A3DyDB: exploring structural aggregation propensities in the yeast proteome

Microbial Cell Factories

Research

Sebastian Kmiecik¹  Aleksander Kuriata¹  Aleksandra E. Badaczewska-Dawid²  Salvador Ventura³  Carlos Pintado-Grima³  Valentín Iglesias³  Javier Garcia-Pardo³ 

[1]Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland

[2]Genome Informatics Facility, Office of Biotechnology, Iowa State University, 50011, Ames, IA, USA

[3]Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain

关键词: Protein aggregation;    Aggrescan 3D;    AlphaFold;    Yeast;    Saccharomyces cerevisiae;   

DOI  :  10.1186/s12934-023-02182-3

 received in 2023-06-30, accepted in 2023-08-18,  发布年份 2023

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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