Insights on protein thermal stability: a graph representation of molecular interactions

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• dc.contributor.author Miotto, Mattia
• dc.contributor.author Olimpieri, Pier Paolo
• dc.contributor.author Di Rienzo, Lorenzo
• dc.contributor.author Ambrosetti, Francesco
• dc.contributor.author Corsi, Pietro
• dc.contributor.author Lepore, Rosalba
• dc.contributor.author Tartaglia, Gian Gaetano
• dc.contributor.author Milanetti, Edoardo
• dc.date.accessioned 2019-10-29T10:59:54Z
• dc.date.available 2019-10-29T10:59:54Z
• dc.date.issued 2019
• dc.description.abstract Motivation: Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity. Results: Here, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In this approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and area under the receiver operating characteristic curve of 78%. Availability and implementation: Code is available upon request to edoardo.milanetti@uniroma1.it Supplementary information: Supplementary data are available at Bioinformatics online.
• dc.description.sponsorship The research leading to these results was supported by Epigenomics flagship project EPIGEN. G.G.T. is funded by European Research Council [RIBOMYLOME_309545]; Spanish Ministry of Economy and Competitiveness [BFU2014−55054−P⁠, BFU2017−86970−P]; and ‘Fundació La Marató de TV3’ [PI043296].
• dc.format.mimetype application/pdf
• dc.identifier.citation Miotto M, Olimpieri PP, Di Rienzo L, Ambrosetti F, Corsi P, Lepore R, Tartaglia GG, Milanetti E. Insights on protein thermal stability: a graph representation of molecular interactions. Bioinformatics. 2019; 35(15):2569-2577. DOI 10.1093/bioinformatics/bty1011
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/bty1011
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/42543
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2019; 35(15):2569-2577
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-P
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86970-P
• dc.rights © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.title Insights on protein thermal stability: a graph representation of molecular interactions
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion