INDEX
A
Absorbance
isotropic ................................................................... 450
spectrum ........................................412, 416, 457, 461
Acoustic mist ionization ...................................... 217–230
Adenosine diphosphate (ADP) ..........290, 303, 308, 311
Adenosine triphosphate (ATP).................. 274, 290, 293,
295–298, 300–307, 310, 311, 313–315, 401,
402, 404, 407, 412, 444
AlphaScreen technology ............ 202–204, 208, 209, 212
Amino acid analysis .............................................. 110, 144
Analytical ultracentrifugation (AUC) ....... 381, 397–403,
409–419
Antibodies ..................42, 202, 203, 208–210, 212–214,
329, 353
Association constant ............................................ 136, 149
Association rate constant .............................................. 276
ATPases.............101, 289, 292, 293, 295, 298, 301–313
Autoradiography ............................................43, 322, 430
B
Band shift assay .................................................... 430, 432
Bandwidth .................. 43, 51, 53, 58, 73, 277, 457, 461
Beer-Lambert law................................................. 365, 428
Biacore ...................... 53, 54, 66, 68, 370, 373, 376, 377
Binding ...........................15, 47, 84, 105, 135, 162, 184,
201, 231, 248, 274, 289, 321, 342, 351, 369,
383, 398, 427, 454, 465
approach to equilibrium ......................................... 237
curves ............................ 94, 144, 145, 148, 162, 163,
174, 177, 180, 254
equation ................................................................... 337
Binding mechanism
conformational selection......................................... 124
fly-casting hypothesis .............................................. 126
induced fit................................................................ 124
Binding site prediction ................................................... 76
Biolayer interferometry (BLI) ................... 135, 352, 353,
357, 361
Biotinyl Cap PE.................................................... 186, 191
Biosensor .............................................343, 346, 353, 356
Buffer
HEPES........................ 188, 190, 194, 232, 242, 325,
334, 468, 482
mismatch.................................................................... 41
MOPS ...................................................................... 294
optimization .......................................... 20, 37, 39, 40
phosphate-buffered saline (PBS).............28, 356, 388
phosphates ............................. 31, 253, 256, 261, 267,
293, 388, 435
screening .............................19, 36, 39, 205, 257, 268
Tris-Borate EDTA (TBE) .............................. 326, 327
Tris-HCl ........................................................... 22, 220
C
Calibration.............................. 51, 52, 86, 157, 302, 309,
310, 315, 393, 399, 404, 409, 413, 415–417,
473, 474
Cellular thermal shift assay (CETSA
®
) .............. 202–204,
208–210, 213, 214
Chaotropic..................................................................... 110
Chase experiments ........................................................ 275
Chemiluminescent labels .............................................. 322
Chromatin remodeler .......................................... 295, 298
Chromophore
fluorenylmethyloxycarbonyl chloride
(FMOC)....................................................... 459
Clamp loader .............398, 401–404, 407–412, 416, 418
Collision-induced dissociation (CID).......................... 475
Competition ....................... 93, 100, 244, 251, 259, 260,
262, 331, 359, 432
Competitive inhibition ................................................. 240
Complex
formation ............................................... 135, 136, 149
interactions ....................................148, 151, 184, 186
Conformational changes.......................... 12, 15, 84, 109,
118–122, 124, 131, 151, 276, 286, 303, 342,
363, 364, 366, 426, 466, 467, 470
Constant
association constant (K a )................86, 106, 149, 420
association rate constant (K a ) ...................... 108, 126,
345, 362
dissociation constant (K d ) .................. 91, 95, 97, 432
dissociation rate constant ...................................90, 93
half maximal effective concentration
(EC 50 ) ................................................. 162, 229
half maximal inhibitory concentration (IC 50 ) ...... 229,
236, 241, 244, 245
inhibition constant (K i ) ................239, 241, 244, 245
Michaelis–Menten constant (K m ) .........292, 295–303
Tina Daviter et al. (eds.), Protein-Ligand Interactions: Methods and Applications, Methods in Molecular Biology, vol. 2263,
https://doi.org/10.1007/978-1-0716-1197-5, © Springer Science+Business Media, LLC, part of Springer Nature 2021
487
A
Absorbance
isotropic ................................................................... 450
spectrum ........................................412, 416, 457, 461
Acoustic mist ionization ...................................... 217–230
Adenosine diphosphate (ADP) ..........290, 303, 308, 311
Adenosine triphosphate (ATP).................. 274, 290, 293,
295–298, 300–307, 310, 311, 313–315, 401,
402, 404, 407, 412, 444
AlphaScreen technology ............ 202–204, 208, 209, 212
Amino acid analysis .............................................. 110, 144
Analytical ultracentrifugation (AUC) ....... 381, 397–403,
409–419
Antibodies ..................42, 202, 203, 208–210, 212–214,
329, 353
Association constant ............................................ 136, 149
Association rate constant .............................................. 276
ATPases.............101, 289, 292, 293, 295, 298, 301–313
Autoradiography ............................................43, 322, 430
B
Band shift assay .................................................... 430, 432
Bandwidth .................. 43, 51, 53, 58, 73, 277, 457, 461
Beer-Lambert law................................................. 365, 428
Biacore ...................... 53, 54, 66, 68, 370, 373, 376, 377
Binding ...........................15, 47, 84, 105, 135, 162, 184,
201, 231, 248, 274, 289, 321, 342, 351, 369,
383, 398, 427, 454, 465
approach to equilibrium ......................................... 237
curves ............................ 94, 144, 145, 148, 162, 163,
174, 177, 180, 254
equation ................................................................... 337
Binding mechanism
conformational selection......................................... 124
fly-casting hypothesis .............................................. 126
induced fit................................................................ 124
Binding site prediction ................................................... 76
Biolayer interferometry (BLI) ................... 135, 352, 353,
357, 361
Biotinyl Cap PE.................................................... 186, 191
Biosensor .............................................343, 346, 353, 356
Buffer
HEPES........................ 188, 190, 194, 232, 242, 325,
334, 468, 482
mismatch.................................................................... 41
MOPS ...................................................................... 294
optimization .......................................... 20, 37, 39, 40
phosphate-buffered saline (PBS).............28, 356, 388
phosphates ............................. 31, 253, 256, 261, 267,
293, 388, 435
screening .............................19, 36, 39, 205, 257, 268
Tris-Borate EDTA (TBE) .............................. 326, 327
Tris-HCl ........................................................... 22, 220
C
Calibration.............................. 51, 52, 86, 157, 302, 309,
310, 315, 393, 399, 404, 409, 413, 415–417,
473, 474
Cellular thermal shift assay (CETSA
®
) .............. 202–204,
208–210, 213, 214
Chaotropic..................................................................... 110
Chase experiments ........................................................ 275
Chemiluminescent labels .............................................. 322
Chromatin remodeler .......................................... 295, 298
Chromophore
fluorenylmethyloxycarbonyl chloride
(FMOC)....................................................... 459
Clamp loader .............398, 401–404, 407–412, 416, 418
Collision-induced dissociation (CID).......................... 475
Competition ....................... 93, 100, 244, 251, 259, 260,
262, 331, 359, 432
Competitive inhibition ................................................. 240
Complex
formation ............................................... 135, 136, 149
interactions ....................................148, 151, 184, 186
Conformational changes.......................... 12, 15, 84, 109,
118–122, 124, 131, 151, 276, 286, 303, 342,
363, 364, 366, 426, 466, 467, 470
Constant
association constant (K a )................86, 106, 149, 420
association rate constant (K a ) ...................... 108, 126,
345, 362
dissociation constant (K d ) .................. 91, 95, 97, 432
dissociation rate constant ...................................90, 93
half maximal effective concentration
(EC 50 ) ................................................. 162, 229
half maximal inhibitory concentration (IC 50 ) ...... 229,
236, 241, 244, 245
inhibition constant (K i ) ................239, 241, 244, 245
Michaelis–Menten constant (K m ) .........292, 295–303
Tina Daviter et al. (eds.), Protein-Ligand Interactions: Methods and Applications, Methods in Molecular Biology, vol. 2263,
https://doi.org/10.1007/978-1-0716-1197-5, © Springer Science+Business Media, LLC, part of Springer Nature 2021
487