title: Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains.
abstract: Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K(d) correlate with changes in k(off).
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.
authors: S Raza
authors: SR
authors: Haq
authors: Celestine N
authors: CN
authors: Chi
authors: Anders
authors: A
authors: Bach
authors: Jakob
authors: J
authors: Dogan
authors: Åke
authors: Å
authors: Engström
authors: Greta
authors: G
authors: Hultqvist
authors: O Andreas
authors: OA
authors: Karlsson
authors: Patrik
authors: P
authors: Lundström
authors: Linda C
authors: LC
authors: Montemiglio
authors: Kristian
authors: K
authors: Strømgaard
authors: Stefano
authors: S
authors: Gianni
authors: Per
authors: P
authors: Jemth
mesh_terms: D008024:Ligands; D016014:Linear Models; D008958:Models, Molecular; D054731:PDZ Domains; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D008024:Ligands; D010455:Peptides