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A3DyDB: exploring structural aggregation propensities in the yeast proteome

dc.abstract.enBackground: The budding yeast Saccharomyces cerevisiae (S. cerevisiae) is a well-established model system for studying protein aggregation due to the conservation of essential cellular structures and pathways found across eukaryotes. However, limited structural knowledge of its proteome has prevented a deeper understanding of yeast functionalities, interactions, and aggregation. Results: In this study, we introduce the A3D yeast database (A3DyDB), which offers an extensive catalog of aggregation propensity predictions for the S. cerevisiae proteome. We used Aggrescan 3D (A3D) and the newly released protein models from AlphaFold2 (AF2) to compute the structure-based aggregation predictions for 6039 yeast proteins. The A3D algorithm exploits the information from 3D protein structures to calculate their intrinsic aggregation propensities. To facilitate simple and intuitive data analysis, A3DyDB provides a user-friendly interface for querying, browsing, and visualizing information on aggregation predictions from yeast protein structures. The A3DyDB also allows for the evaluation of the influence of natural or engineered mutations on protein stability and solubility. The A3DyDB is freely available at http://biocomp.chem.uw.edu.pl/A3D2/yeast . Conclusion: The A3DyDB addresses a gap in yeast resources by facilitating the exploration of correlations between structural aggregation propensity and diverse protein properties at the proteome level. We anticipate that this comprehensive database will become a standard tool in the modeling of protein aggregation and its implications in budding yeast.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorVentura, Salvador
dc.contributor.authorKmiecik, Sebastian
dc.contributor.authorKuriata, Aleksander
dc.contributor.authorIglesias, Valentín
dc.contributor.authorPintado-Grima, Carlos
dc.contributor.authorBadaczewska-Dawid, Aleksandra E.
dc.contributor.authorGarcia-Pardo, Javier
dc.date.accessioned2024-01-24T15:36:26Z
dc.date.available2024-01-24T15:36:26Z
dc.date.issued2023
dc.description.financeNie dotyczy
dc.description.number1
dc.description.volume22
dc.identifier.doi10.1186/S12934-023-02182-3
dc.identifier.issn1475-2859
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/100103
dc.identifier.weblinkhttps://link.springer.com/content/pdf/10.1186/s12934-023-02182-3.pdf
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofMicrobial Cell Factories
dc.relation.pages186
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.enProtein aggregation, Aggrescan 3D, AlphaFold, Yeast, Saccharomyces cerevisiae
dc.titleA3DyDB: exploring structural aggregation propensities in the yeast proteome
dc.typeJournalArticle
dspace.entity.typePublication