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

Informacje na temat projektu

PhasAGE

Identyfikator umowy o grant: 952334

DOI

10.3030/952334

Projekt został zamknięty

Data podpisania przez KE 2 Lipca 2020

Data rozpoczęcia 1 Stycznia 2021

Data zakończenia 31 Marca 2024

Finansowanie w ramach

• Twinning of research institutions

Koszt całkowity

€ 899 741,25

Wkład UE

€ 899 741,25

Koordynowany przez

INSTITUTO DE BIOLOGIA MOLECULAR E CELULAR-IBMC
Portugal

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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

Publikacje

Peer reviewed articles (42)

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

Autorzy: Attila Meszaros, Junaid Ahmed, Giorgio Russo, Peter Tompa, Tamas Lazar
Opublikowane w: Frontiers in Medicine, 2022, ISSN 2296-858X
Wydawca: Frontiers
DOI: 10.3389/fmed.2022.1019803

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

Autorzy: Carlos Pintado-Grima, Valentín Iglesias, Jaime Santos, Vladimir N Uversky, Salvador Ventura
Opublikowane w: Biomolecules, 2021, ISSN 2218-273X
Wydawca: MDPI
DOI: 10.3390/biom11111596

A3DyDB: exploring structural aggregation propensities in the yeast proteome

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

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

Autorzy: Mainak Guharoy, Tamas Lazar, Mauricio Macossay-Castillo, Peter Tompa
Opublikowane w: Communications Biology, 2022, ISSN 2399-3642
Wydawca: Nature
DOI: 10.1038/s42003-022-03391-z

Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase

Autorzy: Ana S. Figueiredo, Joana R. Loureiro, Sandra Macedo-Ribeiro, Isabel Silveira
Opublikowane w: Cells, 2023, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells12060826

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

Autorzy: Javier Garcia-Pardo, Andrea Bartolomé-Nafría, Antonio Chaves-Sanjuan, Marcos Gil-Garcia, Cristina Visentin, Martino Bolognesi, Stefano Ricagno, Salvador Ventura
Opublikowane w: Nature Communications, 2023, ISSN 2041-1723
Wydawca: 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

Autorzy: Alexander Miguel Monzon, Damiano Piovesan, Monika Fuxreiter
Opublikowane w: Biomolecules, 2022, ISSN 2218-273X
Wydawca: MDPI
DOI: 10.3390/biom12010092

Databases for intrinsically disordered proteins

Autorzy: Damiano Piovesan; Alexander Miguel Monzon; Federica Quaglia; Silvio C. E. Tosatto
Opublikowane w: Acta Crystallographica Section D, Numer 1, 2022, ISSN 0907-4449
Wydawca: Blackwell Publishing Inc.
DOI: 10.1107/s2059798321012109

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

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

Computational methods to predict protein aggregation

Autorzy: Susanna Navarro, Salvador Ventura
Opublikowane w: Current Opinion in Structural Biology, 2022, ISSN 1879-033X
Wydawca: Elsevier
DOI: 10.1016/j.sbi.2022.102343

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

Autorzy: Aleksandra E Badaczewska-Dawid, Aleksander Kuriata, Carlos Pintado-Grima, Javier Garcia-Pardo, Michał Burdukiewicz, Valentín Iglesias, Sebastian Kmiecik and Salvador Ventura
Opublikowane w: Nucleic Acids Research, 2023, Strona(/y) D360–D367, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkad942

Biological colloids: Unique properties of membraneless organelles in the cell

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

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

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

Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies

Autorzy: Javier Garcia-Pardo and Salvador Ventura
Opublikowane w: Trends in Biochemical Sciences, 2023, Strona(/y) 119-133, ISSN 0968-0004
Wydawca: Elsevier BV
DOI: 10.1016/j.tibs.2023.10.005

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

Autorzy: Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C.E. Tosatto; Philippe Le Mercier
Opublikowane w: The FEBS Journal, Numer 1, 2022, ISSN 1742-464X
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

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

Autorzy: Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura
Opublikowane w: Biomolecules, 2022, ISSN 2218-273X
Wydawca: MDPI
DOI: 10.3390/biom12070974

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

Autorzy: Carlos Pintado-Grima; Oriol Bárcenas; Andrea Bartolomé-Nafría; Marc Fornt-Suñé; Valentín Iglesias; Javier Garcia-Pardo; Salvador Ventura
Opublikowane w: Biophysica, Numer 1, 2023, ISSN 2673-4125
Wydawca: MDPI
DOI: 10.3390/biophysica3010001

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

Autorzy: Molood Behbahanipour, Javier García-Pardo, Salvador Ventura
Opublikowane w: Prion, 2021, ISSN 1933-690X
Wydawca: Taylor & Francis
DOI: 10.1080/19336896.2021.1961569

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

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

The Repeating, Modular Architecture of the HtrA Proteases

Autorzy: Matthew Merski, Sandra Macedo-Ribeiro, Rafal M. Wieczorek, Maria W. Górna
Opublikowane w: Biomolecules, 2022, ISSN 2218-273X
Wydawca: MDPI
DOI: 10.3390/biom12060793

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

Autorzy: Sárkány, Z., F. Rocha, A. Bratek-Skicki, P. Tompa, S. Macedo-Ribeiro and P. M. Martins
Opublikowane w: Advanced Science, 2023, ISSN 2198-3844
Wydawca: WILEY
DOI: 10.1002/advs.202301501

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

Autorzy: 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
Opublikowane w: Frontiers in Immunology, 2023, ISSN 1664-3224
Wydawca: Frontiers
DOI: 10.3389/fimmu.2023.1182525

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

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

Intrinsic protein disorder uncouples affinity from binding specificity

Autorzy: Tamas Lazar, Agnes Tantos, Peter Tompa, Eva Schad
Opublikowane w: Protein Science, 2022, ISSN 1469-896X
Wydawca: Wiley
DOI: 10.1002/pro.4455

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

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

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

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

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, 2022, Strona(/y) D1515–D1521, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab1025

Drug repurposing of dopaminergic drugs to inhibit ataxin-3 aggregation

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

FuzDB: a new phase in understanding fuzzy interactions

Autorzy: Andras Hatos, Alexander Miguel Monzon, Silvio C E Tosatto, Damiano Piovesan, Monika Fuxreiter
Opublikowane w: Nucleic Acids Research, 2022, Strona(/y) D509–D517, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab1060

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Autorzy: 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
Opublikowane w: Nature Methods, 2023, Strona(/y) 1291–1303, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/s41592-023-01915-x

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

Autorzy: Aleksandra E Badaczewska-Dawid, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik
Opublikowane w: Bioinformatics, 2022, Strona(/y) 3121–3123, ISSN 1367-4811
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac215

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 1, 2021, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab1082

DisProt in 2024: improving function annotation of intrinsically disordered proteins

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

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

Autorzy: Samuel Peña-Díaz,Javier García-Pardo, Salvador Ventura
Opublikowane w: Pharmaceutics, 2023, ISSN 1999-4923
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15030839

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

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

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

Autorzy: 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
Opublikowane w: Chemistry, 2023, ISSN 0223-5234
Wydawca: 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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 1, 2023, Strona(/y) 806–830, ISSN 1362-4962
Wydawca: 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

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

A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins

Autorzy: Attila Mészáros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Opublikowane w: Biomolecules, 2022, ISSN 2218-273X
Wydawca: MDPI
DOI: 10.3390/biom12111566

A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly

Autorzy: Francisco Figueiredo; Mónica Lopes-Marques; Bruno Almeida; Nena Matscheko; Pedro M. Martins; Alexandra Silva; Sandra Macedo-Ribeiro
Opublikowane w: Cells, Numer Volume 11; Numer 12; Pages: 1969, 2022, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells11121969

Small molecules to target tau amyloid aggregation

Autorzy: Zoe Manglano-Artunedo, Samuel Pena-Diaz, Salvador Ventura
Opublikowane w: Neural Regeneration Research, 2023, Strona(/y) 509-511, ISSN 1673-5374
Wydawca: Neural Regeneration Research
DOI: 10.4103/1673-5374.380900

The structural plasticity of polyglutamine repeats

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