title: The kinetics of PDZ domain-ligand interactions and implications for the binding mechanism.
abstract: PDZ domains are protein adapter modules present in a few hundred human proteins. They play important roles in scaffolding and signal transduction. PDZ domains usually bind to the C termini of their target proteins. To assess the binding mechanism of this interaction we have performed the first in-solution kinetic study for PDZ domains and peptides corresponding to target ligands. Both PDZ3 from postsynaptic density protein 95 and PDZ2 from protein tyrosine phosphatase L1 bind their respective target peptides through an apparent A + B --> A.B mechanism without rate-limiting conformational changes. But a mutant with a fluorescent probe (Trp) outside of the binding pocket suggests that slight changes in the structure take place upon binding in protein tyrosine phosphatase-L1 PDZ2. For PDZ3 from postsynaptic density protein 95 the pH dependence of the binding reaction is consistent with a one-step mechanism with one titratable group. The salt dependence of the interaction shows that the formation of electrostatic interactions is rate-limiting for the association reaction but not for dissociation of the complex.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.
authors.forename: Stefano
authors.initials: S
authors.lastname: Gianni
authors.forename: Ake
authors.initials: A
authors.lastname: Engström
authors.forename: Mårten
authors.initials: M
authors.lastname: Larsson
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Calosci
authors.forename: Francesco
authors.initials: F
authors.lastname: Malatesta
authors.forename: Lars
authors.initials: L
authors.lastname: Eklund
authors.forename: Chi Celestine
authors.initials: CC
authors.lastname: Ngang
authors.forename: Carlo
authors.initials: C
authors.lastname: Travaglini-Allocatelli
authors.forename: Per
authors.initials: P
authors.lastname: Jemth
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D000076122:Disks Large Homolog 4 Protein; D004305:Dose-Response Relationship, Drug; D006801:Humans; D006863:Hydrogen-Ion Concentration; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry*; D007477:Ions; D007700:Kinetics; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry*; D013053:Spectrophotometry; D055672:Static Electricity; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors; D014364:Tryptophan / Q000737:chemistry; D014508:Urea / Q000494:pharmacology
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C501444:DLG4 protein, human; D018076:DNA, Complementary; D000076122:Disks Large Homolog 4 Protein; D047908:Intracellular Signaling Peptides and Proteins; D007477:Ions; D008024:Ligands; D008565:Membrane Proteins; D010455:Peptides; D014364:Tryptophan; D014508:Urea; C516742:PTPN13 protein, human; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13; D017027:Protein Tyrosine Phosphatases