LORENZO VISCONTI

Dottore di ricerca

ciclo: XXXIII


relatore: Stefano Gianni
co-supervisore: Francesca Cutruzzolà

Titolo della tesi: Understanding the folding and binding mechanisms of SH2 domains

The interaction between proteins plays a paramount role in biological functions. Frequently, protein-protein interactions are mediated by specific classes of domains that can recognize a determined consensus sequence. To avoid the misregulation of cell physiology, different protein-protein interaction domains evolved to ensure specificity and proper affinity for their natural ligand(s). Since many signalling pathways are mediated by tyrosine phosphorylation, their regulation is controlled in many cases by specific domains able to recognize phosphorylated tyrosine, the so-called SH2 domains. Proteins that contain such domains can minimize cross-reactivity with non-desired targets thanks to the high specificity of the SH2. The understanding of many complex biological processes relies on our ability to describe the underlying fundamental processes. In this context, the study on the stability and functions of isolated domain plays a critical role in modern molecular biology and many signalling pathways have been successfully described by defining the interaction networks of individual domain. For this reason the aim of this thesis is focused on the description of the mechanisms by which proteins of the SH2 family recognize their specific partners in normal and pathological conditions. Furthermore, we addressed the effect of site directed mutagenesis on the folding and stability of this important class of protein domains. Through a combination of site-directed mutagenesis and biophysical techniques such as Stopped-flow kinetics, and NMR, we characterized the mechanism of folding and binding of different SH2 domains, highlighting some possible general characteristics for this class of proteins. In spite of their importance for cell physiology, there is a lack of information pertaining the details of the mechanism of binding of SH2 domains. Our results highlighted for the first time an allosteric mechanism of interaction for the SH2, which we speculate may represent a possible general mechanism of interaction for this class of proteins. Such allosteric mechanism is characterized by a remarkable structural plasticity, with the binding reaction being mediated by a diffused structural region and not solely by the residues located in the binding pocket. In addition through a biophysical approach named double mutant cycle, we defined potential allosteric sites in the SH2 domain from PI3K, which mediate and control the interaction with the partner. Future investigations will be used to explore more in details the allosteric nature of the binding process of other SH2 domains, with the final aim of defining allosteric sites, which could potentially be used as therapeutic targets. The extensive studied on SH2 domains allowed us to also define the molecular mechanism of a specific mutant of the N-terminal SH2 domain from the protein SHP2 (the T42A mutant), which has been demonstrated to be at the basis of the onset of the Noonan Syndrome. Analysing the binding properties of N-SH2 T42A we defined the molecular details that could explain the role of N-SH2 T42 in the disease and so we provided a possible explanation for the hyper-activation of SHP2 in the Noonan Syndrome.

Produzione scientifica

11573/1579282 - 2021 - Targeting PDZ domains as potential treatment for viral infections, neurodegeneration and cancer
Nardella, Caterina; Visconti, Lorenzo; Malagrinò, Francesca; Pagano, Livia; Bufano, Marianna; Nalli, Marianna; Coluccia, Antonio; La Regina, Giuseppe; Silvestri, Romano; Gianni, Stefano; Toto, Angelo - 01a Articolo in rivista
rivista: BIOLOGY DIRECT (London: BioMed Central) pp. - - issn: 1745-6150 - wos: WOS:000706722300001 (8) - scopus: 2-s2.0-85117321017 (13)

11573/1552783 - 2021 - Probing the effects of local frustration in the folding of a multidomain protein
Pagano, Livia; Malagrinò, Francesca; Visconti, Lorenzo; Troilo, Francesca; Pennacchietti, Valeria; Nardella, Caterina; Toto, Angelo; Gianni, Stefano - 01a Articolo in rivista
rivista: JOURNAL OF MOLECULAR BIOLOGY (-LONDON, ENGLAND: ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD, -London; New York: Academic Press.) pp. 167087- - issn: 0022-2836 - wos: WOS:000672680300017 (6) - scopus: 2-s2.0-85107967375 (6)

11573/1477086 - 2021 - Double mutant cycles as a tool to address folding, binding, and allostery
Pagano, Livia; Toto, Angelo; Malagrinò, Francesca; Visconti, Lorenzo; Jemth, Per; Gianni, Stefano - 01a Articolo in rivista
rivista: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (Basel: MDPI Center) pp. 828- - issn: 1422-0067 - wos: WOS:000611298300001 (9) - scopus: 2-s2.0-85099547793 (11)

11573/1495668 - 2021 - Folding and misfolding of a PDZ tandem repeat
Visconti, Lorenzo; Malagrinò, Francesca; Troilo, Francesca; Pagano, Livia; Toto, Angelo; Gianni, Stefano - 01a Articolo in rivista
rivista: JOURNAL OF MOLECULAR BIOLOGY (-LONDON, ENGLAND: ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD, -London; New York: Academic Press.) pp. 166862- - issn: 0022-2836 - wos: WOS:000630007900009 (7) - scopus: 2-s2.0-85100673226 (8)

11573/1435307 - 2020 - Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate
Gautier, Candice; Troilo, Francesca; Cordier, Florence; Malagrinò, Francesca; Toto, Angelo; Visconti, Lorenzo; Zhu, Yanlei; Brunori, Maurizio; Wolff, Nicolas; Gianni, Stefano - 01a Articolo in rivista
rivista: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (National Academy of Sciences:2101 Constitution Avenue Northwest:Washington, DC 20418:(877)314-2253, (615)377-3322, EMAIL: subspnas@nas.edu, INTERNET: http://www.pnas.org, Fax: (615)377-0525) pp. 19963-19969-19969 - issn: 0027-8424 - wos: WOS:000567818600007 (12) - scopus: 2-s2.0-85089787733 (14)

11573/1456152 - 2020 - Targeting the interaction between the SH3 domain of Grb2 and Gab2
Malagrinò, Francesca; Coluccia, Antonio; Bufano, Marianna; La Regina, Giuseppe; Puxeddu, Michela; Toto, Angelo; Visconti, Lorenzo; Paone, Alessio; Magnifico, Maria Chiara; Troilo, Francesca; Cutruzzolà, Francesca; Silvestri, Romano; Gianni, Stefano - 01a Articolo in rivista
rivista: CELLS (Basel: mdpi-Molecular Diversity Preservation International) pp. 2435- - issn: 2073-4409 - wos: WOS:000592940700001 (6) - scopus: 2-s2.0-85096028884 (6)

11573/1401198 - 2020 - Understanding the binding induced folding of intrinsically disordered proteins by protein engineering: caveats and pitfalls
Malagrinò, Francesca; Visconti, Lorenzo; Pagano, Livia; Toto, Angelo; Troilo, Francesca; Gianni, Stefano - 01a Articolo in rivista
rivista: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (Basel: MDPI Center) pp. 3484- - issn: 1422-0067 - wos: WOS:000539312100080 (11) - scopus: 2-s2.0-85084964055 (12)

11573/1359552 - 2020 - Unveiling the molecular basis of the noonan syndrome-causing mutation T42A of SHP2
Toto, A.; Malagrino, F.; Visconti, L.; Troilo, F.; Gianni, S. - 01a Articolo in rivista
rivista: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (Basel (Matthaeustrasse 11) : Molecular Diversity Preservation International MDPI) pp. 461- - issn: 1661-6596 - wos: WOS:000515380000091 (6) - scopus: 2-s2.0-85077880233 (8)

11573/1435303 - 2020 - Comparing the binding properties of peptides mimicking the envelope protein of sars-cov and sars-cov-2 to the pdz domain of the tight junction-associated pals1 protein
Toto, Angelo; Ma, Sana; Malagrinò, Francesca; Visconti, Lorenzo; Pagano, Livia; Stromgaard, Kristian; Gianni, Stefano - 01a Articolo in rivista
rivista: PROTEIN SCIENCE (Cambridge University Press / New York:40 West 20th Street:New York, NY 10011:(800)872-7423, (212)924-3900, EMAIL: journals_subscriptions@cup.org, INTERNET: http://www.journals.cambridge.org, Fax: (212)691-3239) pp. - - issn: 0961-8368 - wos: WOS:000566781500001 (34) - scopus: 2-s2.0-85090470025 (37)

11573/1401188 - 2020 - Templated folding of intrinsically disordered proteins
Toto, Angelo; Malagrinò, Francesca; Visconti, Lorenzo; Troilo, Francesca; Pagano, Livia; Brunori, Maurizio; Jemth, Per; Gianni, Stefano - 01a Articolo in rivista
rivista: THE JOURNAL OF BIOLOGICAL CHEMISTRY (American Society for Biochemistry and Molecular Biology:9650 Rockville Pike:Bethesda, MD 20814:(301)530-7145, EMAIL: asbmb@asbmb.faseb.org, INTERNET: http://www.faseb.org/asbmb, Fax: (301)571-1824) pp. 6586-6593 - issn: 0021-9258 - wos: WOS:000537685000027 (44) - scopus: 2-s2.0-85084721842 (43)

11573/1359561 - 2020 - The effect of proline cis‐trans isomerization on the folding of the C‐terminal SH2 domain from p85
Troilo, F.; Malagrino, F.; Visconti, L.; Toto, A.; Gianni, S. - 01a Articolo in rivista
rivista: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (Basel (Matthaeustrasse 11) : Molecular Diversity Preservation International MDPI) pp. 125- - issn: 1661-6596 - wos: WOS:000515378000125 (4) - scopus: 2-s2.0-85077263439 (5)

11573/1417653 - 2020 - Understanding the mechanism of recognition of gab2 by the n-sh2 domain of shp2
Visconti, Lorenzo; Malagrinò, Francesca; Pagano, Livia; Toto, Angelo - 01a Articolo in rivista
rivista: LIFE (Basel: MDPI) pp. 85- - issn: 2075-1729 - wos: WOS:000551223300004 (7) - scopus: 2-s2.0-85090739226 (7)

11573/1399303 - 2020 - Demonstration of binding induced structural plasticity in a sh2 domain
Visconti, Lorenzo; Toto, Angelo; Jarvis, James A.; Troilo, Francesca; Malagrinò, Francesca; De Simone, Alfonso; Gianni, Stefano - 01a Articolo in rivista
rivista: FRONTIERS IN MOLECULAR BIOSCIENCES (Lausanne : Frontiers Media S.A., 2014-) pp. - - issn: 2296-889X - wos: WOS:000537268200001 (5) - scopus: (0)

11573/1336088 - 2019 - Binding induced folding: Lessons from the kinetics of interaction between NTAIL and XD
Toto, A.; Troilo, F.; Visconti, L.; Malagrinò, F.; Bignon, C.; Longhi, Sonia Rachele Agata; Gianni, S.; S, - 01a Articolo in rivista
rivista: ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (Attuale:ELSEVIER SCIENCE INC, 360 PARK AVE SOUTH, NEW YORK, USA, NY, 10010-1710 Academic Press Incorporated:6277 Sea Harbor Drive:Orlando, FL 32887:(800)543-9534, (407)345-4100, EMAIL: ap@acad.com, INTERNET: http://www.idealibrary.com, Fax: (407)352-3445) pp. 255-261 - issn: 0003-9861 - wos: WOS:000525438900029 (6) - scopus: 2-s2.0-85069557296 (6)

11573/1336085 - 2019 - Structural characterization of an on-pathway intermediate and transition state in the folding of the N-terminal SH2 domain from SHP2
Visconti, L.; Malagrinò, F.; Gianni, S.; Toto, A. - 01a Articolo in rivista
rivista: THE FEBS JOURNAL (Blackwell Pub., Oxford, UK) pp. 4769-4777 - issn: 1742-4658 - wos: WOS:000499718600012 (7) - scopus: 2-s2.0-85069838702 (8)

11573/1218458 - 2019 - Investigating the molecular basis of the aggregation propensity of the pathological d76n mutant of beta-2 microglobulin: role of the denatured state
Visconti, L; Malagrinò, F; Broggini, L; De Luca, Cmg; Moda, F; Gianni, S; Ricagno, S; Toto, A. - 01a Articolo in rivista
rivista: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (Basel (Matthaeustrasse 11) : Molecular Diversity Preservation International MDPI) pp. - - issn: 1661-6596 - wos: WOS:000459746500164 (5) - scopus: 2-s2.0-85060402058 (5)

11573/1253355 - 2019 - The kinetics of folding of the NSH2 domain from p85
Visconti, Lorenzo; Malagrinò, Francesca; Toto, Angelo; Gianni, Stefano - 01a Articolo in rivista
rivista: SCIENTIFIC REPORTS (London: Springer Nature London: Nature Publishing Group) pp. 4058- - issn: 2045-2322 - wos: WOS:000460751700013 (9) - scopus: 2-s2.0-85062766339 (9)

11573/1014992 - 2017 - Addressing the role of the α-helical extension in the folding of the third PDZ domain from PSD-95
Gautier, Candice Natacha Anna; Visconti, Lorenzo; Per, Jemth; Gianni, Stefano - 01a Articolo in rivista
rivista: SCIENTIFIC REPORTS (London: Springer Nature London: Nature Publishing Group) pp. - - issn: 2045-2322 - wos: WOS:000412138800029 (10) - scopus: 2-s2.0-85030565452 (10)

11573/956496 - 2017 - The folding pathway of the KIX domain
Troilo, Francesca; Bonetti, Daniela; Toto, Angelo; Visconti, L; Brunori, Maurizio; Longhi, S; Gianni, Stefano - 01a Articolo in rivista
rivista: ACS CHEMICAL BIOLOGY (Washington, D.C. : American Chemical Society, c2006-) pp. 1683-1690 - issn: 1554-8937 - wos: WOS:000403854000030 (6) - scopus: 2-s2.0-85020525210 (6)

11573/866165 - 2016 - Identification and structural characterization of an intermediate in the folding of the measles virus x domain
Bonetti, Daniela; Camilloni, Carlo; Visconti, Lorenzo; Longhi, Sonia; Brunori, Maurizio; Vendruscolo, Michele; Gianni, Stefano - 01a Articolo in rivista
rivista: THE JOURNAL OF BIOLOGICAL CHEMISTRY (American Society for Biochemistry and Molecular Biology:9650 Rockville Pike:Bethesda, MD 20814:(301)530-7145, EMAIL: asbmb@asbmb.faseb.org, INTERNET: http://www.faseb.org/asbmb, Fax: (301)571-1824) pp. 10886-10892 - issn: 0021-9258 - wos: WOS:000377042600038 (18) - scopus: 2-s2.0-84969179536 (18)

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