A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation
Pintado-Grima, Carlos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Bárcenas, Oriol (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Bartolomé-Nafría, Andrea (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Fornt Suñé, Marc (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Garcia-Pardo, Javier (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Universitat Autònoma de Barcelona

Date:	2023
Abstract:	The presence of insoluble protein deposits in tissues and organs is a hallmark of many human pathologies. In addition, the formation of protein aggregates is considered one of the main bottlenecks to producing protein-based therapeutics. Thus, there is a high interest in rationalizing and predicting protein aggregation. For almost two decades, our laboratory has been working to provide solutions for these needs. We have traditionally combined the core tenets of both bioinformatics and wet lab biophysics to develop algorithms and databases to study protein aggregation and its functional implications. Here, we review the computational toolbox developed by our lab, including programs for identifying sequential or structural aggregation-prone regions at the individual protein and proteome levels, engineering protein solubility, finding and evaluating prion-like domains, studying disorder-to-order protein transitions, or categorizing non-conventional amyloid regions of polar nature, among others. In perspective, the succession of the tools we describe illustrates how our understanding of the protein aggregation phenomenon has evolved over the last fifteen years.
Grants:	Agencia Estatal de Investigación PID2019-105017RB-I00
Rights:	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.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Amyloid ; Bioinformatics ; Biophysics ; Computational tools ; Protein aggregation ; Protein folding ; Protein structure
Published in:	Biophysica, Vol. 3 Núm. 1 (January 2023) , ISSN 2673-4125

DOI: 10.3390/biophysica3010001

20 p, 3.7 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Research articles
Articles > Published articles