Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix
1 Identification of PDZ Interactions by Yeast Two-Hybrid Technique . . . . . . . . . .
1
Monica Castro-Cruz, Marta Monserrat-Gomez, Jean-Paul Borg,
Pascale Zimmermann, and Eric Bailly
2 Identification of PDZ Interactions by Affinity Purification
and Mass Spectrometry Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Avais M. Daulat, Ste ´phane Audebert, Mo ˆnica Wagner,
Luc Camoin, and Jean-Paul Borg
3 Identification of PDZ Interactions by Proteomic Peptide Phage Display . . . . . . . 41
Susanne Lu ¨chow, Gustav N. Sundell, and Ylva Ivarsson
4 A Computational Protocol to Analyze PDZ/PBM Affinity
Data Obtained by High-Throughput Holdup Assay. . . . . . . . . . . . . . . . . . . . . . . . . 61
Pau Jane ´, Lionel Chiron, Goran Bich, Gilles Trave ´,
and Yves Nomine ´
5 Study of PDZ–Peptide and PDZ–Lipid Interactions by Surface
Plasmon Resonance/BIAcore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Pascale Zimmermann and Antonio Luis Egea-Jimenez
6 PDZ Sample Quality Assessment by Biochemical and Biophysical
Characterizations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Ce ´lia Caillet-Saguy, Se ´bastien Bru ˆ le ´, Nicolas Wolff,
and Bertrand Raynal
7 Crystallographic Studies of PDZ Domain–Peptide Interactions
of the Scribble Polarity Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Janesha C. Maddumage, Bryce Z. Stewart, Patrick O. Humbert,
and Marc Kvansakul
8 A Fluorescence-Based Assay to Determine PDZ–Ligand Binding
Thermodynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Young Joo Sun and Ernesto J. Fuentes
9 Unveiling the Folding Mechanism of PDZ Domains . . . . . . . . . . . . . . . . . . . . . . . . 149
Candice Gautier and Stefano Gianni
10 Development of Peptide-Based PDZ Domain Inhibitors. . . . . . . . . . . . . . . . . . . . . 157
Dominik J. Essig, Javier R. Balboa, and Kristian Strømgaard
11 Dynamic Control of Signaling by Phosphorylation
of PDZ Binding Motifs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Ma ´ rton A. Simon and La ´ szl o Nyitray
12 Chemical Synthesis of PDZ Domains. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Christin Kossmann, Sana Ma, Louise S. Clemmensen,
and Kristian Strømgaard
vii
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix
1 Identification of PDZ Interactions by Yeast Two-Hybrid Technique . . . . . . . . . .
1
Monica Castro-Cruz, Marta Monserrat-Gomez, Jean-Paul Borg,
Pascale Zimmermann, and Eric Bailly
2 Identification of PDZ Interactions by Affinity Purification
and Mass Spectrometry Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Avais M. Daulat, Ste ´phane Audebert, Mo ˆnica Wagner,
Luc Camoin, and Jean-Paul Borg
3 Identification of PDZ Interactions by Proteomic Peptide Phage Display . . . . . . . 41
Susanne Lu ¨chow, Gustav N. Sundell, and Ylva Ivarsson
4 A Computational Protocol to Analyze PDZ/PBM Affinity
Data Obtained by High-Throughput Holdup Assay. . . . . . . . . . . . . . . . . . . . . . . . . 61
Pau Jane ´, Lionel Chiron, Goran Bich, Gilles Trave ´,
and Yves Nomine ´
5 Study of PDZ–Peptide and PDZ–Lipid Interactions by Surface
Plasmon Resonance/BIAcore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Pascale Zimmermann and Antonio Luis Egea-Jimenez
6 PDZ Sample Quality Assessment by Biochemical and Biophysical
Characterizations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Ce ´lia Caillet-Saguy, Se ´bastien Bru ˆ le ´, Nicolas Wolff,
and Bertrand Raynal
7 Crystallographic Studies of PDZ Domain–Peptide Interactions
of the Scribble Polarity Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Janesha C. Maddumage, Bryce Z. Stewart, Patrick O. Humbert,
and Marc Kvansakul
8 A Fluorescence-Based Assay to Determine PDZ–Ligand Binding
Thermodynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Young Joo Sun and Ernesto J. Fuentes
9 Unveiling the Folding Mechanism of PDZ Domains . . . . . . . . . . . . . . . . . . . . . . . . 149
Candice Gautier and Stefano Gianni
10 Development of Peptide-Based PDZ Domain Inhibitors. . . . . . . . . . . . . . . . . . . . . 157
Dominik J. Essig, Javier R. Balboa, and Kristian Strømgaard
11 Dynamic Control of Signaling by Phosphorylation
of PDZ Binding Motifs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Ma ´ rton A. Simon and La ´ szl o Nyitray
12 Chemical Synthesis of PDZ Domains. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Christin Kossmann, Sana Ma, Louise S. Clemmensen,
and Kristian Strømgaard
vii