Excellence Hub on Phase Transitions in Aging and Age-Related Disorders

Project Information

PhasAGE

Grant agreement ID: 952334

DOI

10.3030/952334

Project closed

EC signature date 2 July 2020

Start date 1 January 2021

End date 31 March 2024

Funded under

• Twinning of research institutions

Total cost

€ 899 741,25

EU contribution

€ 899 741,25

Coordinated by

INSTITUTO DE BIOLOGIA MOLECULAR E CELULAR-IBMC
Portugal

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Open Research Data Pilot (1)

Report on development of protocols to study liquid-liquid phase separation at IBMC/i3S

Documents, reports (6)

Portfolio with innovation potential of research on protein phase separation
Detailed Dissemination, Communication and Outreach Plan (DCOP)

Detailed Dissemination Communication and Outreach Plan DCOP

ESS1 and ESS2 plan
Report on computational analysis of protein phase separations
Report on publications on PhasAGE topics in high impact journals by the coordinating institution

Introduction in the Continuous reporting tool on the Funding and tenders portal of peerreviewed publications on intrinsically disordered proteinsphase separation of the coordinating entity during the three years preceding the start date of the project

PhasAGE Management Handbook

Websites, patent fillings, videos etc. (5)

PhasAGE Wikipedia
Launch of the PhaseAGE HUB
Launch of the PhasAGE website and links to social media

Launch of thePhasAGE website and links to social media

Implementation of a central PhasAGE HelpDesk
Communication Toolkit

Publications

Peer reviewed articles (42)

The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease

Author(s): Attila Meszaros, Junaid Ahmed, Giorgio Russo, Peter Tompa, Tamas Lazar
Published in: Frontiers in Medicine, 2022, ISSN 2296-858X
Publisher: Frontiers
DOI: 10.3389/fmed.2022.1019803

DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH

Author(s): Carlos Pintado-Grima, Valentín Iglesias, Jaime Santos, Vladimir N Uversky, Salvador Ventura
Published in: Biomolecules, 2021, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom11111596

A3DyDB: exploring structural aggregation propensities in the yeast proteome

Author(s): Javier Garcia-Pardo, Aleksandra E. Badaczewska-Dawid, Carlos Pintado-Grima, Valentín Iglesias, Aleksander Kuriata, Sebastian Kmiecik and Salvador Ventura
Published in: Microbial Cell Factories, 2023, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-023-02182-3

Degron masking outlines degronons, co-degrading functional modules in the proteome

Author(s): Mainak Guharoy, Tamas Lazar, Mauricio Macossay-Castillo, Peter Tompa
Published in: Communications Biology, 2022, ISSN 2399-3642
Publisher: Nature
DOI: 10.1038/s42003-022-03391-z

Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase

Author(s): Ana S. Figueiredo, Joana R. Loureiro, Sandra Macedo-Ribeiro, Isabel Silveira
Published in: Cells, 2023, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells12060826

Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3

Author(s): Javier Garcia-Pardo, Andrea Bartolomé-Nafría, Antonio Chaves-Sanjuan, Marcos Gil-Garcia, Cristina Visentin, Martino Bolognesi, Stefano Ricagno, Salvador Ventura
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-35854-0

Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates

Author(s): Alexander Miguel Monzon, Damiano Piovesan, Monika Fuxreiter
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12010092

Databases for intrinsically disordered proteins

Author(s): Damiano Piovesan; Alexander Miguel Monzon; Federica Quaglia; Silvio C. E. Tosatto
Published in: Acta Crystallographica Section D, Issue 1, 2022, ISSN 0907-4449
Publisher: Blackwell Publishing Inc.
DOI: 10.1107/s2059798321012109

NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation

Author(s): Zsuzsa Sárkány, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins
Published in: Molecular Biology of the Cell, 2024, ISSN 1059-1524
Publisher: American Society for Cell Biology
DOI: 10.1091/mbc.e23-07-0289

Computational methods to predict protein aggregation

Author(s): Susanna Navarro, Salvador Ventura
Published in: Current Opinion in Structural Biology, 2022, ISSN 1879-033X
Publisher: Elsevier
DOI: 10.1016/j.sbi.2022.102343

A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms

Author(s): Aleksandra E Badaczewska-Dawid, Aleksander Kuriata, Carlos Pintado-Grima, Javier Garcia-Pardo, Michał Burdukiewicz, Valentín Iglesias, Sebastian Kmiecik and Salvador Ventura
Published in: Nucleic Acids Research, 2023, Page(s) D360–D367, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad942

Biological colloids: Unique properties of membraneless organelles in the cell

Author(s): Anna Bratek-Skicki, Margot Van Nerom, Dominique Maes, Peter Tompa
Published in: Advances in Colloid and Interface Science, 2022, ISSN 1873-3727
Publisher: ELSEVIER
DOI: 10.1016/j.cis.2022.102777

CARs-DB: A Database of Cryptic Amyloidogenic Regions in Intrinsically Disordered Proteins

Author(s): Carlos Pintado-Grima; Oriol Bárcenas; Zoe Manglano-Artuñedo; Rita Vilaça; Sandra Macedo-Ribeiro; Irantzu Pallarès; Jaime Santos; Salvador Ventura
Published in: Frontiers in Molecular Biosciences, Issue 1, 2022, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2022.882160

Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies

Author(s): Javier Garcia-Pardo and Salvador Ventura
Published in: Trends in Biochemical Sciences, 2023, Page(s) 119-133, ISSN 0968-0004
Publisher: Elsevier BV
DOI: 10.1016/j.tibs.2023.10.005

SARS‐CoV‐2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion

Author(s): Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C.E. Tosatto; Philippe Le Mercier
Published in: The FEBS Journal, Issue 1, 2022, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins

Author(s): Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12070974

A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation

Author(s): Carlos Pintado-Grima; Oriol Bárcenas; Andrea Bartolomé-Nafría; Marc Fornt-Suñé; Valentín Iglesias; Javier Garcia-Pardo; Salvador Ventura
Published in: Biophysica, Issue 1, 2023, ISSN 2673-4125
Publisher: MDPI
DOI: 10.3390/biophysica3010001

Decoding the role of coiled-coil motifs in human prion-like proteins

Author(s): Molood Behbahanipour, Javier García-Pardo, Salvador Ventura
Published in: Prion, 2021, ISSN 1933-690X
Publisher: Taylor & Francis
DOI: 10.1080/19336896.2021.1961569

F/YGG-motif is an intrinsically disordered nucleic-acid binding motif

Author(s): Joris Van Lindt, Tamas Lazar, Donya Pakravan , Manon Demulder, Attila Meszaros , Ludo Van Den Bosch, Dominique Maes, Peter Tompa
Published in: RNA Biology, 2022, ISSN 1555-8584
Publisher: Taylor and Francis
DOI: 10.1080/15476286.2022.2066336

The Repeating, Modular Architecture of the HtrA Proteases

Author(s): Matthew Merski, Sandra Macedo-Ribeiro, Rafal M. Wieczorek, Maria W. Górna
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12060793

Quantification of Surface Tension Effects and Nucleation-and-Growth Rates during Self-Assembly of Biological Condensates

Author(s): Sárkány, Z., F. Rocha, A. Bratek-Skicki, P. Tompa, S. Macedo-Ribeiro and P. M. Martins
Published in: Advanced Science, 2023, ISSN 2198-3844
Publisher: WILEY
DOI: 10.1002/advs.202301501

Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages

Author(s): Joana Wilton, Filipa Lopes de Mendonça, Filipa Lopes de Mendonça, Isabel Pereira-Castro, Isabel Pereira-Castro, Michael Tellier, Takayuki Nojima, Angela M. Costa, Jaime Freitas, Shona Murphy, Maria Jose Oliveira, Nicholas J. Proudfoot, Alexandra Moreira
Published in: Frontiers in Immunology, 2023, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2023.1182525

aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation

Author(s): Carlos Pintado-Grima, Oriol Bárcenas, Valentín Iglesias, Jaime Santos, Zoe Manglano-Artuñedo, Irantzu Pallarès, Michał Burdukiewicz, Salvador Ventura
Published in: Database: The Journal of Biological Databases and Curation, 2023, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baad084

Intrinsic protein disorder uncouples affinity from binding specificity

Author(s): Tamas Lazar, Agnes Tantos, Peter Tompa, Eva Schad
Published in: Protein Science, 2022, ISSN 1469-896X
Publisher: Wiley
DOI: 10.1002/pro.4455

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Author(s): Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, CAID predictors, Silvio C E Tosatto and Damiano Piovesan
Published in: Nucleic Acids Research, 2023, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad430

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

Author(s): Carlos Pintado-Grima, Jaime Santos, Valentín Iglesias, Zoe Manglano-Artuñedo, Irantzu Pallarès, Salvador Ventura
Published in: Frontiers in Plant Science, 2023, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2022.1060410

ECO: the Evidence and Conclusion Ontology, an update for 2022

Author(s): Suvarna Nadendla, Rebecca Jackson, James Munro, Federica Quaglia, Bálint Mészáros, Dustin Olley, Elizabeth T Hobbs, Stephen M Goralski, Marcus Chibucos, Christopher John Mungall, Silvio C E Tosatto, Ivan Erill, Michelle G Giglio
Published in: Nucleic Acids Research, 2022, Page(s) D1515–D1521, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1025

Drug repurposing of dopaminergic drugs to inhibit ataxin-3 aggregation

Author(s): Francisco Figueiredo, Zsuzsa Sárkány, Alexandra Silva, Daniela Vilasboas-Campos, Patrícia Maciel, Andreia Teixeira-Castro, Pedro M. Martins, Sandra Macedo-Ribeiro
Published in: Biomedicine & Pharmacotherapy, 2023, ISSN 0753-3322
Publisher: Elsevier Masson
DOI: 10.1016/j.biopha.2023.115258

FuzDB: a new phase in understanding fuzzy interactions

Author(s): Andras Hatos, Alexander Miguel Monzon, Silvio C E Tosatto, Damiano Piovesan, Monika Fuxreiter
Published in: Nucleic Acids Research, 2022, Page(s) D509–D517, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1060

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Author(s): Bálint Mészáros, András Hatos, Nicolas Palopoli, Federica Quaglia, Edoardo Salladini, Kim Van Roey, Haribabu Arthanari, Zsuzsanna Dosztányi, Isabella C. Felli, Patrick D. Fischer, Jeffrey C. Hoch, Cy M. Jeffries, Sonia Longhi, Emiliano Maiani, Sandra Orchard, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Iva Pritisanac, Luiggi Tenorio, Thibault Viennet, Peter Tompa, Wim V
Published in: Nature Methods, 2023, Page(s) 1291–1303, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01915-x

A3D database: structure-based predictions of protein aggregation for the human proteome

Author(s): Aleksandra E Badaczewska-Dawid, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik
Published in: Bioinformatics, 2022, Page(s) 3121–3123, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac215

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.

Author(s): Federica Quaglia; Federica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor
Published in: Nucleic Acids Research, Issue 1, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1082

DisProt in 2024: improving function annotation of intrinsically disordered proteins

Author(s): Maria Cristina Aspromonte, Maria Victoria Nugnes, Federica Quaglia, Adel Bouharoua, DisProt Consortium, Silvio C E Tosatto and Damiano Piovesan
Published in: Nucleic Acids Research, 2024, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad928

Development of Small Molecules Targeting α-Synuclein Aggregation: A Promising Strategy to Treat Parkinson’s Disease

Author(s): Samuel Peña-Díaz,Javier García-Pardo, Salvador Ventura
Published in: Pharmaceutics, 2023, ISSN 1999-4923
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15030839

Pathogen-specific structural features of Candida albicans Ras1 activation complex: uncovering new antifungal drug targets

Author(s): José A. Manso, Arturo Carabias, Zsuzsa Sárkány, José M. de Pereda, Pedro José Barbosa Pereira and Sandra Macedo-Ribeiro
Published in: Structural Biology, 2023, ISSN 2150-7511
Publisher: AMER Soc Microbiology
DOI: 10.1128/mbio.00638-23

PITB: A high affinity transthyretin aggregation inhibitor with optimal pharmacokinetic properties

Author(s): Francisca Pinheiro, Nathalia Varejão, Adrià Sánchez-Morales, Filipa Bezerra, Susanna Navarro, Adrián Velázquez-Campoy, Félix Busqué, Maria Rosário Almeida, Ramon Alibés, David Reverter, Irantzu Pallarès and Salvador Ventura
Published in: Chemistry, 2023, ISSN 0223-5234
Publisher: Elsevier BV
DOI: 10.1016/j.ejmech.2023.115837

A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion

Author(s): Mamadou Amadou Diallo; Sébastien Pirotte; Yunlong Hu; Léa Morvan; Krzysztof Rakus; Nicolás M Suárez; Lee PoTsang; Hisao Saneyoshi; Yan Xu; Andrew J Davison; Peter Tompa; Joel L Sussman; Alain Vanderplasschen
Published in: Nucleic Acids Research, Issue 1, 2023, Page(s) 806–830, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac761

SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress

Author(s): Valentín Iglesias, Jaime Santos, Juan Santos-Suárez, Carlos Pintado-Grima, Salvador Ventura
Published in: Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2021.718301

A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins

Author(s): Attila Mészáros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12111566

A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly

Author(s): Francisco Figueiredo; Mónica Lopes-Marques; Bruno Almeida; Nena Matscheko; Pedro M. Martins; Alexandra Silva; Sandra Macedo-Ribeiro
Published in: Cells, Issue Volume 11; Issue 12; Pages: 1969, 2022, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells11121969

Small molecules to target tau amyloid aggregation

Author(s): Zoe Manglano-Artunedo, Samuel Pena-Diaz, Salvador Ventura
Published in: Neural Regeneration Research, 2023, Page(s) 509-511, ISSN 1673-5374
Publisher: Neural Regeneration Research
DOI: 10.4103/1673-5374.380900

The structural plasticity of polyglutamine repeats

Author(s): Barbosa Pereira, P. J., J. A. Manso and S. Macedo-Ribeiro
Published in: Current Opinion in Structural Biology, 2023, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2023.102607