A3DyDB : exploring structural aggregation propensities in the yeast proteome
Garcia-Pardo, Javier (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Badaczewska-Dawid, Aleksandra E. (Iowa State University)
Pintado-Grima, Carlos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Kuriata, Aleksander (University of Warsaw)
Kmiecik, Sebastian (University of Warsaw)
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")

Data:	2023
Resum:	Background: 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.
Ajuts:	Agencia Estatal de Investigación PID2019-105017RB-I00 Agència de Gestió d'Ajuts Universitaris i de Recerca 2023/FI_3-00018 Ministerio de Ciencia e Innovación IJC2019-041039-I
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Protein aggregation ; Aggrescan 3D ; AlphaFold ; Yeast ; Saccharomyces cerevisiae
Publicat a:	Microbial cell factories, Vol. 22, Issue 1 (September 2023) , art. 186, ISSN 1475-2859

DOI: 10.1186/s12934-023-02182-3
PMID: 37716955

10 p, 1.9 MB

El registre apareix a les col·leccions:
Documents de recerca > Documents dels grups de recerca de la UAB > Centres i grups de recerca (producció científica) > Ciències de la salut i biociències > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Articles de recerca
Articles > Articles publicats