JAKOB RUPERT

Dottore di ricerca

ciclo: XXXV



Titolo della tesi: The Effect of RNA on Alpha Synuclein Aggregation

Protein aggregation is a widespread phenomenon, closely linked to protein folding and function. A tightly regulated process, it can lead to a wide variety of polymorphic protein assemblies with incredible thermodynamics stability and mechanical properties. Protein aggregates appear in functional roles in all trees of life, from performing catalytic reactions to regulating gene expression, in processes that are thought to go back to the prebiotic stage of life. Aggregation has also attracted significant attention over the last decades due to the involvement of aggregated proteins in debilitating neurodegenerative diseases. One of these proteins is alpha synuclein, shown to form insoluble aggregated assemblies in a plethora of pathological conditions such as Parkinson’s disease, Lewy-body dementia, multiple systems atrophy etc. Nucleic acids can act as potent modulators of protein aggregation, and RNA has the ability to either hinder or facilitate protein assembly and regulate protein phase transitions. The aim of the research, describe in the following dissertation, was to assess the potential modulating effect RNA has on the aggregation of aS, with the long-term ambition of developing RNA-based therapeutic and diagnostic agents. We have shown that RNA accelerates the amyloid assembly of aS with fluorescence-based aggregation assays and infrared spectroscopy by increasing the rate of aggregation and decreasing the aggregation lag time. We have also determined that RNA influences the structural characteristics of aS aggregates and alters their conformation and mechanical properties. Finally, we have determined that aS aggregated species both directly bind RNA, as well as sequester it during coaggregation in a protein-dependent manner. We have determined the higher affinity of aS fibrils for RNA compared to DNA by means of quantifying the nucleic acids extracted from aggregates after aggregation. We have also shown directly that RNA binds to the fibrils by inhibiting their enzymatic activity and we have determined the approximate binding affinity. In addition, we have computationally determined that aggregation leads to an increase in the aggregation propensity of proteins by partitioning of physicochemical properties in the inner and outer parts of the amyloid core. We have also shown that RNA- and DNA-binding domains tend to remain outside the amyloid core and can thus also contribute to specific RNA sequestration by canonic, aggregation-prone RBPs. Thus, we can conclude that RNA plays an important role and has a high potential as a modulator not only of aS aggregation, but of other aggregation-prone proteins in general.

Produzione scientifica

11573/1700809 - 2024 - Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides
Parisi, G.; Piacentini, R.; Incocciati, A.; Bonamore, A.; Macone, A.; Rupert, J.; Zacco, E.; Miotto, M.; Milanetti, E.; Tartaglia, G. G.; Ruocco, G.; Boffi, A.; Di Rienzo, L. - 01a Articolo in rivista
rivista: FRONTIERS IN MOLECULAR BIOSCIENCES (Lausanne : Frontiers Media S.A., 2014-) pp. - - issn: 2296-889X - wos: WOS:001144542200001 (1) - scopus: 2-s2.0-85182672420 (1)

11573/1707957 - 2023 - Single-photon microscopy to study biomolecular condensates
Perego, Eleonora; Zappone, Sabrina; Castagnetti, Francesco; Mariani, Davide; Vitiello, Erika; Rupert, Jakob; Zacco, Elsa; Tartaglia, Gian Gaetano; Bozzoni, Irene; Slenders, Eli; Vicidomini, Giuseppe - 01a Articolo in rivista
rivista: NATURE COMMUNICATIONS (London: Nature Publishing Group-Springer Nature) pp. - - issn: 2041-1723 - wos: (0) - scopus: (0)

11573/1691133 - 2023 - RNA sequestration driven by amyloid formation: the alpha synuclein case
Rupert, Jakob; Monti, Michele; Zacco, Elsa; Tartaglia, Gian Gaetano - 01a Articolo in rivista
rivista: NUCLEIC ACIDS RESEARCH (Oxford University Press:Journals Department, Great Clarendon Street, Oxford OX2 6DP United Kingdom:011 44 1865 556767, EMAIL: jnlorders@oup.co.uk, INTERNET: http://www.oup.co.uk, Fax: 011 44 1865 267485 Editore precedente: Information Retrieval ltd., London) pp. - - issn: 0305-1048 - wos: WOS:001087686200001 (0) - scopus: 2-s2.0-85176589076 (2)

11573/1615416 - 2022 - Experimental methods to study protein–nucleic acid interactions
Giambruno, Roberto; Rupert, Jakob; Zacco, Elsa - 02a Capitolo o Articolo
libro: Advances in Protein Molecular and Structural Biology Methods - (9780323902649)

11573/1615414 - 2022 - New lessons on TDP‐43 from old N. furzeri killifish
Louka, Alexandra; Bagnoli, Sara; Rupert, Jakob; Esapa, Benjamin; Tartaglia, Gian Gaetano; Cellerino, Alessandro; Pastore, Annalisa; Terzibasi Tozzini, Eva - 01a Articolo in rivista
rivista: AGING CELL (-MALDEN:WILEY-BLACKWELL PUBLISHING, INC. -Oxford : Blackwell, 2002-) pp. - - issn: 1474-9718 - wos: WOS:000733359600001 (4) - scopus: 2-s2.0-85121481761 (4)

11573/1615411 - 2021 - catRAPID omics v2.0: going deeper and wider in the prediction of protein–RNA interactions
Armaos, Alexandros; Colantoni, Alessio; Proietti, Gabriele; Rupert, Jakob; Tartaglia, Gian Gaetano - 01a Articolo in rivista
rivista: NUCLEIC ACIDS RESEARCH (Oxford University Press:Journals Department, Great Clarendon Street, Oxford OX2 6DP United Kingdom:011 44 1865 556767, EMAIL: jnlorders@oup.co.uk, INTERNET: http://www.oup.co.uk, Fax: 011 44 1865 267485 Editore precedente: Information Retrieval ltd., London) pp. W72-W79 - issn: 0305-1048 - wos: WOS:000672775800011 (64) - scopus: 2-s2.0-85110295736 (62)

11573/1450451 - 2020 - Zooming in on protein–RNA interactions: a multilevel workflow to identify interaction partners
Colantoni, A.; Rupert, J.; Vandelli, A.; Tartaglia, G. G.; Zacco, E. - 01d Recensione
rivista: BIOCHEMICAL SOCIETY TRANSACTIONS (Portland Press Limited:Commerce Way, Colchester CO2 8HP Essex United Kingdom:011 44 1206 796351, EMAIL: sales@portland-services.com, INTERNET: http://www.portland-services.com, Fax: 011 44 1206 799331) pp. 1529-1543 - issn: 0300-5127 - wos: WOS:000583062000017 (8) - scopus: 2-s2.0-85090173847 (9)

11573/1450092 - 2020 - Structural analysis of SARS-CoV-2 genome and predictions of the human interactome
Vandelli, Andrea; Monti, Michele; Milanetti, Edoardo; Armaos, Alexandros; Rupert, Jakob; Zacco, Elsa; Bechara, Elias; Delli Ponti, Riccardo; Tartaglia, Gian Gaetano - 01a Articolo in rivista
rivista: NUCLEIC ACIDS RESEARCH (Oxford University Press:Journals Department, Great Clarendon Street, Oxford OX2 6DP United Kingdom:011 44 1865 556767, EMAIL: jnlorders@oup.co.uk, INTERNET: http://www.oup.co.uk, Fax: 011 44 1865 267485 Editore precedente: Information Retrieval ltd., London) pp. - - issn: 0305-1048 - wos: WOS:000606018600011 (57) - scopus: 2-s2.0-85096360925 (61)

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