BIG DATA
Spanish researchers build a comprehensive database for studying protein aggregation
Protein aggregation is a phenomenon associated with aging and several pathologies like Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis. This has been a subject of intensive research for several years. To gain a better understanding of it, a team of researchers at the Institut de Biotecnologia i de Biomedicina of the Universitat Autònoma de Barcelona (IBB-UAB) has developed a comprehensive database called A3D-MOBD. The new resource brings together the proteomes of twelve model organisms, including over half a million predictions of protein regions that have a propensity to form aggregates.
The protein folding and computational diseases group at IBB-UAB, led by Professor Salvador Ventura in collaboration with scientists from the University of Warsaw, developed the new database, which was recently published in the journal Nucleic Acids Research. A3D-MOBD provides pre-calculated aggregation propensity analyses and tools for studying this phenomenon on a proteomic scale, as well as evolutionary comparisons between different species.
The A3D-MOBD expands on a method that the same group designed in 2015, Aggrescan 3D, but with significantly expanded data. It contains more than 500,000 structural predictions for over 160,000 proteins from twelve model organisms, including humans, rats, mice, zebrafish, fruit flies, nematode worms, bacterium, and the COVID-19 causative virus SARS-CoV-2. The new resource's adaptive architecture allows for future additions of other organisms relevant to various sectors, including medical, biological, agricultural, and industrial.
The A3D-MOBD tool provides results on protein solubility and stability and includes additional information to contextualize the aggregation process. Several computational sources, such as artificial intelligence-based protein structure modeling algorithm AlphaFold and TOPCONS for the prediction of protein interaction with lipid membranes, were used to develop the database. The researchers linked A3D-MOBD to organism-specific gold-reference databases such as the Human Protein Atlas or Wormbase.
Professor Salvador Ventura expressed his anticipation that A3D-MOBD will offer solutions to a much wider audience of researchers, not only because of the large collection of structures but also because of its integration with databases from different biological fields. He is confident that the new database will set a new standard in protein aggregation research and that it will become a basic resource in this field.
In conclusion, the A3D-MOBD database developed by researchers at IBB-UAB is the most comprehensive database available for studying protein aggregation. It brings together proteomes of twelve of the most widely studied model organisms and provides pre-calculated aggregation propensity analyses and tools for studying the phenomenon on a proteomic scale. This database expands scientists' understanding of the basis of protein aggregation and offers researchers insights into why certain diseases develop in some species and not others.
To access the A3D-MOBD database, please visit http://biocomp.chem.uw.edu.pl/A3D2/MODB .