Short linear interaction motifs as specificity determinants in the ubiquitin system – discovery, mechanisms and therapeutic opportunities

Project Information

UBIMOTIF

Grant agreement ID: 860517

DOI

10.3030/860517

Project closed

EC signature date 9 August 2019

Start date 1 December 2019

End date 31 May 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 4 143 173,11

EU contribution

€ 4 143 173,11

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (6)

UBIMOTIF newsletter 3
UBIMOTIF newsletter 2
UBIMOTIF newsletter 4
UBIMOTIF newsletter 1
Open access publications from ESR projects
Joint publication form JC work

Joint publication form JC work3UCPHPDEPU48

Websites, patent fillings, videos etc. (1)

Website, LinkedIn, twitter, facebook accounts for network

Other (3)

Advertisement of positions
Presentation of results at meetings

Presentation of results at meetings3UCPHPDEPU42

Online open access SLiM resources

Publications

Peer reviewed articles (14)

On the Effects of Disordered Tails, Supertertiary Structure and Quinary Interactions on the Folding and Function of Protein Domains

Author(s): Francesca Malagrinò, Valeria Pennacchietti, Daniele Santorelli, Livia Pagano, Caterina Nardella, Awa Diop, Angelo Toto, Stefano Gianni
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12020209

Folding and Binding Mechanisms of the SH2 Domain from Crkl

Author(s): Caterina Nardella, Angelo Toto, Daniele Santorelli, Livia Pagano, Awa Diop, Valeria Pennacchietti, Paola Pietrangeli, Lucia Marcocci, Francesca Malagrinò, Stefano Gianni
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12081014

The human GID complex engages two independent modules for substrate recruitment

Author(s): Mohamed, Weaam I.; Park, Sophia L.; Rabl, Julius; id_orcid0000-0001-6375-852X; Leitner, Alexander; Boehringer, Daniel; Peter, Matthias; peter, matthias
Published in: EMBO Reports, 22 (11), Issue 1, 2021, ISSN 1469-221X
Publisher: Nature Publishing Group
DOI: 10.3929/ethz-b-000511960

Unveiling induced folding of intrinsically disordered proteins – Protein engineering, frustration and emerging themes

Author(s): Francesca Malagrinò, Awa Diop, Livia Pagano, Caterina Nardella, Angelo Toto, Stefano Gianni
Published in: Current Opinion in Structural Biology, 2022, ISSN 1879-033X
Publisher: Elsevier
DOI: 10.1016/j.sbi.2021.11.004

Who Binds Better? Let Alphafold2 Decide!

Author(s): Julia K. Varga, Ora Schueler-Furman
Published in: Angewandte Chemie, 2023, ISSN 1521-3773
Publisher: Wiley-VCH GmbH
DOI: 10.1002/anie.202303526

Exploring the effect of tethered domains on the folding of Grb2 protein

Author(s): Livia Pagano, Valeria Pennacchietti, Awa Diop, Daniele Santorelli, Paola Pietrangeli, Lucia Marcocci, Caterina Nardella, Francesca Malagrino, Angelo Toto, Stefano Gianni
Published in: Archives of Biochemistry and Biophysics, 2022, ISSN 0003-9861
Publisher: Academic Press
DOI: 10.1016/j.abb.2022.109444

xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures

Author(s): Hazem M. Kotb, Norman E. Davey
Published in: Biomolecules, 2023, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom13060906

Matching protein surface structural patches for high-resolution blind peptide docking

Author(s): Alisa Khramushin, Ziv Ben-Aharon, Tomer Tsaban, Julia K. Varga, Orly Avraham, Ora Schueler-Furman
Published in: PNAS, 2022, ISSN 1091-6490
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2121153119

Structure-Based Prediction of KDAC6 Substrates Validated by Enzymatic Assay Reveals Determinants of Promiscuity and Detects New Potential Substrates

Author(s): Julia Varga; Kelsey Diffley; Katherine R. Welker Leng; Carol A. Fierke; Ora Schueler-Furman
Published in: Scientific Reports, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-05681-2

SH2 Domains: Folding, Binding and Therapeutical Approaches

Author(s): Awa Diop, Daniele Santorelli, Francesca Malagrinò, Caterina Nardella, Valeria Pennacchietti, Livia Pagano, Lucia Marcocci, Paola Pietrangeli, Stefano Gianni, Angelo Toto
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms232415944

Harnessing protein folding neural networks for peptide–protein docking

Author(s): Tsaban, Tomer; Varga, Julia K.; Avraham, Orly; Ben-Aharon, Ziv; Khramushin, Alisa; Schueler-Furman, Ora
Published in: Nature Communications, Issue 1, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27838-9

Biophysical Characterization of the Binding Mechanism between the MATH Domain of SPOP and Its Physiological Partners

Author(s): Awa Diop, Paola Pietrangeli, Caterina Nardella, Valeria Pennacchietti, Livia Pagano, Angelo Toto, Mariana Di Felice, Sara Di Matteo, Lucia Marcocci, Francesca Malagrinò, Stefano Gianni
Published in: International Journal of Molecular Sciences, 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms241210138

Characterization of early and late transition states of the folding pathway of a SH2 domain

Author(s): Angelo Toto; Francesca Malagrinò; Caterina Nardella; Valeria Pennacchietti; Livia Pagano; Daniele Santorelli; Awa Diop; Stefano Gianni
Published in: Protein Science, 2022, ISSN 1469-896X
Publisher: Wiley
DOI: 10.1002/pro.4332

Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCFβ-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1

Author(s): Camilla S. Colding-Christensen, Ellen S. Kakulidis, Javier Arroyo-Gomez, Ivo A. Hendriks, Connor Arkinson, Zita Fábián, Agnieszka Gambus, Niels Mailand, Julien P. Duxin & Michael L. Nielsen
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-43873-0

Book chapters (1)

A Mass Spectrometry-Based Strategy for Mapping Modification Sites for the Ubiquitin-Like Modifier NEDD8

Author(s): Oliveira, C.A.B., Isaakova, E., Beli, P., Xirodimas, D.P.
Published in: The Ubiquitin Code. Methods in Molecular Biology, vol 2602., 2022, ISBN 978-1-0716-2859-1
Publisher: Humana
DOI: 10.1007/978-1-0716-2859-1_10