title: Sequence-specific long range networks in PSD-95/discs large/ZO-1 (PDZ) domains tune their binding selectivity.
abstract: Protein-protein interactions mediated by modular protein domains are critical for cell scaffolding, differentiation, signaling, and ultimately, evolution. Given the vast number of ligands competing for binding to a limited number of domain families, it is often puzzling how specificity can be achieved. Selectivity may be modulated by intradomain allostery, whereby a remote residue is energetically connected to the functional binding site via side chain or backbone interactions. Whereas several energetic pathways, which could mediate intradomain allostery, have been predicted in modular protein domains, there is a paucity of experimental data to validate their existence and roles. Here, we have identified such functional energetic networks in one of the most common protein-protein interaction modules, the PDZ domain. We used double mutant cycles involving site-directed mutagenesis of both the PDZ domain and the peptide ligand, in conjunction with kinetics to capture the fine energetic details of the networks involved in peptide recognition. We performed the analysis on two homologous PDZ-ligand complexes and found that the energetically coupled residues differ for these two complexes. This result demonstrates that amino acid sequence rather than topology dictates the allosteric pathways. Furthermore, our data support a mechanism whereby the whole domain and not only the binding pocket is optimized for a specific ligand. Such cross-talk between binding sites and remote residues may be used to fine tune target selectivity.
authors.affiliation: Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Gianni
authors.forename: S Raza
authors.initials: SR
authors.lastname: Haq
authors.forename: Linda C
authors.initials: LC
authors.lastname: Montemiglio
authors.forename: Maike C
authors.initials: MC
authors.lastname: Jürgens
authors.forename: Åke
authors.initials: Å
authors.lastname: Engström
authors.forename: Celestine N
authors.initials: CN
authors.lastname: Chi
authors.forename: Maurizio
authors.initials: M
authors.lastname: Brunori
authors.forename: Per
authors.initials: P
authors.lastname: Jemth
mesh_terms: D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins