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Article ; Online: Different electrostatic forces drive the binding kinetics of SARS-CoV, SARS-CoV-2 and MERS-CoV Envelope proteins with the PDZ2 domain of ZO1.

Pennacchietti, Valeria / Toto, Angelo

2023 Volume 13, Issue 1, Page(s) 7906

Abstract: The Envelope protein (E) is a structural protein encoded by the genome of SARS-CoV, SARS-CoV-2 and MERS-CoV Coronaviruses. It is poorly present in the virus but highly expressed in the host cell, with prominent role in virus assembly and virulence. The E ...

Abstract	The Envelope protein (E) is a structural protein encoded by the genome of SARS-CoV, SARS-CoV-2 and MERS-CoV Coronaviruses. It is poorly present in the virus but highly expressed in the host cell, with prominent role in virus assembly and virulence. The E protein possesses a PDZ-binding motif (PBM) at its C terminus that allows it to interact with host PDZ domain containing proteins. ZO1 is a key protein in assembling the cytoplasmic plaque of epithelial and endothelial Tight Junctions (TJs) as well as in determining cell differentiation, proliferation and polarity. The PDZ2 domain of ZO1 is known to interact with the Coronaviruses Envelope proteins, however the molecular details of such interaction have not been established. In this paper we directly measured, through Fluorescence Resonance Energy Transfer and Stopped-Flow methodology, the binding kinetics of the PDZ2 domain of ZO1 with peptides mimicking the C-terminal portion of the Envelope protein from SARS-CoV, SARS-CoV-2 and MERS-CoV in different ionic strength conditions. Interestingly, the peptide mimicking the E protein from MERS-CoV display much higher microscopic association rate constant with PDZ2 compared to SARS-CoV and SARS-CoV-2 suggesting a stronger contribution of electrostatic forces in the early events of binding. A comparison of thermodynamic and kinetic data obtained at increasing ionic strengths put in evidence different contribution of electrostatics in the recognition and complex formation events for the three peptides. Our data are discussed under the light of available structural data of PDZ2 domain of ZO1 and of previous works about these protein systems.
MeSH term(s)	Humans ; SARS-CoV-2/metabolism ; Middle East Respiratory Syndrome Coronavirus/genetics ; Middle East Respiratory Syndrome Coronavirus/metabolism ; COVID-19 ; Static Electricity ; Severe acute respiratory syndrome-related coronavirus/genetics ; Peptides/chemistry ; Protein Binding
Chemical Substances	Peptides
Language	English
Publishing date	2023-05-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-35079-7
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Article: Editorial: Intrinsically Disordered Proteins and Regions: The Challenge to the Structure-Function Relationship.

Toto, Angelo / Sormanni, Pietro / Paissoni, Cristina / Uversky, Vladimir N

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 962643

Language	English
Publishing date	2022-07-06
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.962643
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Article ; Online: Editorial

Angelo Toto / Pietro Sormanni / Cristina Paissoni / Vladimir N. Uversky

Frontiers in Molecular Biosciences, Vol

Intrinsically Disordered Proteins and Regions: The Challenge to the Structure-Function Relationship

2022 Volume 9

Keywords	intrinsically disordered protein ; intrinsically disordered region ; structure-function continuum ; protein-protein interaction ; multifunctional protein ; protein structure ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Understanding Binding-Induced Folding by Temperature Jump.

Toto, Angelo / Troilo, Francesca / Malagrinò, Francesca / Gianni, Stefano

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2141, Page(s) 651–661

Abstract: Temperature jump is a powerful technique for the characterization of fast kinetics and can be readily employed to understand both binding and folding reactions. Here we summarize briefly a temperature-jump prototypical experiment between an intrinsically ...

Abstract	Temperature jump is a powerful technique for the characterization of fast kinetics and can be readily employed to understand both binding and folding reactions. Here we summarize briefly a temperature-jump prototypical experiment between an intrinsically disordered protein and its physiological partner. The model used is the N
MeSH term(s)	Artifacts ; Buffers ; Calibration ; Electric Conductivity ; Equipment Design ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Nucleocapsid Proteins/chemistry ; Nucleocapsid Proteins/metabolism ; Osmolar Concentration ; Protein Binding ; Protein Domains ; Protein Folding ; Temperature ; Tryptophan/analogs & derivatives ; Tryptophan/analysis
Chemical Substances	Buffers ; Intrinsically Disordered Proteins ; Nucleocapsid Proteins ; measles virus nucleocapsid protein ; N-acetyltryptophanamide (2382-79-8) ; Tryptophan (8DUH1N11BX)
Language	English
Publishing date	2020-07-21
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0524-0_33
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Article: Understanding the Mechanism of Recognition of Gab2 by the N-SH2 Domain of SHP2.

Visconti, Lorenzo / Malagrinò, Francesca / Pagano, Livia / Toto, Angelo

Life (Basel, Switzerland)

2020 Volume 10, Issue 6

Abstract: Gab2 is a scaffold protein with a crucial role in colocalizing signaling proteins and it is involved in the regulation of several important molecular pathways. SHP2 is a protein phosphatase that binds, through its two SH2 domains, specific consensus ... ...

Abstract	Gab2 is a scaffold protein with a crucial role in colocalizing signaling proteins and it is involved in the regulation of several important molecular pathways. SHP2 is a protein phosphatase that binds, through its two SH2 domains, specific consensus sequences presenting a phosphorylated tyrosine located on the disordered tail of Gab2. To shed light on the details of such a fundamental interaction for the physiology of the cell, we present a complete mutational analysis of the kinetics of binding between the N-SH2 domain of SHP2 and a peptide mimicking a specific region of Gab2. By analyzing kinetic data, we determined structural features of the transition state of the N-SH2 domain binding to Gab2, highlighting a remarkable cooperativity of the binding reaction. Furthermore, comparison of these data with ones previously obtained for another SH2 domain suggests the presence of underlying general features characterizing the binding process of SH2 domains. Data are discussed under the light of previous works on SH2 domains.
Language	English
Publishing date	2020-06-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life10060085
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Article ; Online: Experimental Characterization of the Interaction between the N-Terminal SH3 Domain of Crkl and C3G.

Pagano, Livia / Malagrinò, Francesca / Nardella, Caterina / Gianni, Stefano / Toto, Angelo

International journal of molecular sciences

2021 Volume 22, Issue 24

Abstract: Crkl is a protein involved in the onset of several cancer pathologies that exerts its function only through its protein-protein interaction domains, a SH2 domain and two SH3 domains. SH3 domains are small protein interaction modules that mediate the ... ...

Abstract	Crkl is a protein involved in the onset of several cancer pathologies that exerts its function only through its protein-protein interaction domains, a SH2 domain and two SH3 domains. SH3 domains are small protein interaction modules that mediate the binding and recognition of proline-rich sequences. One of the main physiological interactors of Crkl is C3G (also known as RAPGEF1), an interaction with key implications in regulating cellular growth and differentiation, cell morphogenesis and adhesion processes. Thus, understanding the interaction between Crkl and C3G is fundamental to gaining information about the molecular determinants of the several cancer pathologies in which these proteins are involved. In this paper, through a combination of fast kinetics at different experimental conditions and site-directed mutagenesis, we characterize the binding reaction between the N-SH3 domain of Crkl and a peptide mimicking a specific portion of C3G. Our results show a clear effect of pH on the stability of the complex, due to the protonation of negatively charged residues in the binding pocket of N-SH3. Our results are discussed under the light of previous work on SH3 domains.
MeSH term(s)	Adaptor Proteins, Signal Transducing/chemistry ; Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Binding Sites ; Cell Adhesion ; Cell Differentiation ; Cell Proliferation ; Guanine Nucleotide-Releasing Factor 2/chemistry ; Guanine Nucleotide-Releasing Factor 2/metabolism ; Humans ; Models, Molecular ; Mutagenesis, Site-Directed/methods ; Protein Binding ; Protein Conformation ; Protein Domains ; Static Electricity
Chemical Substances	Adaptor Proteins, Signal Transducing ; CRKL protein ; Guanine Nucleotide-Releasing Factor 2 ; RAPGEF1 protein, human
Language	English
Publishing date	2021-12-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222413174
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Article ; Online: Understanding the molecular basis of folding cooperativity through a comparative analysis of a multidomain protein and its isolated domains.

Santorelli, Daniele / Marcocci, Lucia / Pennacchietti, Valeria / Nardella, Caterina / Diop, Awa / Pietrangeli, Paola / Pagano, Livia / Toto, Angelo / Malagrinò, Francesca / Gianni, Stefano

The Journal of biological chemistry

2023 Volume 299, Issue 3, Page(s) 102983

Abstract: Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multidomain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of ... ...

Abstract	Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multidomain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of a multidomain protein may either fold independently on each other or exhibit interdependent supradomain phenomena. To address this issue, here we present the comparative analysis of the folding of a tandem repeat protein, comprising two contiguous PDZ domains, in comparison to that of its isolated constituent domains. By analyzing in detail the equilibrium and kinetics of folding at different experimental conditions, we demonstrate that despite each of the PDZ domains in isolation being capable of independent folding, at variance with previously characterized PDZ tandem repeats, the full-length construct folds and unfolds as a single cooperative unit. By exploiting quantitatively, the comparison of the folding of the tandem repeat to those observed for its constituent domains, as well as by characterizing a truncated variant lacking a short autoinhibitory segment, we successfully rationalize the molecular basis of the observed cooperativity and attempt to infer some general conclusions for multidomain systems.
MeSH term(s)	Kinetics ; Models, Molecular ; Protein Folding ; Proteins/chemistry ; Protein Conformation ; Protein Domains
Chemical Substances	Proteins
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.102983
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Article: The Role of BIA Analysis in Osteoporosis Risk Development: Hierarchical Clustering Approach.

Sgarro, Giacinto Angelo / Grilli, Luca / Valenzano, Anna Antonia / Moscatelli, Fiorenzo / Monacis, Domenico / Toto, Giusi / De Maria, Antonella / Messina, Giovanni / Polito, Rita

Diagnostics (Basel, Switzerland)

2023 Volume 13, Issue 13

Abstract: Osteoporosis is a common musculoskeletal disorder among the elderly and a chronic condition which, like many other chronic conditions, requires long-term clinical management. It is caused by many factors, including lifestyle and obesity. Bioelectrical ... ...

Abstract	Osteoporosis is a common musculoskeletal disorder among the elderly and a chronic condition which, like many other chronic conditions, requires long-term clinical management. It is caused by many factors, including lifestyle and obesity. Bioelectrical impedance analysis (BIA) is a method to estimate body composition based on a weak electric current flow through the body. The measured voltage is used to calculate body bioelectrical impedance, divided into resistance and reactance, which can be used to estimate body parameters such as total body water (TBW), fat-free mass (FFM), fat mass (FM), and muscle mass (MM). This study aims to find the tendency of osteoporosis in obese subjects, presenting a method based on hierarchical clustering, which, using BIA parameters, can group patients who show homogeneous characteristics. Grouping similar patients into clusters can be helpful in the field of medicine to identify disorders, pathologies, or more generally, characteristics of significant importance. Another added value of the clustering process is the possibility to define cluster prototypes, i.e., imaginary patients who represent models of "states", which can be used together with clustering results to identify subjects with similar characteristics in a classification context. The results show that hierarchical clustering is a method that can be used to provide the detection of states and, consequently, supply a more personalized medicine approach. In addition, this method allowed us to elect BIA as a potential prognostic and diagnostic instrument in osteoporosis risk development.
Language	English
Publishing date	2023-07-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics13132292
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Article ; Online: The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State.

Pietrangeli, Paola / Marcocci, Lucia / Pennacchietti, Valeria / Diop, Awa / Di Felice, Mariana / Pagano, Livia / Malagrinò, Francesca / Toto, Angelo / Brunori, Maurizio / Gianni, Stefano

Journal of molecular biology

2024 Volume 436, Issue 10, Page(s) 168555

Abstract: The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing ... ...

Abstract	The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart. Through an extensive site-directed mutagenesis, we employed a Φ -value analysis to map native-like contacts in the folding transition state. The presence of a broad energy barrier facilitated the exploration of such contacts in both early and late folding events. We compared results from yeast and human frataxin providing insights into the impact of native topology on the folding mechanism and elucidating the properties of the underlying free energy landscape. The findings are discussed in the context of the funneled energy landscape theory of protein folding.
Language	English
Publishing date	2024-03-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2024.168555
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Article ; Online: The binding selectivity of the C-terminal SH3 domain of Grb2, but not its folding pathway, is dictated by its contiguous SH2 domain.

Di Felice, Mariana / Pagano, Livia / Pennacchietti, Valeria / Diop, Awa / Pietrangeli, Paola / Marcocci, Lucia / Di Matteo, Sara / Malagrinò, Francesca / Toto, Angelo / Gianni, Stefano

The Journal of biological chemistry

2024 Volume 300, Issue 4, Page(s) 107129

Abstract: The adaptor protein Grb2, or growth factor receptor-bound protein 2, possesses a pivotal role in the transmission of fundamental molecular signals in the cell. Despite lacking enzymatic activity, Grb2 functions as a dynamic assembly platform, ... ...

Abstract	The adaptor protein Grb2, or growth factor receptor-bound protein 2, possesses a pivotal role in the transmission of fundamental molecular signals in the cell. Despite lacking enzymatic activity, Grb2 functions as a dynamic assembly platform, orchestrating intracellular signals through its modular structure. This study delves into the energetic communication of Grb2 domains, focusing on the folding and binding properties of the C-SH3 domain linked to its neighboring SH2 domain. Surprisingly, while the folding and stability of C-SH3 remain robust and unaffected by SH2 presence, significant differences emerge in the binding properties when considered within the tandem context compared with isolated C-SH3. Through a double mutant cycle analysis, we highlighted a subset of residues, located at the interface with the SH2 domain and far from the binding site, finely regulating the binding of a peptide mimicking a physiological ligand of the C-SH3 domain. Our results have mechanistic implications about the mechanisms of specificity of the C-SH3 domain, indicating that the presence of the SH2 domain optimizes binding to its physiological target, and emphasizing the general importance of considering supramodular multidomain protein structures to understand the functional intricacies of protein-protein interaction domains.
MeSH term(s)	GRB2 Adaptor Protein/metabolism ; GRB2 Adaptor Protein/chemistry ; GRB2 Adaptor Protein/genetics ; src Homology Domains ; Humans ; Protein Folding ; Protein Binding ; Binding Sites
Chemical Substances	GRB2 Adaptor Protein ; GRB2 protein, human
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.107129
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