title: Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments.
abstract: BACKGROUND
  PDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the prevalence, specificity, affinity, and molecular determinants of PDZ-PtdInsPs interactions and on their impact on PDZ-protein interactions is very limited.
  
  
  RESULTS
  We screened the human proteome for PtdInsPs interacting PDZ domains by a combination of in vivo cell-localization studies and in vitro dot blot and Surface Plasmon Resonance (SPR) experiments using synthetic lipids and recombinant proteins. We found that PtdInsPs interactions contribute to the cellular distribution of some PDZ domains, intriguingly also in nuclear organelles, and that a significant subgroup of PDZ domains interacts with PtdInsPs with affinities in the low-to-mid micromolar range. In vitro specificity for the head group is low, but with a trend of higher affinities for more phosphorylated PtdInsPs species. Other membrane lipids can assist PtdInsPs-interactions. PtdInsPs-interacting PDZ domains have generally high pI values and contain characteristic clusters of basic residues, hallmarks that may be used to predict additional PtdInsPs interacting PDZ domains. In tripartite binding experiments we established that peptide binding can either compete or cooperate with PtdInsPs binding depending on the combination of ligands.
  
  
  CONCLUSIONS
  Our screen substantially expands the set of PtdInsPs interacting PDZ domains, and shows that a full understanding of the biology of PDZ proteins will require a comprehensive insight into the intricate relationships between PDZ domains and their peptide and lipid ligands.
authors: Department of Human Genetics, K. U. Leuven, Leuven, Belgium.
authors: Ylva
authors: Y
authors: Ivarsson
authors: Anna Maria
authors: AM
authors: Wawrzyniak
authors: Rudra
authors: R
authors: Kashyap
authors: Jolanta
authors: J
authors: Polanowska
authors: Stéphane
authors: S
authors: Betzi
authors: Frédérique
authors: F
authors: Lembo
authors: Elke
authors: E
authors: Vermeiren
authors: Driss
authors: D
authors: Chiheb
authors: Nicolas
authors: N
authors: Lenfant
authors: Xavier
authors: X
authors: Morelli
authors: Jean-Paul
authors: JP
authors: Borg
authors: Jérôme
authors: J
authors: Reboul
authors: Pascale
authors: P
authors: Zimmermann
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D001665:Binding Sites; D045744:Cell Line, Tumor; D017930:Genes, Reporter; D057166:High-Throughput Screening Assays; D006801:Humans; D015151:Immunoblotting; D007700:Kinetics; D008024:Ligands; D008164:Luminescent Proteins; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D054731:PDZ Domains; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D010716:Phosphatidylinositols / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D020349:Surface Plasmon Resonance; D053676:Syntenins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D008164:Luminescent Proteins; D008565:Membrane Proteins; D010455:Peptides; D010716:Phosphatidylinositols; D011994:Recombinant Proteins; D053676:Syntenins; C054562:yellow fluorescent protein, Bacteria
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