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

Informazioni relative al progetto

PhasAGE

ID dell’accordo di sovvenzione: 952334

DOI

10.3030/952334

Progetto chiuso

Data della firma CE 2 Luglio 2020

Data di avvio 1 Gennaio 2021

Data di completamento 31 Marzo 2024

Finanziato da

• Twinning of research institutions

Costo totale

€ 899 741,25

Contributo UE

€ 899 741,25

Coordinato da

INSTITUTO DE BIOLOGIA MOLECULAR E CELULAR-IBMC
Portugal

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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

Pubblicazioni

Peer reviewed articles (42)

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

Autori: Attila Meszaros, Junaid Ahmed, Giorgio Russo, Peter Tompa, Tamas Lazar
Pubblicato in: Frontiers in Medicine, 2022, ISSN 2296-858X
Editore: Frontiers
DOI: 10.3389/fmed.2022.1019803

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

Autori: Carlos Pintado-Grima, Valentín Iglesias, Jaime Santos, Vladimir N Uversky, Salvador Ventura
Pubblicato in: Biomolecules, 2021, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom11111596

A3DyDB: exploring structural aggregation propensities in the yeast proteome

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

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

Autori: Mainak Guharoy, Tamas Lazar, Mauricio Macossay-Castillo, Peter Tompa
Pubblicato in: Communications Biology, 2022, ISSN 2399-3642
Editore: Nature
DOI: 10.1038/s42003-022-03391-z

Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase

Autori: Ana S. Figueiredo, Joana R. Loureiro, Sandra Macedo-Ribeiro, Isabel Silveira
Pubblicato in: Cells, 2023, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells12060826

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

Autori: Javier Garcia-Pardo, Andrea Bartolomé-Nafría, Antonio Chaves-Sanjuan, Marcos Gil-Garcia, Cristina Visentin, Martino Bolognesi, Stefano Ricagno, Salvador Ventura
Pubblicato in: Nature Communications, 2023, ISSN 2041-1723
Editore: 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

Autori: Alexander Miguel Monzon, Damiano Piovesan, Monika Fuxreiter
Pubblicato in: Biomolecules, 2022, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom12010092

Databases for intrinsically disordered proteins

Autori: Damiano Piovesan; Alexander Miguel Monzon; Federica Quaglia; Silvio C. E. Tosatto
Pubblicato in: Acta Crystallographica Section D, Numero 1, 2022, ISSN 0907-4449
Editore: Blackwell Publishing Inc.
DOI: 10.1107/s2059798321012109

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

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

Computational methods to predict protein aggregation

Autori: Susanna Navarro, Salvador Ventura
Pubblicato in: Current Opinion in Structural Biology, 2022, ISSN 1879-033X
Editore: Elsevier
DOI: 10.1016/j.sbi.2022.102343

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

Autori: Aleksandra E Badaczewska-Dawid, Aleksander Kuriata, Carlos Pintado-Grima, Javier Garcia-Pardo, Michał Burdukiewicz, Valentín Iglesias, Sebastian Kmiecik and Salvador Ventura
Pubblicato in: Nucleic Acids Research, 2023, Pagina/e D360–D367, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad942

Biological colloids: Unique properties of membraneless organelles in the cell

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

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

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

Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies

Autori: Javier Garcia-Pardo and Salvador Ventura
Pubblicato in: Trends in Biochemical Sciences, 2023, Pagina/e 119-133, ISSN 0968-0004
Editore: Elsevier BV
DOI: 10.1016/j.tibs.2023.10.005

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

Autori: Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C.E. Tosatto; Philippe Le Mercier
Pubblicato in: The FEBS Journal, Numero 1, 2022, ISSN 1742-464X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

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

Autori: Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura
Pubblicato in: Biomolecules, 2022, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom12070974

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

Autori: Carlos Pintado-Grima; Oriol Bárcenas; Andrea Bartolomé-Nafría; Marc Fornt-Suñé; Valentín Iglesias; Javier Garcia-Pardo; Salvador Ventura
Pubblicato in: Biophysica, Numero 1, 2023, ISSN 2673-4125
Editore: MDPI
DOI: 10.3390/biophysica3010001

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

Autori: Molood Behbahanipour, Javier García-Pardo, Salvador Ventura
Pubblicato in: Prion, 2021, ISSN 1933-690X
Editore: Taylor & Francis
DOI: 10.1080/19336896.2021.1961569

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

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

The Repeating, Modular Architecture of the HtrA Proteases

Autori: Matthew Merski, Sandra Macedo-Ribeiro, Rafal M. Wieczorek, Maria W. Górna
Pubblicato in: Biomolecules, 2022, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom12060793

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

Autori: Sárkány, Z., F. Rocha, A. Bratek-Skicki, P. Tompa, S. Macedo-Ribeiro and P. M. Martins
Pubblicato in: Advanced Science, 2023, ISSN 2198-3844
Editore: WILEY
DOI: 10.1002/advs.202301501

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

Autori: 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
Pubblicato in: Frontiers in Immunology, 2023, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2023.1182525

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

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

Intrinsic protein disorder uncouples affinity from binding specificity

Autori: Tamas Lazar, Agnes Tantos, Peter Tompa, Eva Schad
Pubblicato in: Protein Science, 2022, ISSN 1469-896X
Editore: Wiley
DOI: 10.1002/pro.4455

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

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

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

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

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

Autori: 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
Pubblicato in: Nucleic Acids Research, 2022, Pagina/e D1515–D1521, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab1025

Drug repurposing of dopaminergic drugs to inhibit ataxin-3 aggregation

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

FuzDB: a new phase in understanding fuzzy interactions

Autori: Andras Hatos, Alexander Miguel Monzon, Silvio C E Tosatto, Damiano Piovesan, Monika Fuxreiter
Pubblicato in: Nucleic Acids Research, 2022, Pagina/e D509–D517, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab1060

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Autori: 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
Pubblicato in: Nature Methods, 2023, Pagina/e 1291–1303, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-023-01915-x

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

Autori: Aleksandra E Badaczewska-Dawid, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik
Pubblicato in: Bioinformatics, 2022, Pagina/e 3121–3123, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac215

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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 1, 2021, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkab1082

DisProt in 2024: improving function annotation of intrinsically disordered proteins

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

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

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

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

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

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

Autori: 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
Pubblicato in: Chemistry, 2023, ISSN 0223-5234
Editore: 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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 1, 2023, Pagina/e 806–830, ISSN 1362-4962
Editore: 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

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

A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins

Autori: Attila Mészáros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Pubblicato in: Biomolecules, 2022, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom12111566

A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly

Autori: Francisco Figueiredo; Mónica Lopes-Marques; Bruno Almeida; Nena Matscheko; Pedro M. Martins; Alexandra Silva; Sandra Macedo-Ribeiro
Pubblicato in: Cells, Numero Volume 11; Numero 12; Pages: 1969, 2022, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells11121969

Small molecules to target tau amyloid aggregation

Autori: Zoe Manglano-Artunedo, Samuel Pena-Diaz, Salvador Ventura
Pubblicato in: Neural Regeneration Research, 2023, Pagina/e 509-511, ISSN 1673-5374
Editore: Neural Regeneration Research
DOI: 10.4103/1673-5374.380900

The structural plasticity of polyglutamine repeats

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