ArticleMicrobial cell factories2023
A3DyDB: exploring structural aggregation propensities in the yeast proteome.
Article in Microbial cell factories, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 6 citations in OpenAlex.
- Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.Protein science : a publication of the Protein Society · 2024Review
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms.Nucleic acids research · 2024Article
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7 authors at 3 institutions in 3 countries.
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Abstract
backgroundThe 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.
resultsIn 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 .
conclusionThe 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.
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