Hybrid approaches ........................................................ 126
Hydrogen/deuterium exchange ......................... 193–217
I
IgG ................................................ 60, 62, 70, 73, 75, 101
Immunodiagnostics ........................................................ 79
Immunofluorescence .................................................... 288
Inhibitor .............................................................. 9, 11, 12,
43, 60, 66, 105, 109, 115, 117, 260, 306, 307,
323, 324, 332
K
Kallikrein-related protease 7 (KLK7)......................60–62,
66, 69, 70, 75
Kinetics .............................................................. 59–62, 65,
70, 73, 75, 138, 140, 145–153, 159, 160, 168,
217, 275
L
Lysine deacetylases ............................................... 319–335
M
Mammalian target of rapamycin (mTOR).......... 287, 288
Membrane protein complexes ........................... 3–15, 190
Membrane proteins................................................. 3, 4, 6,
7, 77, 78, 189, 223, 245, 257–267
Microcalorimetry........................................................... 130
Modelling restraints .................................... 221, 224, 235
Multiprotein complexes ............................ 17–37, 39, 189
N
Native-PAGE................................................259–261, 265
Negative stain electron microscopy ............................. 245
Non-canonical amino acids .......................................... 319
Non-covalent mass spectrometry ............... 173, 174, 181
Non-homologous endjoining (NHEJ)............... 126, 127
Nucleo-protein complexes............................................ 125
O
Oligomeric states.................................184, 185, 247, 259
P
Panning....................................... 106, 107, 111–118, 120
Phage display ..........................60, 61, 106, 107, 111–116
Phage ELISA ................................................110, 116–120
Polyproteins................................................. 78, 79, 89, 93
Protein complexes .............................................12, 17, 39,
59, 126, 155, 181, 188, 189, 223, 224, 230, 246,
251, 255, 303–317, 320
Protein-DNA binding......................................... 181, 203,
214, 215
Protein-fragment complementation assay ................... 303
Protein heterogeneity .......................................... 155–169
Protein interactions...........................................18, 39, 61,
105, 126, 155, 156, 195, 288, 289, 291, 295,
296, 303
Protein-protein interaction (PPI) ....................... 303, 304
Proteomics...........................................190, 193, 303–317
R
Recombinant antibodies ........................... 60, 66, 77–102
Recombinant antibody formats...................................... 70
Research reagents .......................................................... 105
Restriction free (RF) .........................................18, 24, 32,
34, 35, 184, 186, 187
S
ScFv-Fc ........................................................ 60, 62, 70, 73
Secretory expression........................................................ 78
Sedimentation coefficients.................................. 156, 160,
162, 163, 169
Sedimentation velocity (SV) ................................... 79, 85,
91, 155–164, 168
Sequence and ligation independent cloning
(SLIC) .................................................... 18, 23–25,
30, 32, 34, 55, 62
Single-chain variable fragment format
(scFv).............................................. 60, 61, 63, 102
Single-molecule localization microscopy
(SMLM)................................................... 271, 272,
275, 277–279, 281, 283
Single particle electron microscopy ............................. 244
Size exclusion chromatography (SEC) .................. 10, 13,
15, 89, 93, 99, 127, 133, 156, 161, 162, 164,
181–183, 259, 266, 267
Solubilization .............................................................9, 12,
257–259, 261–263, 266
Stabilization ....................................................84, 257–267
Stoichiometries..................................................6, 61, 126,
127, 133, 135, 136, 140, 141, 156, 173, 174,
181, 222, 224, 230, 233, 236, 272, 283
Structural mass spectrometry ............................. 174, 193,
194, 209, 221–223, 239
Subcomplexes .............................................. 226, 229, 238
Super-resolution microscopy ............................... 126, 271
SwitchSENSE technology ................................... 145, 146
T
Therapeutic antibodies .......................................... 79, 100
Thermodynamic parameters ................................ 126, 133
Thermophoresis ................................................... 125–142
Three-color.................................................................... 299
Timecorrelated single-photon counting cards
(TCSPC) ................................................... 295, 296
Transcription factor (TF)............................ 181, 195, 210
Transient gene expression.........................................59–75
Translocon ..................................................5–8, 11, 13–15
340
MULTIPROTEIN COMPLEXES: METHODS AND PROTOCOLS
Index
Hydrogen/deuterium exchange ......................... 193–217
I
IgG ................................................ 60, 62, 70, 73, 75, 101
Immunodiagnostics ........................................................ 79
Immunofluorescence .................................................... 288
Inhibitor .............................................................. 9, 11, 12,
43, 60, 66, 105, 109, 115, 117, 260, 306, 307,
323, 324, 332
K
Kallikrein-related protease 7 (KLK7)......................60–62,
66, 69, 70, 75
Kinetics .............................................................. 59–62, 65,
70, 73, 75, 138, 140, 145–153, 159, 160, 168,
217, 275
L
Lysine deacetylases ............................................... 319–335
M
Mammalian target of rapamycin (mTOR).......... 287, 288
Membrane protein complexes ........................... 3–15, 190
Membrane proteins................................................. 3, 4, 6,
7, 77, 78, 189, 223, 245, 257–267
Microcalorimetry........................................................... 130
Modelling restraints .................................... 221, 224, 235
Multiprotein complexes ............................ 17–37, 39, 189
N
Native-PAGE................................................259–261, 265
Negative stain electron microscopy ............................. 245
Non-canonical amino acids .......................................... 319
Non-covalent mass spectrometry ............... 173, 174, 181
Non-homologous endjoining (NHEJ)............... 126, 127
Nucleo-protein complexes............................................ 125
O
Oligomeric states.................................184, 185, 247, 259
P
Panning....................................... 106, 107, 111–118, 120
Phage display ..........................60, 61, 106, 107, 111–116
Phage ELISA ................................................110, 116–120
Polyproteins................................................. 78, 79, 89, 93
Protein complexes .............................................12, 17, 39,
59, 126, 155, 181, 188, 189, 223, 224, 230, 246,
251, 255, 303–317, 320
Protein-DNA binding......................................... 181, 203,
214, 215
Protein-fragment complementation assay ................... 303
Protein heterogeneity .......................................... 155–169
Protein interactions...........................................18, 39, 61,
105, 126, 155, 156, 195, 288, 289, 291, 295,
296, 303
Protein-protein interaction (PPI) ....................... 303, 304
Proteomics...........................................190, 193, 303–317
R
Recombinant antibodies ........................... 60, 66, 77–102
Recombinant antibody formats...................................... 70
Research reagents .......................................................... 105
Restriction free (RF) .........................................18, 24, 32,
34, 35, 184, 186, 187
S
ScFv-Fc ........................................................ 60, 62, 70, 73
Secretory expression........................................................ 78
Sedimentation coefficients.................................. 156, 160,
162, 163, 169
Sedimentation velocity (SV) ................................... 79, 85,
91, 155–164, 168
Sequence and ligation independent cloning
(SLIC) .................................................... 18, 23–25,
30, 32, 34, 55, 62
Single-chain variable fragment format
(scFv).............................................. 60, 61, 63, 102
Single-molecule localization microscopy
(SMLM)................................................... 271, 272,
275, 277–279, 281, 283
Single particle electron microscopy ............................. 244
Size exclusion chromatography (SEC) .................. 10, 13,
15, 89, 93, 99, 127, 133, 156, 161, 162, 164,
181–183, 259, 266, 267
Solubilization .............................................................9, 12,
257–259, 261–263, 266
Stabilization ....................................................84, 257–267
Stoichiometries..................................................6, 61, 126,
127, 133, 135, 136, 140, 141, 156, 173, 174,
181, 222, 224, 230, 233, 236, 272, 283
Structural mass spectrometry ............................. 174, 193,
194, 209, 221–223, 239
Subcomplexes .............................................. 226, 229, 238
Super-resolution microscopy ............................... 126, 271
SwitchSENSE technology ................................... 145, 146
T
Therapeutic antibodies .......................................... 79, 100
Thermodynamic parameters ................................ 126, 133
Thermophoresis ................................................... 125–142
Three-color.................................................................... 299
Timecorrelated single-photon counting cards
(TCSPC) ................................................... 295, 296
Transcription factor (TF)............................ 181, 195, 210
Transient gene expression.........................................59–75
Translocon ..................................................5–8, 11, 13–15
340
MULTIPROTEIN COMPLEXES: METHODS AND PROTOCOLS
Index
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