title: The mechanism of binding of the second PDZ domain from the Protein Tyrosine Phosphatase-BL to the Adenomatous Polyposis Coli tumor suppressor.
abstract: Many biological processes are regulated by the interaction between protein domains and their corresponding binding partners. The PDZ domain is one of the most common protein-protein interaction modules in mammalian cells, whose role is to bind C-terminal sequences of specific targets. The second PDZ domain from the Protein Tyrosine Phosphatase-BL (PDZ2) binds to the C-terminal of Adenomatous Polyposis Coli protein (APC), one of the major tumor suppressor whose task is to regulate cell adhesion and proliferation. Here, we present a detailed kinetics analysis of the interaction between PDZ2 domain and a peptide mimicking the PDZ binding motif of APC. By analyzing data obtained at different experimental conditions, we propose a plausible mechanism for binding. Furthermore, a comparison between the dissociation rate constant measured by different methodologies allow us to identify an additional kinetic step, which is likely to arise from a conformational change of PDZ2 occurring after binding. The data are discussed on the light of previous work on PDZ domains.
authors.affiliation: Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy.
authors.forename: Eva
authors.initials: E
authors.lastname: Di Silvio
authors.affiliation: Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Bonetti
authors.affiliation: Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy.
authors.forename: Angelo
authors.initials: A
authors.lastname: Toto
authors.affiliation: Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy.
authors.forename: Angela
authors.initials: A
authors.lastname: Morrone
authors.affiliation: Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK stefano.gianni@uniroma1.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Gianni
mesh_terms: D025601:Adenomatous Polyposis Coli Protein / Q000737:chemistry / Q000378:metabolism*; D000818:Animals; D001665:Binding Sites; D007700:Kinetics; D051379:Mice; D008958:Models, Molecular; D054731:PDZ Domains; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D060066:Protein Interaction Maps; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13 / Q000737:chemistry / Q000378:metabolism*
chemical_list: D025601:Adenomatous Polyposis Coli Protein; D010455:Peptides; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13
keywords: kinetics; peptide binding; protein–protein interaction