Dottorato in BIOCHIMICA

email: stefano.gianni@uniroma1.it
telefono: 067886799

Stefano GIANNI
Curriculum Vitae

Parte I – Informazioni Generali

Nome Cognome Stefano GIANNI
Data di nascita 27 Gennaio 1976
Luogo di nascita Rome
Cittadinanza Italiana
Indirizzo Via Tommaso da Celano 94, 00179, Roma, Italia
Telefono 338-8964614
E-mail stefano.gianni@uniroma1.it
Lingue Italian (madre lingua), English (fluente)
ORCID 0000-0003-1653-1925

Parte II – Titoli di Studio


Laurea Dic 1999 Sapienza Università di Roma Laurea in Biologia
PhD Marzo 2003 Sapienza Università di Roma PhD in Biochimica
Pre-doctorate training Ott 2001 – Mazo 2003 Medical Research Council – Centre for Protein Engineering, Cambridge (UK) Visiting Scientist
Post-doctorate training Mar 2003 – Genn 2004 Medical Research Council – Centre for Protein Engineering, Cambridge (UK) Visiting Scientist
Post-doctorate training Mar 2004 – Mag 2005 Sapienza University of Rome Assegnista di Ricerca
Post-doctorate training Giu 2005 – Dic 2005 Sapienza Università di Roma Borsista Istituto Pasteur –Fondazione Cenci Bolognetti (borse di studio per l’Italia per il rientro dall’estero)


Parte III – Incarichi

IIIA – Incarichi Accademici


Dic 2005 Dic 2012 CNR – Consiglio Nazionale delle Ricerche – Istituto di Biologia e Patologia Molecolari, Roma, Italia Ricercatore
Dic 2012 Ott 2016 Sapienza Università di Roma Professore Associato
Maggio 2013 Lug 2016 University of Cambridge, Dept. of Chemistry, Cambridge (UK) Visiting Professor
Nov 2016 oggi Sapienza Università di Roma Professore Ordinario


IIIB – Altro Incarichi


Lug 2013 oggi Sapienza Università di Roma – Facoltà di Farmacia e Medicina – Corso di Laurea in Scienze Farmaceutiche Applicate Commissione Pratiche studenti
2015 date Sapienza Università di Roma – Facoltà di Farmacia e Medicina – Corsi di Laurea in: Scienze Farmaceutiche Applicate; Inform. scientifica sul farmaco; Scienze e Tecn. dei Prod. Erbor. Referente Incaricato per le procedure part-time
2014 oggi Sapienza Università di Roma – Facoltà di Farmacia e Medicina – Corsi di Laurea in: Medicina e Chirurgia; Scienze Farmaceutiche Applicate Presidente d’Aula Commissioni test di Ingresso
2013 oggi Sapienza Università di Roma – Facoltà di Farmacia e Medicina PhD Course of Biochemistry, Membro del Collegio dei Docenti
2013 oggi MIUR Membro dell' Albo Revisori Progetti
2015 oggi European Union COST Action BM1405 – Non globular proteins – MC Member
2016 oggi ANVUR Evaluator VQR 2011-2014
2016 oggi European Union Member of the Evaluator Panels of FET-OPEN - NOVEL IDEAS FOR RADICALLY NEW TECHNOLOGIES







Part IV – Attività didattica



2004-2010 Sapienza, Università di Roma Modulo “Struttura della Cellula e Meccanismi di duplicazione Cellulare”, Professioni Sanitarie in Tecniche Audioprotesiche;
2004-2010 Sapienza, Università di Roma Modulo “Struttura della Cellula e Meccanismi di duplicazione Cellulare”, Professioni Sanitarie in Tecniche Audiometristiche
2004-2012 Sapienza, Università di Roma Member of the commission for the exam of “Chimica e Propedeutica Biochimica” in the course of “Medicina e Chirurgia”
2013-2015 Sapienza, Università di Roma Corso di Laurea in Medicina e Chirurgia – CLMMC “E” - Corso di “Chimica e Prop. Biochimica”
2013-oggi Sapienza, Università di Romae Corso di Laurea in Scienze Farmaceutiche Applicate – Corso di “Biotecnologie Modecolari”
2015-oggi Sapienza, Università di Roma Corso di Laurea in Tecnico di Laboratorio Biomedico (Sede di Pozzilli –NEUROMED) – Corso di Basi Fisiche e Chimiche – Titolare del Corso in Chimica e Prop. Biochimica e Co-ordinatore di corso Integrato
2015-oggi Sapienza, Università di Roma Corso di Laurea in Tecniche di Radiologia Medica per Immagini e Radioterapia (Sede di Pozzilli –NEUROMED) – Corso di Basi Fisiche e Chimiche – Titolare del Corso in Chimica e Prop. Biochimica
2013 -oggi Sapienza, Università di Roma Relatore di tesi di Laurea per tesi di Laurea in Fisica, Chimica e Scienze Farmacuetiche Applicate.
2013 - oggi Sapienza, Università di Roma Docente Guida presso il Dottorato di Ricerca in Biochimica di PhD students.

2017-oggi Coordinatore del Dottorato di Ricerca in Scienze Biochimiche, Sapienza, Università di Roma













Part V - - Membro di Società, Editorial Board, Premi


2009 Accademia Nazionale delle Scienze, detta dei XL, e Accademia Nazionale dei Lincei. “Vincenzo Caglioti" International Prize for Chemistry
2010 Young Researcher Prize, CNR Department of Life Sciences (awarded by the Director and including a grant of 5.000 Euro for research)
2008-2014 Membro of the Italian Society of Biochemistry and Molecular Biology (SIB)
2005-oggi Membro dell'Editorial Board di Protein Engineering Design & Selection (Oxford Journals)
2008-2015 Membro dell'Editorial Board di Research Letters in Biochemistry (Hindawi)
2014-oggi Membro dell'Editorial Board di Scientific Reports (Nature Publishing Group)
2015-oggi Membro dell'Editorial Board di Biophysical Chemistry (Elsevier)
2017-oggi Membro dell'Editorial Board di Protein and Peptide Letter (Bentham Science)
2017-oggi Membro dell'Editorial Board di International Journal of Molecular Sciences (MDPI)
2020 Accademia Nazionale delle Scienze, detta dei X, Medaglia "Emilia Chiancone" per la Biologia Molecolare
2020 Accademia Nazionale dei Lincei, Premio Tartufari per la Biologia

Part VI - Funding Information [grants as PI-principal investigator or I-investigator]


2011 -2013 The dark side of protein folding: denatured states and misfolded species in molecular recognition and pathological processes. Istituto Pasteur Fondazione Cenci Bolognetti – Investigator 60k Euro
2013 No structure but function: the new paradigm of modern biophysics (C26A13T9NB) Sapienza Progetti di Ricerca di Università - Principal Investigator
12k Euro
2014 - 2016 PDZ Domains and Cancer Istituto Pasteur Fondazione Cenci Bolognetti – Progetti di Ricerca Under 40 – Principal Investigator 90k Euro
2015 - 2018 Meccanismi molecolari del folding di proteine intrinsecamente disordinate
Università Italo Francese – Bando Vinci – Principal Investigator 60k Euro
2015 - 2018 Unveiling the role protein disorder in molecular interaction and signaling (C26A155S48)
Sapienza Progetti di Ricerca di Università - Principal Investigator
31k Euro
2016 - 2019 PDZnet (EU proposal 675341) European Union – Marie Curie International Training Network – Beneficiary Investigator 250k Euro
2017 - 2020 AIRC My First AIRC Grant - Principal Investigator - 205k Euro
2020 - 2024 UBIMOTIF (EU proposal 860517) European Union – Marie Curie International Training Network – Beneficiary Investigator 250k Euro
2021 - 2025 AIRC Investigator Grant - Principal Investigator - 400k Euro
2023 - 2027 IDPro (EU proposal 10119633) European Union – Marie Curie International Training Network – Beneficiary Investigator 250k Euro

Part VII – Pubblicazioni e comunicazioni

Pubblicazioni internazionali 153

Hirsch (H) index 38


Invited Talks e seminari:

Il Prof. Gianni ha comunicato oltre 30 seminari in conferenze nazionali ed internazionali (Comprese una FEBS annual meeting e due Protein Society annual meetings)
Membro dell' Organizing Committee of the International Conference
Protein Structure and Dynamics, 1-3 Dec 2010, Acc. Naz. Dei Lincei, Rome Italy
Membro dello Scientific Committee of the International Conference
Proteine, 31 Mar-1 Apr 2014, Padua, Italy.

PUBBLICAZIONI

1) Gianni, S., Travaglini-Allocatelli, C., Cutruzzolà, F., Bigotti, M.G. & Brunori, M. (2001). Snapshots of protein folding. A study on the multiple transition state pathway of cytochrome c551 from Pseudomonas aeruginosa. J. Mol. Biol., 309, 1177-87.

2) Gianni, S., Brunori, M. & Travaglini-Allocatelli, C. (2001). Refolding kinetics of cytochrome c551 reveals mechanistic defference between urea and guanidine. Protein Science, 10, 1685-1688

3) Arcovito, A., Gianni, S., Brunori, M., Travaglini-Allocatelli, C. & Bellelli, A. (2001). Fast coordination changes in cytochrome c do not necessarily imply folding. J. Biol. Chem. 276, 41073-41078.

4) Brunori, M., Bigotti, M.G., Cutruzzolà, F., Gianni, S. & Travaglini-Allocatelli, C. (2003) Cytochrome c551 as a model system for protein folding. Biophys. Chem. 100, 409-419.

5) Gianni, S., Travaglini-Allocatelli, C., Cutruzzolà, F., Brunori, M., Ramachandra Shastry, M.C. & Roder, H. (2003) Parallel pathways in cytochrome c551 folding. J. Mol. Biol. 330, 1145-1152 .

6) Travaglini-Allocatelli, C., Gianni, S., Morea, V., Tramontano, A., Soulimane, T. & Brunori, M. (2003) Exploring the cytochrome c folding mechanisms: cyt c552 from Thermus thermophilus folds through an on-pathway intermediate. J. Biol. Chem., 278, 41136-41140 .

7) Gianni, S., Guydosh, N.R., Khan, F., Caldas, T.D., Mayor, U., White, G.W.N., DeMarco, M.L., Daggett, V. & Fersht A.R. (2003) Unifying features in protein folding mechanisms. Proc. Natl. Acad. Sci USA, 100, 13286-13291.

8) Khan, F., Chuang, J.I., Gianni, S. and Fersht, A.R. (2003)The kinetic pathway of folding of barnase. J. Mol. Biol., 333, 169-186.

9) Gianni, S., Mayor, U. and Fersht, A.R. (2003) Structural insights in the folding of single domain proteins. Ital. J. Biochem., 52, 157-161.

10) Jemth, P.*, Gianni S.*, Day, R., Li, B., Johnson, C.M., Daggett, V. and Fersht, A.R. (2004) Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proc. Natl. Acad. Sci USA, 101, 6450-6455.

11) Travaglini-Allocatelli, C., Gianni, S. and Brunori, M. (2004) A common folding mechanism in the cytochrome c family. Trends Bioch. Sci., 29, 535-541.

12) White, G.W.N.*, Gianni, S.*, Grossman, J.G., Jemth, P., Fersht, A.R., and Daggett, V. (2005) Simulation and Experiment Conspire to reveal Cryptic Intermediates and the Slide from Framework to Nucleation-Condensation Mechanism in the Folding of the Homeodomain Superfamily. J. Mol. Biol., 350, 757-775.

13) Jemth, P., Day, R., Gianni, S., Khan, F., Allen, M. D., Daggett, V., and Fersht, A. R. (2005) The structure of the major transition state for folding of an FF domain from experiment and simulation. J. Mol. Biol., 350, 363-378

14) Travaglini-Allocatelli, C.*, Gianni, S.*, Dubey, V.K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzolà, F., Bren, K.L. and Brunori, M. (2005) An obligatory intermediate in the folding of cytochrome c552 from Hydrogenobacter thermophilus. J. Biol. Chem., 280, 25729-25734

15) Gianni S., Calosci, N., Aelen, J., Vuister, G.W., Brunori, M. and Travaglini-Allocatelli C. (2005) Kinetic folding mechanism of PDZ2 from PTP-BL, Protein Eng. Des. Sel., 18, 389-395.

16) Gianni, S., Engström, A., Larsson, M., Calosci, N., Malatesta, F., Eklund, L., Ngang, C.C., Travaglini-Allocatelli, C., and Jemth P., (2005) The Kinetics Of Pdz Domain – Ligand Interactions And Implications For The Binding Mechanism, J. Biol. Chem., 280, 34805-34812.

17) Chi, C.N, Engstrom, Å, Gianni, S., Larsson, M. and Jemth, P. (2006) Two conserved residues govern the salt and pH dependencies of the binding reaction of a PDZ domain. J.Biol. Chem., 281, 36811-36888.

18) Gianni, S., Walma, T., Arcovito, A., Calosci, N., Bellelli, A., Engstrom, Å, Travaglini-Allocatelli, C., Brunori, M., Jemth, P. and Vuister, G.W. (2006) Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering. Structure, 14, 1801-1809.

19) Gianni, S., Geeierhaas, C.D., Calosci, N., Jemth, P., Vuister, G.W., Travaglini-Allocatelli, C., Vendruscolo, M. and Brunori M. (2007) A PDZ domain recapitulates a unifying mechanism for protein folding. Proc. Natl. Acad. Sci USA, 104, 128-133.

20) Federici, L., Masulli, M., Bonivento, D., Di Matteo, A., Gianni, S., Favaloro, B., Di Ilio, C. and Allocati, N., (2007) Role of Ser11 in the stabilization of the structure of Ochrobactrum anthropi glutathione transferase. Biochem J. 2007 403, 267-274

21) Ivarsson, Y., Travaglini-Allocatelli, C., Jemth, P., Malatesta, F., Brunori, M. and Gianni, S.† (2007) An on-pathway intermediate in the folding of a PDZ domain.
J Biol Chem. 282, 8568-8572

22) Chi, C.N*, Gianni, S.*†, Calosci, N., Travaglini-Allocatelli, C. Engstrom, Å, and Jemth, P. (2007) A conserved folding mechanism for PDZ domains. FEBS Letters 2007 581, 1109-1113.

23) Gianni, S.†, Ivarsson, Y., Jemth, P., Brunori, M., Travaglini-Allocatelli, C. (2007) Identification and characterization of protein folding intermediates. Biophys. Chem 128, 105-113.

24) Gianni, S., Brunori, M., Travaglini-Allocatelli, C., (2007) Plasticity of the protein folding landscape: switching between on and off-pathway intermediates Arch. Biochem. Biophys. 466 172-176.

25) Di Matteo, A., Gianni, S., Schininà, M.E., Giorgi, A., Altieri, F., Calosci, N., Brunori, M., Travaglini-Allocatelli, C. (2007) A strategic protein in cytochrome c maturation: 3D structure of CcmH and binding to apocytochrome c. J. Biol. Chem. 282, 27012-27019.

26) Jemth, P., Gianni, S.† (2007) PDZ domains: folding and binding. Biochemistry 46, 8701-8708

27) Gianni, S.†, Ivarsson, Y., Bah, A., Bush-Pelic, L.A., Di Cera, E. (2007) Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics. Biophys. Chem. 131, 111-114.

28) Ivarsson, Y., Travaglini-Allocatelli, C., Morea, V., Brunori, M., Gianni, S.† (2008) The folding pathway of an engineered circularly permuted PDZ domain. Protein Eng. Des. Sel 21 155-160.

29) Ivarsson, Y., Travaglini-Allocatelli, C., Brunori, M., Gianni, S.† (2008) Mechanisms of proten folding. Eur. Biophys. J. 37, 721-728

30) Jemth, P., Johnson, C.M., Gianni, S., Fersht, A.R. (2008) Demonstration by burst phase analysis of a robust folding intermediate in the FF domain Protein Eng. Des. Sel. 21, 207-214.

31) Ivarsson, Y, Travaglini-Allocatelli, C., Brunori, M., Gianni, S.†, (2008) Folding and Misfolding in a naturally circularly permuted PDZ domain. J. Biol. Chem. 283, 8954-8960.

32) Borgia, A., Gianni, S., Brunori, M., Travaglini-Allocatelli, C., (2008) Fast folding kinetics and stabilization of apo-cytochrome c FEBS Letters .582 1003-1007.

33) Parrini, C., Bemporad, F., Baroncelli, A., Gianni, S., Travaglini-Allocatelli, C., Kohn, J.E., Ramazzotti, M., Chiti, F., Taddei, N., (2008) The folding process of acylphosphatase from Escherichia coli is remarkably accelerated by the presence of a disulfide bond. J. Mol. Biol. 379, 1107-1118.

34) Calosci, N., Chi, C.N., Richter, B., Camilloni, C., Engstrom, A, Eklund, L, Travaglini-Allocatelli, C., Gianni, S.†, Vendruscolo, M.†, Jemth, P.†, (2008) Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins Proc. Natl. Acad. Sci. USA, 105, 19241-19246.

35) Sicorello, A., Torrassa, S., Soldi, G., Gianni, S., Travaglini-Allocatelli, C., Taddei, N., Relini, A., Chiti, F., (2009) Agitation and high ionic strength induce amyloidogenesis of a folded PDZ domain in native conditions Biophys. J 96, 2289-2298.

36) Travaglini-Allocatelli, C., Ivarsson, Y., Jemth, P., and Gianni, S.,† (2009) Folding and stability of globular proteins and implications for function. Curr. Opin. Struct. Biol. 19, 3-7.

37) Scaloni, F., Gianni, S., Federici, L., Falini, B., Brunori, M. (2009) Folding mechanism of the C-terminal domain of nucleophosmin: residual structure in the denatured state and its pathophysiological significance. FASEB J. 23, 2360-2365.

38) Federici, L., Masulli, M., Gianni, S., Di Ilio, C., Allocati, N. (2009) A conserved hydrogen-bond network stabilizes the structure of Beta class glutathione S-transferases. Biochem Biophys Res Commun. 382: 525-529.

39) Ivarsson, Y., Travaglini-Allocatelli, C., Brunori, M., Gianni, S., (2009) Engineered symmetric connectivity highlights malleability in protein folding pathways J. Am. Chem. Soc. 131, 11727-11733.

40) Chi, C.N., Bach, A., Engström, A., Wang, H., Strømgaard, K., Gianni, S.†, Jemth, P. † (2009) A sequential binding mechanism in a PDZ domain. Biochemistry. 48, 7089-7097.

41) Savino, C., Montemiglio, L.C., Sciara, G., Miele, A.E., Kendrew, S.G., Jemth, P., Gianni, S.†, Vallone, B., (2009) Investigating the structural plasticity of a cytochrome P450: three-dimensional structures of P450 EryK and binding to its physiological substrate. J. Biol. Chem. 284, 29170-29179.

42) Gianni, S., Brunori, M., Jemth, P., Oliveberg, M., Zhang, M., (2009) Distinguishing between smooth and rough free energy barriers in protein folding. Biochemistry 48, 11825-11830.

43) Giansanti, F., Di Leandro, L., Koutris, I., Pitari, G., Fabbrini, M.S., Lombardi, A., Flavell, D.J., Flavell, S.U., Gianni, S. †, Ippoliti, R. (2010) Engineering a switchable toxin: the potential use of PDZ domains in the expression, targeting and activation of modified saporin variants. Protein Eng. Des, Sel. 23. 61-68.

44) Scaloni, F., Federici, L., Brunori, M., Gianni, S., (2010) Deciphering the folding transition state structure and denatured state properties of nucleophosmin C-terminal domain. Proc. Natl. Acad. Sci, USA 107, 5447-5452.

45) Haq, S.R., Jurgens, M.C., Chi, C.N., Koh, C.S., Elfstrom, L., Selmer, M., Gianni, S†, Jemth, P (2010) The plastic energy landscape of protein folding: a triangular folding mechanism with an equilibrium intermediate for a small protein domain. J Biol Chem. 285, 18051-18059

46) Di Matteo, A., Calosci, N., Gianni ,S., Jemth, P., Brunori, M., Travaglini-Allocatelli, C. (2010) Structural and functional characterization of CcmG from Pseudomonas aeruginosa, a key component of the bacterial cytochrome c maturation apparatus. Proteins. Struct. Funct. Bioinf. 78, 2213-21.

47) Montemiglio, L.C., Gianni, S., Vallone, B., Savino, C. (2010) Azole drugs trap cytochrome P450 EryK in alternative conformational states. Biochemistry 49, 9199-9206.

48) Gianni, S., Ivarsson, Y., De Simone, A., Travaglini-Allocatelli, C., Brunori, M., Vendruscolo M., (2010) Characterization of the Structure of a Misfolded Intermediate Populated during the Folding Process of a PDZ domain Nature Struct. Mol Biol. 17, 1431-1437.

49) Morrone, A., McCully, M.E., Bryan, P.N., Brunori, M., Daggett, V., Gianni, S.†, Travaglini-Allocatelli, C., (2011) The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function. J. Biol., Chem. . 286, 3863-3872.

50) Gianni, S., Haq, S.R., Montemiglio, L.C., Jürgens, M.C., Engström, Å., Chi, C.N., Brunori, M., Jemth, P. (2011) Sequence-specific long range networks in PSD-95/discs large/ZO-1 (PDZ) domains tune their binding selectivity. J. Biol. Chem. 286, 27167-27175.

51) Morrone, A., Giri, R., Toofanny, R.D., Travaglini-Allocatelli, C., Brunori, M., Daggett, V., Gianni, S.†, (2011) GB1 is not a two-state folder: identification and characterization of an on-pathway intermadiate. Biophys. J 101, 2053-2060.

52) Giardina, G., Montioli, R., Gianni, S., Cellini, B., Paiardini, A., Borri-Voltattorni, C., Cutruzzolà, F., (2011) The open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases. Proc. Natl. Acad. Sci. USA 108, 20514-20519.

53) Haq SR, Chi CN, Bach A, Dogan J, Engström A, Hultqvist G, Karlsson A, Lundström P, Montemiglio LC, Strømgaard K, Gianni S, Jemth P. (2011) Side chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains. J. Am. Chem. Soc. 134, 599-605


54) Brunori, M., Gianni, S., Giri, R., Morrone, A., Travaglini-Allocatelli, C., (2012) Morphogenesis of a protein: folding pathways and the energy landscape Bioch. Soc. Trans 40(2):429-32.

55) Hultqvist G, Pedersen SW, Chi CN, Strømgaard K, Gianni S, Jemth P. (2012) An expanded view of the protein folding landscape of PDZ domains. Biochem Biophys Res Commun. 421, 550-553.

56) Chi, C.N., Bach, A., Stromgaard, K., Gianni, S., Jemth, P., (2012) Ligand binding by PDZ domains. Biofactors, 38, 338-348.

57) Giri., R., Morrone, A., Travaglini-Allocatelli C., Jemth, P., Brunori, M., Gianni, S.†, (2012) The folding pathways of proteins with increasing degree of sequence identities but different structure and function. Proc. Natl. Acad. Sci. USA. 109, 17772-17776.

58) Morrone, A., Giri, R., Brunori, M., Gianni S. †, (2012) Reassessing the folding of the KIX domain: Evidence for a two-state mechanism Protein Sci. 21, 1775-1779.

59) Gianni, S. †, Morrone, A., Giri, R., Brunori, M. (2012) A folding-after-binding mechanism describes the recognition between the transactivation domain of c-Myb and the KIX domain of the CREB-binding protein. Biochem Biophys Res Commun. 428, 205-209

60) Chi CN, Haq SR, Rinaldo S, Dogan J, Cutruzzolà F, Engström A, Gianni S, Lundström P, Jemth P. (2012) Interactions outside the Boundaries of the Canonical Binding Groove of a PDZ Domain Influence Ligand Binding. Biochemistry. 51, 8971-8979

61) Polticelli, F., Caprari, S., Gianni, S., Ascenzi, P., (2012) GA/GB Fold switching may modulate fatty acid transfer from human serum albumin to bacteria. IUBMB Life 64, 885-888.

62) Hultqvist, G., Punekar, A., Morrone, A., Chi, C.N., Engstrom, A, Selmer, M, Gianni, S. †, Jemth, P., (2012) Tolerance of protein folding to a circular permutation in a PDZ domain, PLOS ONE, 7, e50055

63) Chiarella, S., Federici, L., Di Matteo, A., Brunori, M., Gianni, S. †, (2013) The folding pathway of a functionally competent C-terminal domain of nucleophosmin: protein stability and denatured state residual structure. Biochem Biophys Res Commun. 435, 64-68.

64) Ascenzi, P., and Gianni S. †, (2013) On the functional role of reaction intermediates: rediscovering "chronosteric effects" thirty years later. IUBMB Life, 65, 836-844

65) Eildal JN, Hultqvist G, Balle T, Stuhr-Hansen N, Padrah S, Gianni S, Strømgaard K, Jemth P. (2013) Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations J. Am. Chem. Soc. 135, 12998-13007

66) Hultqvist G, Haq SR, Punekar AS, Chi CN, Engström Å, Bach A, Strømgaard K, Selmer M, Gianni, S. †, Jemth P. (2013) Energetic pathway sampling in a protein interaction domain. Structure. 21, 1193-1202.

67) Giri R, Morrone A, Toto A, Brunori M, Gianni, S. † (2013) Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system. Proc Natl Acad Sci U S A. 110, 149422-149427

68) Dogan, J., Gianni, S. †, Jemth, P. (2014) The binding mechanisms of intrinsically disordered proteins Phys. Chem. Chem. Phys. 16, 6323-6331

69) Bonetti D, Toto A, Giri R, Morrone A, Sanfelice D, Pastore A, Temussi P, Gianni, S. †, Brunori M. (2014) The kinetics of folding of frataxin. Phys Chem Chem Phys. 16, 6391-6397.

70) Gianni, S. †, Dogan J, Jemth P. (2014) Distinguishing induced fit from conformational selection. Biophys. Chem. 189, 33-39.

71) Toto A, Giri R, Brunori M, Gianni, S. † (2014) The mechanism of binding of the KIX domain to the mixed lineage leukemia protein and its allosteric role in the recognition of c-Myb. Protein Sci. 23, 962-969.

72) Di Silvio, E., Bonetti, D., Toto, A., Morrone, A., Gianni, S. † (2014) The mechanism of binding of the second PDZ domain from the Protein Tyrosine Phosphatase-BL to the Adenomatous Polyposis Coli tumor suppressor. Protein Eng. Des. Sel. 27, 249-253

73) Gianni, S. † Jemth, P., (2014) Conserved nucleation sites reinforce the significance of Phi value analysis in protein-folding studies. IUBMB Life 66, 449-452

74) Conti, S., Li, X., Gianni, S., Ghadami, S. A., Buxbaum, J., Cecchi, C., Chiti, F., Bemporad, F., (2014) A complex equilibrium among partially unfolded conformations in monomeric transthyretin. Biochemistry 53, 4381-4392

75) Gianni, S. †, Camilloni, C., Giri, R., Toto, A., Bonetti, D., Morrone, A., Sormanni, P, Brunori, M., Vendruscolo, M. (2014) Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein. Proc. Natl. Acad. Sci. USA 111, 14141-14146

76) Dosnon, M., Bonetti, D., Morrone, A., Erales, J., Di Silvio, E., Longhi, S., Gianni, S. † (2015) Demonstration of a Folding after Binding Mechanism in the Recognition between the Measles Virus NTAIL and X Domains. ACS Chem Biol 10, 795-802.

77) Di Silvio, E., Toto, A., Bonetti, D., Morrone, A., Gianni, S. † (2015) Understanding the effect of alternative splicing in the folding and function of the second PDZ from protein tyrosine phosphatase-BL. Sci Rep. 5: 9299.

78) Di Silvio, E., Brunori, M., Gianni, S. † (2015) Frustration Scuplts the early stages of protein folding Angew Chem Int Ed Engl 54, 10867-10869.

79) Gruet A, Dosnon M, Blocquel D, Brunel J, Gerlier D, Das RK, Bonetti D, Gianni, S., Fuxreiter M, Longhi S, Bignon C. (2016) Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions. FEBS J.

80) Gianni, S., Dogan, J., Jemth, P. (2016) Coupled binding and folding of intrinsically disordered proteins: what can we learn from kinetics? Curr. Opin. Struct. Biol. 38, 18-24.

81) Toto A, Camilloni C, Giri R, Brunori M, Vendruscolo M, Gianni, S. † (2016) Molecular Recognition by Templated Folding of an Intrinsically Disordered Protein Sci. Rep. 6 21994

82) Toto A, Pedersen SW, Karlsson OA, Moran GE, Andersson E, Chi CN, Strømgaard K, Gianni, S. † Jemth P. (2016) Ligand binding to the PDZ domains of postsynaptic density protein 95. Protein Eng. Des. Sel. Mar 2 [epub ahead of print]

83) Gianni, S. †, Jemth, P. (2016) Protein Folding: Vexing debates on a fundamental problem. Biophys. Chem 212, 17-21

84) Bonetti D, Camilloni C, Visconti L, Longhi S, Brunori M, Vendruscolo M, Gianni, S. † (2016) Identification and Structural Characterization of an Intermediate in the Folding of the Measles Virus X domain. J. Biol. Chem. Mar 21 [epub ahead of print]

85) Camilloni, C., Bonetti, D., Morrone, D., Giri, R., Dobson, C. M., Brunori, M., Gianni, S. † , Vendruscolo, M. (2016) Structural Biology of the hydrophobic effect in protein folding Sci. Rep. Accepted for publication.

86) Toto, A., Gianni, S. † (2016) Mutational Analysis of the Binding-Induced Folding Reaction of the Mixed-Lineage Leukemia Protein to the KIX Domain. Biochemistry. 55, 3957-3962

87) Dogan J, Toto A, Andersson E, Gianni, S. †, Jemth P. (2016) Activation Barrier-Limited Folding and Conformational Sampling of a Dynamic Protein Domain. Biochemistry. 55, 5289-5295.

88) Toto A, Mattei A, Jemth P, Gianni, S. †, (2016) Understanding the role of phosphorylation in the binding mechanism of a PDZ domain. Protein Eng Des Sel. 2016 Oct 19. [Epub ahead of print]

89) Brunori M, Gianni, S. † .(2016) Molecuar Medicine – To be or not to be Biophys Chem. 2016 Jul-Aug;214-215:33-46.

90) Kukic P, Pustovalova Y, Camilloni C, Gianni, S., Korzhnev DM, Vendruscolo M. (2017) Structural Characterization of the Early Events in the Nucleation- Condensation Mechanism in a Protein Folding Process. J Am Chem Soc. 139, 6899- 6910.

91) Troilo F, Bonetti D, Toto A, Visconti L, Brunori M, Longhi S, Gianni, S. † (2017) The folding pathway of the KIX domain ACS Chem. Biol. 12, 1683-1690

92) Longhi S, Bloyet LM, Gianni, S., Gerlier D. (2017) How order and disorder within paramyxoviral nucleoproteins and phosphoproteins orchestrate the molecular interplay of transcription and replication. Cell Mol Life Sci. 74, 3091-3118.

93) Bonetti D, Troilo F, Toto A, Brunori M, Longhi S, Gianni, S. † (2017) Analyzing the Folding and Binding Steps of an Intrinsically Disordered Protein by Protein Engineering. Biochemistry 56, 3780-3786.

94) Caillet-Saguy C, Toto A, Guerois R, Maisonneuve P, di Silvio E, Sawyer K, Gianni, S. † Wolff N. (2017) Regulation of the Human Phosphatase PTPN4 by the inter-domain linker connecting the PDZ and the phosphatase domains. Sci Rep. 7, 7875.

95) Toto, A., Bonetti, D., De Simone A., Gianni, S. † (2017) Understanding the mechanism of binding between Gab2 and the C terminal SH3 domain from Grb2 Oncotarget 8, 82344-82351.

96) Gautier C, Visconti L, Jemth P, Gianni S. † (2017) Addressing the role of the α-helical extension in the folding of the third PDZ domain from PSD-95. Sci Rep. 7, 12593.

97) Gianni S†, Jemth P. (2017) How Fast Is Protein-Ligand Association? Trends Biochem Sci. 42, 847-849.

98) Bignon C, Troilo F, Gianni S, Longhi S. (2017) Partner-Mediated Polymorphism of an Intrinsically Disordered Protein. J Mol Biol. S0022-2836(17)30562-4.

99) Schramm A, Lieutaud P, Gianni S, Longhi S, Bignon C. (2017) InSiDDe: A Server for Designing Artificial Disordered Proteins. Int J Mol Sci. 19: E91.

100) Saponaro, C., Sergio, S., Coluccia, A., De Luca, M., La Regina, G., Mologni, L., Famiglini, V.,Naccarato, V., Bonetti, D., Gautier, C., Gianni, S., Vergara, D., Salzet, M., Fournier, I., Bucci, C., Silvestri, R., Gambacorti Passerini, C., Maffia, M., Coluccia, A.M.L (2018) β-Catenin knockdown promotes NHERF1-mediated survival of colorectal cancer cells: implications for a double-targeted therapy Oncogene. 2018 Mar 19.

101) Caflisch, A., Gianni, S.†, (2018) Curr Opin Struct. Biol. 48:iv-vii.

102) Bonetti D, Troilo F, Brunori M, Longhi S, Gianni S. (2018) How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein? Biophys J.114, 1889-1894.

103) Del Poggetto E, Toto A, Aloise C, Di Piro F, Gori L, Malatesta F, Gianni S, Chiti F, Bemporad F. (2018) Stability of an aggregation-prone partially folded state of human profilin-1 correlates with aggregation propensity. J Biol Chem. 2018 May 14. pii: jbc.RA118.002087.

104) Malgieri G, D'Abrosca G, Pirone L, Toto A, Palmieri M, Russo L, Sciacca MFM, Tatè R, Sivo V, Baglivo I, Majewska R, Coletta M, Pedone PV, Isernia C, De Stefano M, Gianni S, Pedone EM, Milardi D, Fattorusso R. (2018) Folding mechanisms steer the amyloid fibril formation propensity of highly homologous proteins. Chem Sci. 9: 3290-3298.

105) Bignon C, Troilo F, Gianni S, Longhi S. Modulation of Measles Virus NTAIL Interactions through Fuzziness and Sequence Features of Disordered Binding Sites. (2018) Biomolecules. 2018; 9, E8.

106) Karlsson E, Andersson E, Dogan J, Gianni S, Jemth P, Camilloni C. A structurally heterogeneous transition state underlies coupled binding and folding of disordered proteins. (2019) J Biol Chem. 294, 1230-1239

107) Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. (2018) Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol. 611:137-192.

108) Gianni S, McCully ME, Malagrinò F, Bonetti D, De Simone A, Brunori M, Daggett V. (2018) A Carboxylate to Amide Substitution That Switches Protein Folds. Angew Chem Int Ed Engl. 2018 57:12795-12798.

109) Troilo F, Bonetti D, Camilloni C, Toto A, Longhi S, Brunori M, Gianni S†. (2018) Folding Mechanism of the SH3 Domain from Grb2. J Phys Chem B. 122(49):11166-11173.

110) Bonetti D, Troilo F, Toto A, Travaglini-Allocatelli C, Brunori M, Gianni S†. (2018) Mechanism of Folding and Binding of the N-Terminal SH2 Domain from SHP2. J Phys Chem B. 122(49):11108-11114.

111) Visconti L, Malagrinò F, Toto A, Gianni S.† (2019) The kinetics of folding of the NSH2 domain from p85. Sci Rep. 9, 4058

112) Troilo F, Bonetti D, Bignon C, Longhi S, Gianni S.†(2019) Understanding Intramolecular Crosstalk in an Intrinsically Disordered Protein. ACS Chem Biol. 14, 337-341.

113) Visconti L, Malagrinò F, Broggini L, De Luca CMG, Moda F, Gianni S†, Ricagno S, Toto A. (2019) Investigating the Molecular Basis of the Aggregation Propensity of the Pathological D76N Mutant of Beta-2 Microglobulin: Role of the Denatured State. Int J Mol Sci. 20 pii: E396.

114) Coluccia A, La Regina G, Naccarato V, Nalli M, Orlando V, Biagioni S, De Angelis ML, Baiocchi M, Gautier C, Gianni S, Di Pastena F, Di Magno L, Canettieri G, Coluccia AML, Silvestri R. (2019) Drug Design and Synthesis of First in Class PDZ1 Targeting NHERF1 Inhibitors as Anticancer Agents. ACS Med Chem Lett, 10, 499-503

115) Malagrinò F, Troilo F, Bonetti D, Toto A, Gianni, S. † (2019) Mapping the allosteric network within a SH3 domain. Sci Rep. 2019 9:8279.

116) Visconti L, Malagrinò F, Gianni, S. †, Toto A. (2019) Structural characterization of an on-pathway intermediate and transition state in the folding of the N-terminal SH2 domain from SHP2. FEBS J. 286(23):4769-4777.

117) Gianni, S. †, Jemth P. (2019) Affinity versus specificity in coupled binding and folding reactions. Protein Eng Des Sel. 32:203.

118) Toto A, Troilo F, Visconti L, Malagrinò F, Bignon C, Longhi S, Gianni, S. †, (2019) Binding induced folding: Lessons from the kinetics of interaction between NTAIL and XD. Arch Biochem Biophys. 671:255-261.

119) Petrosino M, Pasquo A, Novak L, Toto A, Gianni S, Mantuano E, Veneziano L, Minicozzi V, Pastore A, Puglisi R, Capriotti E, Chiaraluce R, Consalvi V. (2019) Characterization of human frataxin missense variants in cancer tissues. Hum Mutat. 2019 Sep;40(9):1400-1413.

120) Troilo F, Malagrinò F, Visconti L, Toto A, Gianni S. (2019) The Effect of Proline cis-trans Isomerization on the Folding of the C-Terminal SH2 Domain from p85. Int J Mol Sci. 2019 Dec 23;21(1). pii: E125.

121) Laursen, L, Karlsson, E., Gianni, S. †, Jemth, P., (2020) Functional interplay between protein domains in a supramodular structure J. Biol. Chem, J Biol Chem. 2020 Feb 14;295(7):1992-2000.

122) Toto A, Malagrinò F, Visconti L, Troilo F, Gianni S. (2020) Unveiling the Molecular Basis of the Noonan Syndrome-Causing Mutation T42A of SHP2. Int J Mol Sci. 2020 Jan 10;21(2). pii: E461.

123) Gautier, C., Gianni, S. †, (2020) Unveiling the folding mechanism of PDZ domains Methods Mol. Biol. Accepted for publication

124) Toto, A., Troilo, F., Malagrinò, F., Gianni, S. †, (2020) Understanding binding induced folding by temperature jump Methods Mol. Biol.2141:651-661.

125) Toto A, Malagrinò F, Visconti L, Troilo F, Pagano L, Brunori M, Jemth P, Gianni S. (2020) Templated folding of intrinsically disordered proteins J Biol Chem. 2020 May 8;295(19):6586-6593.

126) Malagrinò F, Visconti L, Pagano L, Toto A, Troilo F, Gianni S. (2020) Understanding the Binding Induced Folding of Intrinsically Disordered Proteins by Protein Engineering: Caveats and Pitfalls Int J Mol Sci. 2020 May 15;21(10):3484.

127) Visconti L, Toto A, Jarvis JA, Troilo F, Malagrinò F, De Simone A, Gianni S. (2020) Demonstration of Binding Induced Structural Plasticity in a SH2 Domain Front Mol Biosci. 2020 May 12;7:89.

128) Gautier C, Troilo F, Cordier F, Malagrinò F, Toto A, Visconti L, Zhu Y, Brunori M, Wolff N, Gianni S. (2020) Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):19963-19969.

129) Toto A, Ma S, Malagrinò F, Visconti L, Pagano L, Stromgaard K, Gianni S. (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 Protein Sci. 2020 Oct;29(10):2038-2042.

130) Laursen L, Kliche J, Gianni S, Jemth P. (2020) Supertertiary protein structure affects an allosteric network. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24294-24304.

131) Gianni S, Jemth P. (2020) Direct Quantification of Protein Dimerization Preference Shed Light on SOD1-associated ALS J Mol Biol. 2020 Nov 20;432(23):6003-6004.

132) Malagrinò F, Coluccia A, Bufano M, Regina G, Puxeddu M, Toto A, Visconti L, Paone A, Magnifico MC, Troilo F, Cutruzzolà F, Silvestri R, Gianni S. (2020) Targeting the Interaction between the SH3 Domain of Grb2 and Gab2. Cells. 2020 Nov 7;9(11):2435.

133) Pagano L, Toto A, Malagrinò F, Visconti L, Jemth P, Gianni S. (2021) Double Mutant Cycles as a Tool to Address Folding, Binding, and Allostery. Int J Mol Sci. 2021 Jan 15;22(2):828.

134) Visconti L, Malagrinò F, Troilo F, Pagano L, Toto A, Gianni S. (2021) Folding and Misfolding of a PDZ Tandem Repeat. J Mol Biol. 2021 Apr 2;433(7):166862

135) Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. (2021) Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly Acc Chem Res. 2021 Mar 2;54(5):1251-1259.

136) Fusco G, Gianni S. (2021) Function, Regulation, and Dysfunction of Intrinsically Disordered Proteins Life (Basel) 2021 Feb 12;11(2):140.

137) Nalli M, Puxeddu M, La Regina G, Gianni S, Silvestri R. Emerging Therapeutic Agents for Colorectal Cancer. Molecules. 2021 Dec 9;26(24):7463. doi: 10.3390/molecules26247463.

138) Pagano L, Malagrinò F, Nardella C, Gianni S, Toto A. Experimental Characterization of the Interaction between the N-Terminal SH3 Domain of Crkl and C3G. Int J Mol Sci. 2021 Dec 7;22(24):13174.

139) Nardella C, Malagrinò F, Pagano L, Rinaldo S, Gianni S, Toto A. Determining folding and binding properties of the C-terminal SH2 domain of SHP2. Protein Sci. 2021 Dec;30(12):2385-2395. doi: 10.1002/pro.4201.

140) Nardella C, Visconti L, Malagrinò F, Pagano L, Bufano M, Nalli M, Coluccia A, La Regina G, Silvestri R, Gianni S, Toto A. Targeting PDZ domains as potential treatment for viral infections, neurodegeneration and cancer. Biol Direct. 2021 Oct 12;16(1):15. doi: 10.1186/s13062-021-00303-9.

141) Laursen L, Gianni S, Jemth P. Dissecting Inter-domain Cooperativity in the Folding of a Multi Domain Protein. J Mol Biol. 2021 Sep 3;433(18):167148. doi: 10.1016/j.jmb.2021.167148. Epub 2021 Jul 8.

142) Pagano L, Malagrinò F, Visconti L, Troilo F, Pennacchietti V, Nardella C, Toto A, Gianni S. Probing the Effects of Local Frustration in the Folding of a Multidomain Protein. J Mol Biol. 2021 Jul 23;433(15):167087. doi: 10.1016/j.jmb.2021.167087. Epub 2021 Jun 3.

143) Malagrinò F, Pennacchietti V, Santorelli D, Pagano L, Nardella C, Diop A, Toto A, Gianni S. On the Effects of Disordered Tails, Supertertiary Structure and Quinary Interactions on the Folding and Function of Protein Domains Biomolecules. 2022 Jan 26;12(2):209. doi: 10.3390/biom12020209

144) Malagrinò F, Diop A, Pagano L, Nardella C, Toto A, Gianni S. Unveiling induced folding of intrinsically disordered proteins - Protein engineering, frustration and emerging themes Curr Opin Struct Biol . 2022 Feb;72:153-160. doi: 10.1016/j.sbi.2021.11.004.

145) Coluccia A, Bufano M, La Regina G, Puxeddu M, Toto A, Paone A, Bouzidi A, Musto G, Badolati N, Orlando V, Biagioni S, Masci D, Cantatore C, Cirilli R, Cutruzzolà F, Gianni S, Stornaiuolo M, Silvestri R. Anticancer Activity of ( S)-5-Chloro-3-((3,5-dimethylphenyl)sulfonyl)- N-(1-oxo-1-((pyridin-4-ylmethyl)amino)propan-2-yl)-1 H-indole-2-carboxamide (RS4690), a New Dishevelled 1 Inhibitor Cancers (Basel). 2022 Mar 7;14(5):1358. doi: 10.3390/cancers14051358.

146) Toto A, Malagrinò F, Nardella C, Pennacchietti V, Pagano L, Santorelli D, Diop A, Gianni S. Characterization of early and late transition states of the folding pathway of a SH2 domain Protein Sci. 2022 Jun;31(6):e4332. doi: 10.1002/pro.4332.

147) Brunori M, Gianni S. An Outlook on the Complexity of Protein Morphogenesis in Health and Disease. Front Mol Biosci. 2022 Jun 13;9:909567. doi: 10.3389/fmolb.2022.909567.

148) Nardella C, Toto A, Santorelli D, Pagano L, Diop A, Pennacchietti V, Pietrangeli P, Marcocci L, Malagrinò F, Gianni S. Folding and Binding Mechanisms of the SH2 Domain from Crkl. Biomolecules. 2022 Jul 22;12(8):1014. doi: 10.3390/biom12081014.

149) Malagrinò F, Fusco G, Pennacchietti V, Toto A, Nardella C, Pagano L, de Simone A, Gianni S. Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat. Protein Sci. 2022 Sep;31(9):e4396. doi: 10.1002/pro.4396.

150) Gautier C, Gianni S. A short structural extension dictates the early stages of folding of a PDZ domain. Biochim Biophys Acta Proteins Proteom. 2022 Nov 1;1870(11-12):140852.

151) Pagano L, Pennacchietti V, Diop A, Santorelli D, Pietrangeli P, Marcocci L, Nardella C, Malagrinò F, Toto A, Gianni S. Exploring the effect of tethered domains on the folding of Grb2 protein.
Arch Biochem Biophys. 2022 Nov 30;731:109444.

152) Hollås H, Ramirez J, Nominé Y, Kostmann C, Toto A, Gianni S, Travé G, Vedeler A. The cooperative folding of annexin A2 relies on a transient nonnative intermediate. Biophys J. 2022 Dec 6;121(23):4492-4504.

153) Diop A, Santorelli D, Malagrinò F, Nardella C, Pennacchietti V, Pagano L, Marcocci L, Pietrangeli P, Gianni S, Toto A. SH2 Domains: Folding, Binding and Therapeutical Approaches. Int J Mol Sci. 2022 Dec 15;23(24):15944.

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* Shared First-Author