A sequential binding mechanism in a PDZ domain
2009 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 30, 7089-7097 p.Article in journal (Refereed) Published
Conformational selection and induced fit are two well-known mechanisms of allosteric protein-ligand interaction. Some proteins, like ubiquitin, have recently been found to exist in multiple conformations at equilibrium, suggesting that the conformational selection may be a general mechanism of interaction, in particular for single-domain proteins. Here, we found that the PDZ2 domain of SAP97 binds its ligand via a sequential (induced fit) mechanism. We performed binding experiments using SAP97 PDZ2 and peptide ligands and observed biphasic kinetics with the stopped-flow technique, indicating that ligand binding involves at least a two-step process. By using an ultrarapid continuous-flow mixer, we then detected a hyperbolic dependence of binding rate constants on peptide concentration, corroborating the two-step binding mechanism. Furthermore, we found a similar dependence of the rate constants on both PDZ and peptide concentration, demonstrating that the PDZ2-peptide interaction involves a precomplex, which then undergoes a conformational change, and thereby follows an induced fit mechanism.
Place, publisher, year, edition, pages
2009. Vol. 48, no 30, 7089-7097 p.
Medical and Health Sciences
IdentifiersURN: urn:nbn:se:uu:diva-119523DOI: 10.1021/bi900559kISI: 000268231800002PubMedID: 19496620OAI: oai:DiVA.org:uu-119523DiVA: diva2:300369