PHASAGE
PhasAGE – Excellence Hub on Phase Transitions in Aging and Age-Related Disorders
PUBLICATIONS
List of scientific publications funded by the PhasAGE project relevant to the field of phase separation and protein aggregation in aging and disease.
2024
Behbahanipour M, Navarro S, Bárcenas O, Garcia-Pardo J, Ventura S. Bioengineered self-assembled nanofibrils for high-affinity SARS-CoV-2 capture and neutralization. J Colloid Interface Sci. 2024 Jun 24;674:753-765. doi: 10.1016/j.jcis.2024.06.175 
Bartolomé-Nafría A, García-Pardo J, Ventura S. Mutations in human prion-like domains: pathogenic but not always amyloidogenic. Prion. 2024 Dec;18(1):28-39. doi: 10.1080/19336896.2024.2329186
Diogo Costa-Rodrigues, José P. Leite, et al. Transthyretin monomers: a new plasma biomarker for pre-symptomatic transthyretin-related amyloidosis. Amyloid. 2024 Jul 1:1-7. doi: 10.1080/13506129.2024.2368860
Aspromonte MC, Del Conte A, Zhu S, et al. CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs). Human Genetics. In Review.
Manglano-Artuñedo Z, Peña-Díaz S, Ventura S. Small molecules to target tau amyloid aggregation. Neural Regen Res. 2024 Mar;19(3):509-511. doi: 10.4103/1673-5374.380900.
Garcia-Pardo J, Fornt-Suñé M, Ventura S. Assembly and catalytic activity of short prion-inspired peptides. Methods Enzymol. 2024;697:499-526. doi: 10.1016/bs.mie.2024.01.015.
Pintado-Grima C, Bárcenas O, Ventura S. Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins. Methods Mol Biol. 2024;2714:171-185. doi: 10.1007/978-1-0716-3441-7_10.
Badaczewska-Dawid AE, Kuriata A, Pintado-Grima C, Garcia-Pardo J, Burdukiewicz M, Iglesias V, Kmiecik S, Ventura S. A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms. Nucleic Acids Res. 2023 Oct 28:gkad942.
Garcia-Pardo J, Ventura S. Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies. Trends Biochem Sci. 2023 Nov 3:S0968-0004(23)00260-8. doi: 10.1016/j.tibs.2023.10.005.
2023
Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Mol Biol Cell. 2023 Dec 20:mbcE23070289. doi: 10.1091/mbc.E23-07-0289
Pintado-Grima C, Bárcenas O, Iglesias V, Santos J, Manglano-Artuñedo Z, Pallarès I, Burdukiewicz M, Ventura S. aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation Database. 2023. baad084 doi: 10.1093/database/baad084
Aspromonte MC, Nugnes MV, Quaglia F, Bouharoua A; DisProt Consortium; Tosatto SCE, Piovesan D. DisProt in 2024: improving function annotation of intrinsically disordered proteins. Nucleic Acids Res. 2023 Oct 30:gkad928. doi: 10.1093/nar/gkad928.
Garcia-Pardo J, Badaczewska-Dawid AE, Pintado-Grima C, Iglesias V, Kuriata A, Kmiecik S, Ventura S. A3DyDB: exploring structural aggregation propensities in the yeast proteome. Microb Cell Fact. 2023 Sep 16;22(1):186. doi: 10.1186/s12934-023-02182-3.
Mészáros B, et al. Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions. Nat Methods. 2023 Sep;20(9):1291-1303. doi: 10.1038/s41592-023-01915-x
Figueiredo F, Sárkány Z, Silva A, Vilasboas-Campos D, Maciel P, Teixeira-Castro A, Martins PM, Macedo-Ribeiro S. Drug repurposing of dopaminergic drugs to inhibit ataxin-3 aggregation. Biomed Pharmacother. 2023 Sep;165:115258. doi: 10.1016/j.biopha.2023.115258.
Manso JA, Carabias A, Sárkány Z, de Pereda JM, Pereira PJB, Macedo-Ribeiro S. Pathogen-specific structural features of Candida albicans Ras1 activation complex: uncovering new antifungal drug targets. mBio. 2023 Aug 31;14(4):e0063823. doi: 10.1128/mbio.00638-23.
Sárkány Z, Rocha F, Bratek-Skicki A, Tompa P, Macedo-Ribeiro S, Martins PM. Quantification of Surface Tension Effects and Nucleation-and-Growth Rates during Self-Assembly of Biological Condensates. Adv Sci (Weinh). 2023 Aug;10(23):e2301501. doi: 10.1002/advs.202301501.
Del Conte A, Bouhraoua A, Mehdiabadi M, Clementel D, Monzon AM; CAID predictors; Tosatto SCE, Piovesan D. CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 2023 Jul 5;51(W1):W62-W69. doi: 10.1093/nar/gkad430.
Barbosa Pereira PJ, Manso JA, Macedo-Ribeiro S. The structural plasticity of polyglutamine repeats. Curr Opin Struct Biol. 2023 Jun;80:102607. doi: 10.1016/j.sbi.2023.102607.
Wilton J, de Mendonça FL, Pereira-Castro I, et al. Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages. Front Immunol. 2023 Jun 8;14:1182525. doi: 10.3389/fimmu.2023.1182525.
Figueiredo AS, Loureiro JR, Macedo-Ribeiro S, Silveira I. Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase. Cells. 2023 Mar 7;12(6):826. doi: 10.3390/cells12060826.
Peña-Díaz S, García-Pardo J, Ventura S. Development of Small Molecules Targeting α-Synuclein Aggregation: A Promising Strategy to Treat Parkinson’s Disease. Pharmaceutics. 2023 Mar 3;15(3):839. doi: 10.3390/pharmaceutics15030839.
Garcia-Pardo J, Bartolomé-Nafría A, Chaves-Sanjuan A, Gil-Garcia M, Visentin C, Bolognesi M, Ricagno S, Ventura S. Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3. Nat Commun. 2023 Jan 16;14(1):239. doi: 10.1038/s41467-023-35854-0.
Pintado-Grima C, Bárcenas O, Bartolomé-Nafría A, Fornt-Suñé M, Iglesias V, Garcia-Pardo J, Ventura S. A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation. Biophysica. 2023; 3(1):1-20.
Pintado-Grima C, Santos J, Iglesias V, Manglano-Artuñedo Z, Pallarès I, Ventura S. Exploring cryptic amyloidogenic regions in prion-like proteins from plants. Front Plant Sci. 2023 Jan 16;13:1060410. doi: 10.3389/fpls.2022.1060410.
Diallo MA, et al. A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion. Nucleic Acids Res. 2023 Jan 25;51(2):806-830. doi: 10.1093/nar/gkac761.
2022
Bratek-Skicki A, Van Nerom M, Maes D, Tompa P. Biological colloids: Unique properties of membraneless organelles in the cell. Adv Colloid Interface Sci. 2022 Dec;310:102777. doi: 10.1016/j.cis.2022.102777.
Lazar T, Tantos A, Tompa P, Schad E. Intrinsic protein disorder uncouples affinity from binding specificity. Protein Sci. 2022 Nov;31(11):e4455. doi: 10.1002/pro.4455.
Mészáros A, Muwonge K, Janvier S, Ahmed J, Tompa P. A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins. Biomolecules. 2022 Oct 26;12(11):1566. doi: 10.3390/biom12111566
Meszaros A, Ahmed J, Russo G, Tompa P, Lazar T. The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease. Front Med (Lausanne). 2022 Oct 20;9:1019803. doi: 10.3389/fmed.2022.1019803.
Van Lindt J, Lazar T, Pakravan D, Demulder M, Meszaros A, Van Den Bosch L, Maes D, Tompa P. F/YGG-motif is an intrinsically disordered nucleic-acid binding motif. RNA Biol. 2022;19(1):622-635. doi: 10.1080/15476286.2022.2066336.
Pintado-Grima C, Bárcenas O, Ventura S. In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins. Biomolecules. 2022 Jul 12;12(7):974. doi: 10.3390/biom12070974.
Quaglia F, Salladini E, Carraro M, Minervini G, Tosatto SCE, Le Mercier P. SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion. FEBS J. 2022 Jul;289(14):4240-4250. doi: 10.1111/febs.16379.
Merski M, Macedo-Ribeiro S, Wieczorek RM, Górna MW. The Repeating, Modular Architecture of the HtrA Proteases. Biomolecules. 2022 Jun 7;12(6):793. doi: 10.3390/biom12060793.
Figueiredo F, Lopes-Marques M, Almeida B, Matscheko N, Martins PM, Silva A, Macedo-Ribeiro S. A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly. Cells. 2022 Jun 19;11(12):1969. doi: 10.3390/cells11121969
Guharoy M, Lazar T, Macossay-Castillo M, Tompa P. Degron masking outlines degronons, co-degrading functional modules in the proteome. Commun Biol. 2022 May 11;5(1):445. doi: 10.1038/s42003-022-03391-z.
Pintado-Grima C, Bárcenas O, Manglano-Artuñedo Z, Vilaça R, Macedo-Ribeiro S, Pallarès I, Santos J, Ventura S. CARs-DB: A Database of Cryptic Amyloidogenic Regions in Intrinsically Disordered Proteins. Front Mol Biosci. 2022 May 18;9:882160. doi: 10.3389/fmolb.2022.882160.
Badaczewska-Dawid AE, Garcia-Pardo J, Kuriata A, Pujols J, Ventura S, Kmiecik S. A3D database: structure-based predictions of protein aggregation for the human proteome. Bioinformatics. 2022 May 26;38(11):3121-3123. doi: 10.1093/bioinformatics/btac215.
Navarro S, Ventura S. Computational methods to predict protein aggregation. Curr Opin Struct Biol. 2022 Apr;73:102343. doi: 10.1016/j.sbi.2022.102343
Piovesan D, Monzon AM, Quaglia F, Tosatto SCE. Databases for intrinsically disordered proteins. Acta Crystallogr D Struct Biol. 2022 Feb 1;78(Pt 2):144-151. doi:10.1107/S2059798321012109.
Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs ET, Goralski SM, Chibucos M, Mungall CJ, Tosatto SCE, Erill I, Giglio MG. ECO: the Evidence and Conclusion Ontology, an update for 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D1515-D1521.
Hatos A, Monzon AM, Tosatto SCE, Piovesan D, Fuxreiter M. FuzDB: a new phase in understanding fuzzy interactions. Nucleic Acids Res. 2022 Jan 7;50(D1):D509-D517.
Quaglia, F., B. Meszaros, E. Salladini, A. Hatos, R. Pancsa, L. B. et al. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res. 2022 Jan 7;50(D1):D480-D487. doi: 10.1093/nar/gkab1082.
Monzon AM, Piovesan D, Fuxreiter M. Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates. Biomolecules. 2022 Jan 6;12(1):92. doi: 10.3390/biom1201009
2021
Behbahanipour, M., J. Garcia-Pardo and S. Ventura (2021). “Decoding the role of coiled-coil motifs in human prion-like proteins.” Prion 15(1): 143-154
Pintado-Grima, C., V. Iglesias, J. Santos, V. N. Uversky and S. Ventura (2021). “DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH.” Biomolecules 11(11)
Iglesias, V., J. Santos, J. Santos-Suarez, C. Pintado-Grima and S. Ventura (2021). “SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress.” Front Mol Biosci 8: 718301
Publications from other scientific communities
CD-CODE: crowdsourcing condensate database and encyclopedia. Rostam N, et al. Nat Methods (2023)
The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates. Vandelli A, Arnal Segura M, et al. Bioinformatics (2023)
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins. Hatos, A., Tosatto, S.C.E., et al. Nucleic Acids Res. (2022)
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation. Vendruscolo M, Fuxreiter M. J Mol Biol. (2021)
The role of ordered cooperative assembly in biomolecular condensates. Korkmazhan E, Tompa P, Dunn AR. Nat Rev Mol Cell Biol. (2021)
“Protein” no longer means what it used to. Parisi G, Palopoli N, Tosatto SCE, Fornasari MS, Tompa P. Curr Res Struct Biol. (2021)
Functionalized Prion-Inspired Amyloids for Biosensor Applications. Díaz-Caballero M, Navarro S, Ventura S. Biomacromolecules. (2021)
Exploring Curated Conformational Ensembles of Intrinsically Disordered Proteins in the Protein Ensemble Database. Quaglia F, Lazar T, Hatos A, Tompa P, Piovesan D, Tosatto SCE. Curr Protoc. (2021)
SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins.” Pintado C, Santos J, Iglesias V, Ventura S. Bioinformatics. (2021)
Generic nature of the condensed states of proteins.” Fuxreiter M, Vendruscolo M. Nat Cell Biol. (2021)
α-Helical peptidic scaffolds to target α-synuclein toxic species with nanomolar affinity. Santos J, Gracia P, Navarro S, Peña-Díaz S, Pujols J, Cremades N, Pallarès I, Ventura S. Nat Commun. (2021)
Critical assessment of protein intrinsic disorder prediction. Necci M, Piovesan D; CAID Predictors; DisProt Curators, Tosatto SCE. Nat Methods. (2021)
AlphaFold and the amyloid landscape. Pinheiro F, Santos J, Ventura S. J Mol Biol. (2021)
FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. J Mol Biol. (2021)
Liquid-Liquid Phase Separation Enhances TDP-43 LCD Aggregation but Delays Seeded Aggregation. Pakravan D, Michiels E, Bratek-Skicki A, De Decker M, Van Lindt J, Alsteens D, Derclaye S, Van Damme P, Schymkowitz J, Rousseau F, Tompa P, Van Den Bosch L. Biomolecules. (2021)
“Spot in a drop: mutations in aberrant condensates.” Fuxreiter M. Nat Rev Mol Cell Biol. (2021)
Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers. Farahi N, Lazar T, Wodak SJ, Tompa P, Pancsa R. Int J Mol Sci. (2021)
“MobiDB: intrinsically disordered proteins in 2021.” Piovesan D, Necci M, Escobedo N, Monzon AM, Hatos A, Mičetić I, Quaglia F, Paladin L, Ramasamy P, Dosztányi Z, Vranken WF, Davey NE, Parisi G, Fuxreiter M, Tosatto SCE. Nucleic Acids Res. (2021)
A generic approach to study the kinetics of liquid-liquid phase separation under near-native conditions. Van Lindt J, Bratek-Skicki A, Nguyen PN, Pakravan D, Durán-Armenta LF, Tantos A, Pancsa R, Van Den Bosch L, Maes D, Tompa P. Commun Biol. (2021)
Widespread occurrence of the droplet state of proteins in the human proteome.” Hardenberg M, Horvath A, Ambrus V, Fuxreiter M, Vendruscolo M. Proc Natl Acad Sci U S A. (2020)
A guide to the regulation of the formation of biomolecular condensates. Bratek-Skicki A, Pancsa R, Meszaros B, Van Lindt J, Tompa P. FEBS J. (2020)
Small-molecule inhibition of aging-associated chromosomal instability delays cellular senescence.” Barroso-Vilares M, Macedo JC, Reis M, Warren JD, Compton D, Logarinho E. EMBO Rep. (2020)
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies. Marton Miskei, Csaba Antal and Monika Fuxreiter. Nucleic Acids Research. (2017)
ACKNOWLEDGEMENT – INFORMATION ON EU FUNDING
Please use the following statement to acknowledge the PhasAGE participation in collaborative publications:
“This [insert type of result] is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 952334.”