E. Johnson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1f7e0bc6a42e477ca0376c7ad633ba17
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:1f7e0bc6a42e477ca0376c7ad633ba17
record_format	dspace
spelling	oai:doaj.org-article:1f7e0bc6a42e477ca0376c7ad633ba172021-12-02T12:32:06ZProtein-protein binding selectivity and network topology constrain global and local properties of interface binding networks10.1038/s41598-017-05686-22045-2322https://doaj.org/article/1f7e0bc6a42e477ca0376c7ad633ba172017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05686-2https://doaj.org/toc/2045-2322Abstract Protein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this study we analyze four independently constructed IINs from yeast and humans and find a conserved structure of these networks with a unique topology distinct from the parent PPIN. Using an IIN sampling algorithm and a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly explained as a balance between limits on interface diversity and a need for physico-chemical binding complementarity. This complementarity must be optimized both for functional interactions and against mis-interactions, and this selectivity is encoded in the IIN motifs. To test whether the parent PPIN shapes IINs, we compared optimal IINs in biological PPINs versus random PPINs. We found that the hubs in biological networks allow for selective binding with minimal interfaces, suggesting that binding specificity is an additional pressure for a scale-free-like PPIN. We confirm through phylogenetic analysis that hub interfaces are strongly conserved and rewiring of interactions between proteins involved in endocytosis preserves interface binding selectivity.David O. HollandBenjamin H. ShapiroPei XueMargaret E. JohnsonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q David O. Holland Benjamin H. Shapiro Pei Xue Margaret E. Johnson Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
description	Abstract Protein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this study we analyze four independently constructed IINs from yeast and humans and find a conserved structure of these networks with a unique topology distinct from the parent PPIN. Using an IIN sampling algorithm and a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly explained as a balance between limits on interface diversity and a need for physico-chemical binding complementarity. This complementarity must be optimized both for functional interactions and against mis-interactions, and this selectivity is encoded in the IIN motifs. To test whether the parent PPIN shapes IINs, we compared optimal IINs in biological PPINs versus random PPINs. We found that the hubs in biological networks allow for selective binding with minimal interfaces, suggesting that binding specificity is an additional pressure for a scale-free-like PPIN. We confirm through phylogenetic analysis that hub interfaces are strongly conserved and rewiring of interactions between proteins involved in endocytosis preserves interface binding selectivity.
format	article
author	David O. Holland Benjamin H. Shapiro Pei Xue Margaret E. Johnson
author_facet	David O. Holland Benjamin H. Shapiro Pei Xue Margaret E. Johnson
author_sort	David O. Holland
title	Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
title_short	Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
title_full	Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
title_fullStr	Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
title_full_unstemmed	Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
title_sort	protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/1f7e0bc6a42e477ca0376c7ad633ba17
work_keys_str_mv	AT davidoholland proteinproteinbindingselectivityandnetworktopologyconstrainglobalandlocalpropertiesofinterfacebindingnetworks AT benjaminhshapiro proteinproteinbindingselectivityandnetworktopologyconstrainglobalandlocalpropertiesofinterfacebindingnetworks AT peixue proteinproteinbindingselectivityandnetworktopologyconstrainglobalandlocalpropertiesofinterfacebindingnetworks AT margaretejohnson proteinproteinbindingselectivityandnetworktopologyconstrainglobalandlocalpropertiesofinterfacebindingnetworks
_version_	1718394145440006144

Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks

Ejemplares similares