Chapter 5
Study of PDZ–Peptide and PDZ–Lipid Interactions
by Surface Plasmon Resonance/BIAcore
Pascale Zimmermann and Antonio Luis Egea-Jimenez
Abstract
Surface plasmon resonance (SPR)/BIAcore technology enables the characterization of molecular interactions, including determination of affinities and kinetics. In BIAcore, one of the interaction partners (the
ligand) is immobilized on a chip and the other (the analyte) is provided in solution. BIAcore allows to study
association and dissociation rates in real time without the use of labeling. BIAcore can be applied to
molecular interactions involving small compounds and biological macromolecules such as proteins, lipids,
nucleic acids, or carbohydrates. Here we describe protocols for the measurements of PDZ domain–peptide
(oriented biotinylated peptides), PDZ domain–liposomes (lipid membranes), and PDZ–lipid–peptide
tripartite interactions.
Key words PDZ, Lipids, Lipid interaction, Liposomes, Peptide interaction, BIAcore, L1 sensor chip,
SA sensor chip
1 Introduction
PDZ domains are globular domains composed of approximately
90 amino acids. They share a common fold comprising six β-strands
arranged in a β-sandwich and two α-helices capping each end
[1]. There are approximately 270 PDZ domains in the human
proteome, distributed in more than 150 PDZ proteins [2]. PDZ
domains are the most common interacting modules in humans,
recognizing short peptide motifs, called PDZ binding motifs, most
often situated at the cytosolic tail of target proteins such as membrane receptors, adhesion molecules, or ion channels, among
others [3]. Involved in the formation and function of signal transduction complexes, PDZ domain–peptide interactions are key regulators in many cellular pathways [4]. Some PDZ domains can
interact with lipids and even act as dual specificity modules displaying both peptide and membrane lipid binding activities. Lipid
partners of PDZ domains include phospholipids such as phosphoinositides [5–10] and phosphatidylserine [11] or the neutral lipid
Jean-Paul Borg (ed.), PDZ Mediated Interactions: Methods and Protocols, Methods in Molecular Biology, vol. 2256,
https://doi.org/10.1007/978-1-0716-1166-1_5, © Springer Science+Business Media, LLC, part of Springer Nature 2021
75
Study of PDZ–Peptide and PDZ–Lipid Interactions
by Surface Plasmon Resonance/BIAcore
Pascale Zimmermann and Antonio Luis Egea-Jimenez
Abstract
Surface plasmon resonance (SPR)/BIAcore technology enables the characterization of molecular interactions, including determination of affinities and kinetics. In BIAcore, one of the interaction partners (the
ligand) is immobilized on a chip and the other (the analyte) is provided in solution. BIAcore allows to study
association and dissociation rates in real time without the use of labeling. BIAcore can be applied to
molecular interactions involving small compounds and biological macromolecules such as proteins, lipids,
nucleic acids, or carbohydrates. Here we describe protocols for the measurements of PDZ domain–peptide
(oriented biotinylated peptides), PDZ domain–liposomes (lipid membranes), and PDZ–lipid–peptide
tripartite interactions.
Key words PDZ, Lipids, Lipid interaction, Liposomes, Peptide interaction, BIAcore, L1 sensor chip,
SA sensor chip
1 Introduction
PDZ domains are globular domains composed of approximately
90 amino acids. They share a common fold comprising six β-strands
arranged in a β-sandwich and two α-helices capping each end
[1]. There are approximately 270 PDZ domains in the human
proteome, distributed in more than 150 PDZ proteins [2]. PDZ
domains are the most common interacting modules in humans,
recognizing short peptide motifs, called PDZ binding motifs, most
often situated at the cytosolic tail of target proteins such as membrane receptors, adhesion molecules, or ion channels, among
others [3]. Involved in the formation and function of signal transduction complexes, PDZ domain–peptide interactions are key regulators in many cellular pathways [4]. Some PDZ domains can
interact with lipids and even act as dual specificity modules displaying both peptide and membrane lipid binding activities. Lipid
partners of PDZ domains include phospholipids such as phosphoinositides [5–10] and phosphatidylserine [11] or the neutral lipid
Jean-Paul Borg (ed.), PDZ Mediated Interactions: Methods and Protocols, Methods in Molecular Biology, vol. 2256,
https://doi.org/10.1007/978-1-0716-1166-1_5, © Springer Science+Business Media, LLC, part of Springer Nature 2021
75