INDEX
A
Actomyosin................................. 261, 263, 264, 266–268
Adherens junctions (AJ) ............................................... 222
Amide-to ester mutation ....................197, 206, 210–211
AVLX-144 ................................................... 158, 159, 163
B
BIAcore......................................................................75–86
Biomolecular fragment complementation assay.......... 187
Biophysical techniques .................................................... 90
C
Calcium/calmodulin-dependent serine protein
kinase (CASK) ........................... 34, 138–140, 143
Computational approach ....................................... 66, 237
E
Electropherogram superimposition ............................... 67
Epithelial cell polarity ................................................... 224
Equilibrium ......................... 62, 78, 84, 95, 99, 149–154
Expressed protein ligation (EPL)....................... 194–197,
199, 200, 211, 212
F
Fluorescence ............................................... 66, 67, 73, 99,
107, 116, 137–147, 150, 151, 153, 161, 163,
169, 170, 180, 181, 184–186
Fluorescence anisotropy ............................................... 138
Fluorescence polarization (FP) ............................ 73, 161,
163, 169, 170, 180, 181, 184–186, 188
Folding ................................................... 3, 90, 91, 97–99,
104, 105, 114–119, 127, 130, 149–155
Forces.....................................................95, 238, 246, 247
G
GAL4 ............................................................................. 1, 2
H
Holdup assay .................................................... 61–72, 180
I
Identity ..............................................90, 92–94, 138, 227
Implicit solvent............................................ 239, 240, 245
Inhibition......................................................157, 224–226
Isothermal titration calorimetry (ITC).......................127,
129, 130, 132, 170, 175, 180, 181, 186, 187, 190
K
Kinetics ....................................................... 77, 78, 81–84,
86, 115, 149, 150, 152–155, 180, 196
L
Ligand binding.................... 41, 117, 127, 137–147, 242
Lipid interactions ......................................................75–86
Liposomes....................................... 76–78, 80, 82, 83, 86
L1 sensor chips......................................78, 82, 83, 85, 86
M
MC simulations .................................................... 242, 243
Molecular mechanics............................................ 238–240
Molecular modeling............................280, 281, 283–286
N
NanoBiT ..............................................180, 183, 187–189
Native chemical ligation (NCL)................. 194, 212, 213
Next-generation sequencing (NGS) ...................... 42, 43,
46, 51, 56, 58
P
Pathogenesis ...................... 221, 223, 225–227, 230, 232
PDZ-Binding Motifs (PBM).................................. 3, 5, 7,
11, 12, 14, 19, 24, 41, 61–73, 75, 86, 89, 99, 115,
117, 126, 129, 132, 137, 139–142, 145,
179–190, 217–232
PDZ/PBM interaction ............................... 137, 138, 145
Peptide interactions ..........................................75, 81, 82,
84, 85, 125–132
Phage display ........................................... 41–58, 126, 130
Phosphorylation ..............................................42, 48, 126,
179–190, 197, 206, 224, 239
Protein complexes .............................................17, 18, 21,
22, 24, 26, 30–31, 34, 37, 76, 127, 129, 223, 258
Protein design ...................................................... 237, 250
Protein engineering ...................................................... 116
Protein modifications.................................................... 193
Protein-protein binding................................................ 218
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, © Springer Science+Business Media, LLC, part of Springer Nature 2021
291
A
Actomyosin................................. 261, 263, 264, 266–268
Adherens junctions (AJ) ............................................... 222
Amide-to ester mutation ....................197, 206, 210–211
AVLX-144 ................................................... 158, 159, 163
B
BIAcore......................................................................75–86
Biomolecular fragment complementation assay.......... 187
Biophysical techniques .................................................... 90
C
Calcium/calmodulin-dependent serine protein
kinase (CASK) ........................... 34, 138–140, 143
Computational approach ....................................... 66, 237
E
Electropherogram superimposition ............................... 67
Epithelial cell polarity ................................................... 224
Equilibrium ......................... 62, 78, 84, 95, 99, 149–154
Expressed protein ligation (EPL)....................... 194–197,
199, 200, 211, 212
F
Fluorescence ............................................... 66, 67, 73, 99,
107, 116, 137–147, 150, 151, 153, 161, 163,
169, 170, 180, 181, 184–186
Fluorescence anisotropy ............................................... 138
Fluorescence polarization (FP) ............................ 73, 161,
163, 169, 170, 180, 181, 184–186, 188
Folding ................................................... 3, 90, 91, 97–99,
104, 105, 114–119, 127, 130, 149–155
Forces.....................................................95, 238, 246, 247
G
GAL4 ............................................................................. 1, 2
H
Holdup assay .................................................... 61–72, 180
I
Identity ..............................................90, 92–94, 138, 227
Implicit solvent............................................ 239, 240, 245
Inhibition......................................................157, 224–226
Isothermal titration calorimetry (ITC).......................127,
129, 130, 132, 170, 175, 180, 181, 186, 187, 190
K
Kinetics ....................................................... 77, 78, 81–84,
86, 115, 149, 150, 152–155, 180, 196
L
Ligand binding.................... 41, 117, 127, 137–147, 242
Lipid interactions ......................................................75–86
Liposomes....................................... 76–78, 80, 82, 83, 86
L1 sensor chips......................................78, 82, 83, 85, 86
M
MC simulations .................................................... 242, 243
Molecular mechanics............................................ 238–240
Molecular modeling............................280, 281, 283–286
N
NanoBiT ..............................................180, 183, 187–189
Native chemical ligation (NCL)................. 194, 212, 213
Next-generation sequencing (NGS) ...................... 42, 43,
46, 51, 56, 58
P
Pathogenesis ...................... 221, 223, 225–227, 230, 232
PDZ-Binding Motifs (PBM).................................. 3, 5, 7,
11, 12, 14, 19, 24, 41, 61–73, 75, 86, 89, 99, 115,
117, 126, 129, 132, 137, 139–142, 145,
179–190, 217–232
PDZ/PBM interaction ............................... 137, 138, 145
Peptide interactions ..........................................75, 81, 82,
84, 85, 125–132
Phage display ........................................... 41–58, 126, 130
Phosphorylation ..............................................42, 48, 126,
179–190, 197, 206, 224, 239
Protein complexes .............................................17, 18, 21,
22, 24, 26, 30–31, 34, 37, 76, 127, 129, 223, 258
Protein design ...................................................... 237, 250
Protein engineering ...................................................... 116
Protein modifications.................................................... 193
Protein-protein binding................................................ 218
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, © Springer Science+Business Media, LLC, part of Springer Nature 2021
291