Ligand-dependent intra- and interdomain motions in the PDZ12 tandem regulate binding interfaces in postsynaptic density protein-95

Bertalan Kovács, Nóra Zajácz-Epresi, Zoltán Gáspári

Research output: Contribution to journalArticle


The postsynaptic density protein-95 (PSD-95) regulates synaptic plasticity through interactions mediated by its peptide-binding PDZ domains. The two N-terminal PDZ domains of PSD-95 form an autonomous structural unit, and their interdomain orientation and dynamics depend on ligand binding. To understand the mechanistic details of the effect of ligand binding, we generated conformational ensembles using available experimentally determined nuclear Overhauser effect interatomic distances and S2 order parameters. In our approach, the fast dynamics of the two domains is treated independently. We find that intradomain structural changes induced by ligand binding modulate the probability of the occurrence of specific domain–domain orientations. Our results suggest that the β2-β3 loop in the PDZ domains is a key regulatory region, which influences both intradomain motions and supramodular rearrangement.

Original languageEnglish
Pages (from-to)887-902
Number of pages16
JournalFEBS letters
Issue number5
Publication statusPublished - Mar 1 2020



  • PDZ tandem
  • PSD-95
  • molecular dynamics simulation
  • structural ensembles
  • supramodular dynamics

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this