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

Informations projet

PhasAGE

N° de convention de subvention: 952334

DOI

10.3030/952334

Projet clôturé

Date de signature de la CE 2 Juillet 2020

Date de début 1 Janvier 2021

Date de fin 31 Mars 2024

Financé au titre de

• Twinning of research institutions

Coût total

€ 899 741,25

Contribution de l’UE

€ 899 741,25

Coordonné par

INSTITUTO DE BIOLOGIA MOLECULAR E CELULAR-IBMC
Portugal

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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

Auteurs: Attila Meszaros, Junaid Ahmed, Giorgio Russo, Peter Tompa, Tamas Lazar
Publié dans: Frontiers in Medicine, 2022, ISSN 2296-858X
Éditeur: Frontiers
DOI: 10.3389/fmed.2022.1019803

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

Auteurs: Carlos Pintado-Grima, Valentín Iglesias, Jaime Santos, Vladimir N Uversky, Salvador Ventura
Publié dans: Biomolecules, 2021, ISSN 2218-273X
Éditeur: MDPI
DOI: 10.3390/biom11111596

A3DyDB: exploring structural aggregation propensities in the yeast proteome

Auteurs: Javier Garcia-Pardo, Aleksandra E. Badaczewska-Dawid, Carlos Pintado-Grima, Valentín Iglesias, Aleksander Kuriata, Sebastian Kmiecik and Salvador Ventura
Publié dans: Microbial Cell Factories, 2023, ISSN 1475-2859
Éditeur: BioMed Central
DOI: 10.1186/s12934-023-02182-3

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

Auteurs: Mainak Guharoy, Tamas Lazar, Mauricio Macossay-Castillo, Peter Tompa
Publié dans: Communications Biology, 2022, ISSN 2399-3642
Éditeur: Nature
DOI: 10.1038/s42003-022-03391-z

Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase

Auteurs: Ana S. Figueiredo, Joana R. Loureiro, Sandra Macedo-Ribeiro, Isabel Silveira
Publié dans: Cells, 2023, ISSN 2073-4409
Éditeur: MDPI
DOI: 10.3390/cells12060826

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

Auteurs: Javier Garcia-Pardo, Andrea Bartolomé-Nafría, Antonio Chaves-Sanjuan, Marcos Gil-Garcia, Cristina Visentin, Martino Bolognesi, Stefano Ricagno, Salvador Ventura
Publié dans: Nature Communications, 2023, ISSN 2041-1723
Éditeur: 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

Auteurs: Alexander Miguel Monzon, Damiano Piovesan, Monika Fuxreiter
Publié dans: Biomolecules, 2022, ISSN 2218-273X
Éditeur: MDPI
DOI: 10.3390/biom12010092

Databases for intrinsically disordered proteins

Auteurs: Damiano Piovesan; Alexander Miguel Monzon; Federica Quaglia; Silvio C. E. Tosatto
Publié dans: Acta Crystallographica Section D, Numéro 1, 2022, ISSN 0907-4449
Éditeur: Blackwell Publishing Inc.
DOI: 10.1107/s2059798321012109

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

Auteurs: Zsuzsa Sárkány, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins
Publié dans: Molecular Biology of the Cell, 2024, ISSN 1059-1524
Éditeur: American Society for Cell Biology
DOI: 10.1091/mbc.e23-07-0289

Computational methods to predict protein aggregation

Auteurs: Susanna Navarro, Salvador Ventura
Publié dans: Current Opinion in Structural Biology, 2022, ISSN 1879-033X
Éditeur: Elsevier
DOI: 10.1016/j.sbi.2022.102343

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

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

Biological colloids: Unique properties of membraneless organelles in the cell

Auteurs: Anna Bratek-Skicki, Margot Van Nerom, Dominique Maes, Peter Tompa
Publié dans: Advances in Colloid and Interface Science, 2022, ISSN 1873-3727
Éditeur: ELSEVIER
DOI: 10.1016/j.cis.2022.102777

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

Auteurs: Carlos Pintado-Grima; Oriol Bárcenas; Zoe Manglano-Artuñedo; Rita Vilaça; Sandra Macedo-Ribeiro; Irantzu Pallarès; Jaime Santos; Salvador Ventura
Publié dans: Frontiers in Molecular Biosciences, Numéro 1, 2022, ISSN 2296-889X
Éditeur: Frontiers
DOI: 10.3389/fmolb.2022.882160

Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies

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

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

Auteurs: Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C.E. Tosatto; Philippe Le Mercier
Publié dans: The FEBS Journal, Numéro 1, 2022, ISSN 1742-464X
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

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

Auteurs: Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura
Publié dans: Biomolecules, 2022, ISSN 2218-273X
Éditeur: MDPI
DOI: 10.3390/biom12070974

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

Auteurs: Carlos Pintado-Grima; Oriol Bárcenas; Andrea Bartolomé-Nafría; Marc Fornt-Suñé; Valentín Iglesias; Javier Garcia-Pardo; Salvador Ventura
Publié dans: Biophysica, Numéro 1, 2023, ISSN 2673-4125
Éditeur: MDPI
DOI: 10.3390/biophysica3010001

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

Auteurs: Molood Behbahanipour, Javier García-Pardo, Salvador Ventura
Publié dans: Prion, 2021, ISSN 1933-690X
Éditeur: Taylor & Francis
DOI: 10.1080/19336896.2021.1961569

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

Auteurs: Joris Van Lindt, Tamas Lazar, Donya Pakravan , Manon Demulder, Attila Meszaros , Ludo Van Den Bosch, Dominique Maes, Peter Tompa
Publié dans: RNA Biology, 2022, ISSN 1555-8584
Éditeur: Taylor and Francis
DOI: 10.1080/15476286.2022.2066336

The Repeating, Modular Architecture of the HtrA Proteases

Auteurs: Matthew Merski, Sandra Macedo-Ribeiro, Rafal M. Wieczorek, Maria W. Górna
Publié dans: Biomolecules, 2022, ISSN 2218-273X
Éditeur: MDPI
DOI: 10.3390/biom12060793

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

Auteurs: Sárkány, Z., F. Rocha, A. Bratek-Skicki, P. Tompa, S. Macedo-Ribeiro and P. M. Martins
Publié dans: Advanced Science, 2023, ISSN 2198-3844
Éditeur: WILEY
DOI: 10.1002/advs.202301501

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

Auteurs: 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
Publié dans: Frontiers in Immunology, 2023, ISSN 1664-3224
Éditeur: Frontiers
DOI: 10.3389/fimmu.2023.1182525

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

Auteurs: Carlos Pintado-Grima, Oriol Bárcenas, Valentín Iglesias, Jaime Santos, Zoe Manglano-Artuñedo, Irantzu Pallarès, Michał Burdukiewicz, Salvador Ventura
Publié dans: Database: The Journal of Biological Databases and Curation, 2023, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baad084

Intrinsic protein disorder uncouples affinity from binding specificity

Auteurs: Tamas Lazar, Agnes Tantos, Peter Tompa, Eva Schad
Publié dans: Protein Science, 2022, ISSN 1469-896X
Éditeur: Wiley
DOI: 10.1002/pro.4455

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

Auteurs: Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, CAID predictors, Silvio C E Tosatto and Damiano Piovesan
Publié dans: Nucleic Acids Research, 2023, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad430

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

Auteurs: Carlos Pintado-Grima, Jaime Santos, Valentín Iglesias, Zoe Manglano-Artuñedo, Irantzu Pallarès, Salvador Ventura
Publié dans: Frontiers in Plant Science, 2023, ISSN 1664-462X
Éditeur: Frontiers Media S. A.
DOI: 10.3389/fpls.2022.1060410

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

Auteurs: 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
Publié dans: Nucleic Acids Research, 2022, Page(s) D1515–D1521, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkab1025

Drug repurposing of dopaminergic drugs to inhibit ataxin-3 aggregation

Auteurs: Francisco Figueiredo, Zsuzsa Sárkány, Alexandra Silva, Daniela Vilasboas-Campos, Patrícia Maciel, Andreia Teixeira-Castro, Pedro M. Martins, Sandra Macedo-Ribeiro
Publié dans: Biomedicine & Pharmacotherapy, 2023, ISSN 0753-3322
Éditeur: Elsevier Masson
DOI: 10.1016/j.biopha.2023.115258

FuzDB: a new phase in understanding fuzzy interactions

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

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Auteurs: 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
Publié dans: Nature Methods, 2023, Page(s) 1291–1303, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-023-01915-x

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

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

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 1, 2021, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkab1082

DisProt in 2024: improving function annotation of intrinsically disordered proteins

Auteurs: Maria Cristina Aspromonte, Maria Victoria Nugnes, Federica Quaglia, Adel Bouharoua, DisProt Consortium, Silvio C E Tosatto and Damiano Piovesan
Publié dans: Nucleic Acids Research, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad928

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

Auteurs: Samuel Peña-Díaz,Javier García-Pardo, Salvador Ventura
Publié dans: Pharmaceutics, 2023, ISSN 1999-4923
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15030839

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

Auteurs: José A. Manso, Arturo Carabias, Zsuzsa Sárkány, José M. de Pereda, Pedro José Barbosa Pereira and Sandra Macedo-Ribeiro
Publié dans: Structural Biology, 2023, ISSN 2150-7511
Éditeur: AMER Soc Microbiology
DOI: 10.1128/mbio.00638-23

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

Auteurs: 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
Publié dans: Chemistry, 2023, ISSN 0223-5234
Éditeur: 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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 1, 2023, Page(s) 806–830, ISSN 1362-4962
Éditeur: 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

Auteurs: Valentín Iglesias, Jaime Santos, Juan Santos-Suárez, Carlos Pintado-Grima, Salvador Ventura
Publié dans: Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Éditeur: Frontiers
DOI: 10.3389/fmolb.2021.718301

A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins

Auteurs: Attila Mészáros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Publié dans: Biomolecules, 2022, ISSN 2218-273X
Éditeur: MDPI
DOI: 10.3390/biom12111566

A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly

Auteurs: Francisco Figueiredo; Mónica Lopes-Marques; Bruno Almeida; Nena Matscheko; Pedro M. Martins; Alexandra Silva; Sandra Macedo-Ribeiro
Publié dans: Cells, Numéro Volume 11; Numéro 12; Pages: 1969, 2022, ISSN 2073-4409
Éditeur: MDPI
DOI: 10.3390/cells11121969

Small molecules to target tau amyloid aggregation

Auteurs: Zoe Manglano-Artunedo, Samuel Pena-Diaz, Salvador Ventura
Publié dans: Neural Regeneration Research, 2023, Page(s) 509-511, ISSN 1673-5374
Éditeur: Neural Regeneration Research
DOI: 10.4103/1673-5374.380900

The structural plasticity of polyglutamine repeats

Auteurs: Barbosa Pereira, P. J., J. A. Manso and S. Macedo-Ribeiro
Publié dans: Current Opinion in Structural Biology, 2023, ISSN 0959-440X
Éditeur: Elsevier BV
DOI: 10.1016/j.sbi.2023.102607