An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

Abstract Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Struc...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Juan Salamanca Viloria, Maria Francesca Allega, Matteo Lambrughi, Elena Papaleo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/45282f6203174d848f5d2da71acc4a59
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:45282f6203174d848f5d2da71acc4a59
record_format	dspace
spelling	oai:doaj.org-article:45282f6203174d848f5d2da71acc4a592021-12-02T12:31:49ZAn optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass10.1038/s41598-017-01498-62045-2322https://doaj.org/article/45282f6203174d848f5d2da71acc4a592017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01498-6https://doaj.org/toc/2045-2322Abstract Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to use the centers of mass of the side chains as nodes. It becomes thus critical to evaluate the minimal distance cutoff between the centers of mass which will provide stable network properties. Moreover, when the PSN is derived from a structural ensemble collected by molecular dynamics (MD), the impact of the MD force field has to be evaluated. We selected a dataset of proteins with different fold and size and assessed the two fundamental properties of the PSN, i.e. hubs and connected components. We identified an optimal cutoff of 5 Å that is robust to changes in the force field and the proteins. Our study builds solid foundations for the harmonization and standardization of the PSN approach.Juan Salamanca ViloriaMaria Francesca AllegaMatteo LambrughiElena PapaleoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Juan Salamanca Viloria Maria Francesca Allega Matteo Lambrughi Elena Papaleo An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
description	Abstract Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to use the centers of mass of the side chains as nodes. It becomes thus critical to evaluate the minimal distance cutoff between the centers of mass which will provide stable network properties. Moreover, when the PSN is derived from a structural ensemble collected by molecular dynamics (MD), the impact of the MD force field has to be evaluated. We selected a dataset of proteins with different fold and size and assessed the two fundamental properties of the PSN, i.e. hubs and connected components. We identified an optimal cutoff of 5 Å that is robust to changes in the force field and the proteins. Our study builds solid foundations for the harmonization and standardization of the PSN approach.
format	article
author	Juan Salamanca Viloria Maria Francesca Allega Matteo Lambrughi Elena Papaleo
author_facet	Juan Salamanca Viloria Maria Francesca Allega Matteo Lambrughi Elena Papaleo
author_sort	Juan Salamanca Viloria
title	An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
title_short	An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
title_full	An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
title_fullStr	An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
title_full_unstemmed	An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
title_sort	optimal distance cutoff for contact-based protein structure networks using side-chain centers of mass
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/45282f6203174d848f5d2da71acc4a59
work_keys_str_mv	AT juansalamancaviloria anoptimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT mariafrancescaallega anoptimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT matteolambrughi anoptimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT elenapapaleo anoptimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT juansalamancaviloria optimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT mariafrancescaallega optimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT matteolambrughi optimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass AT elenapapaleo optimaldistancecutoffforcontactbasedproteinstructurenetworksusingsidechaincentersofmass
_version_	1718394274539634688

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

Ejemplares similares