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

Deliverables

Documents, reports (2)

UBIMOTIF newsletter 2
UBIMOTIF newsletter 1

Websites, patent fillings, videos etc. (1)

Website, LinkedIn, twitter, facebook accounts for network

Other (1)

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Publications

Peer reviewed articles (13)

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

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