A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Biophysica |
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| Online Access: | https://www.mdpi.com/2673-4125/3/1/1 |
| _version_ | 1797858465243201536 |
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| author | Carlos Pintado-Grima Oriol Bárcenas Andrea Bartolomé-Nafría Marc Fornt-Suñé Valentín Iglesias Javier Garcia-Pardo Salvador Ventura |
| author_facet | Carlos Pintado-Grima Oriol Bárcenas Andrea Bartolomé-Nafría Marc Fornt-Suñé Valentín Iglesias Javier Garcia-Pardo Salvador Ventura |
| author_sort | Carlos Pintado-Grima |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-09T21:13:49Z |
| format | Article |
| id | doaj.art-1f94c3e420fa44458982adf40c6c7cd0 |
| institution | Directory Open Access Journal |
| issn | 2673-4125 |
| language | English |
| last_indexed | 2024-04-09T21:13:49Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biophysica |
| spelling | doaj.art-1f94c3e420fa44458982adf40c6c7cd02023-03-28T13:12:50ZengMDPI AGBiophysica2673-41252023-01-013112010.3390/biophysica3010001A Review of Fifteen Years Developing Computational Tools to Study Protein AggregationCarlos Pintado-Grima0Oriol Bárcenas1Andrea Bartolomé-Nafría2Marc Fornt-Suñé3Valentín Iglesias4Javier Garcia-Pardo5Salvador Ventura6Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainDepartament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainDepartament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainDepartament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainDepartament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainDepartament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainDepartament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, SpainThe 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.https://www.mdpi.com/2673-4125/3/1/1protein aggregationbioinformaticsbiophysicscomputational toolsamyloidprotein structure |
| spellingShingle | Carlos Pintado-Grima Oriol Bárcenas Andrea Bartolomé-Nafría Marc Fornt-Suñé Valentín Iglesias Javier Garcia-Pardo Salvador Ventura A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation Biophysica protein aggregation bioinformatics biophysics computational tools amyloid protein structure |
| title | A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation |
| title_full | A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation |
| title_fullStr | A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation |
| title_full_unstemmed | A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation |
| title_short | A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation |
| title_sort | review of fifteen years developing computational tools to study protein aggregation |
| topic | protein aggregation bioinformatics biophysics computational tools amyloid protein structure |
| url | https://www.mdpi.com/2673-4125/3/1/1 |
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