Alexa fluors ..................................................... 232, 338
1,8-ANS..................................................................... 37
coumarins ................................................................ 290
CPM......................................................................... 212
Cy ............................................................................. 232
Cyanine-5 ....................................................... 165, 166
DCVJ ....................................................................... 212
6-FAM ..................................................................... 328
fluorescein....................................................... 232, 325
fluorescein isothiocyanate (FITC)......................... 401,
403, 404, 407–412
green fluorescent protein (GFP) ............................ 400
Mant......................................................................... 282
rhodamine ............................................................... 232
SYBR Green II ........................................................ 328
SYBR Safe ....................................................... 328, 336
SYPRO Orange ..................... 37, 201, 203, 205, 206,
212, 213
tryptophan ............................................. 101, 274, 282
tyrosine ........................................................... 274, 282
yellow fluorescent protein (YFP) ........................... 400
Folding ............................. 12, 15, 16, 86, 106, 107, 109,
110, 112, 121, 122, 125, 128, 130, 150, 458
Fo ¨rster resonance energy transfer ................................ 274
Fragment-based lead discovery (FBLD)............. 247, 248
Free energy (ΔG) .............................. 103, 125, 128, 136,
149, 150, 367
G
GTPases ......................................289, 292, 303, 304, 312
Guanosine
triphosphate (GTP)................................................. 293
H
Heat capacity (ΔC p ) ........................................... 16, 18, 77
High-throughput screening ......................................... 217
AMI-MS .................................................................. 222
CETSA HT..................................................... 202, 204
fluorescence polarization ............................... 231–245
Hill slope .............................................................. 241, 245
Homology modelling ................................................... 444
Hybridization .................... 342, 344, 345, 347–349, 371
Hydrogen-deuterium exchange (HDX) ............ 469–473,
475, 479, 481, 482
Hydrophobicity ............................................................. 470
I
Inhibition......... 213, 222, 223, 225, 227, 292, 295, 298
Instrumental response function (instrumental time
constant) ........................................................ 88
Interaction
complexes ................... 105, 107, 119, 124, 161, 322,
329, 335, 337, 361, 362, 397, 398, 402, 403,
406, 408, 418
Intermediates........................ 84, 97, 106, 107, 110, 112,
113, 116, 122, 124, 125, 130, 131, 238, 245,
303, 304, 307, 438
Intrinsically disordered protein (IDP) ............... 106, 107,
110, 118, 119, 121, 122, 124–126
Isomerisation ................................................................... 97
Isothermal titration calorimetry (ITC)........................ 274
baseline .....................................................66, 142, 153
c-value .......................................................67, 143, 144
data analysis ............................................................... 78
heat ...................49, 65–67, 144, 147–149, 151–153,
156–158
heat capacity ............................................................ 150
measurement ..................................... 48, 64, 135, 141
stoichiometry............................................65, 136, 145
Isotherms .......................... 65–68, 70, 76, 120, 143, 337,
406, 407, 410, 413, 415, 419
K
Kinetics
amplitudes .......... 112, 121, 123, 124, 307, 315, 365
Burst phase .............................................................. 307
exponential equations ............................................. 305
Lag phase ............................................... 305, 311, 314
membrane binding.................................................. 454
pre-steady state ........................................................ 292
second order ............................................................ 118
steady state.............50, 292, 295, 297, 303, 305, 307
L
Labelling
fluorescence ...................................................... 76, 243
Lamp
xenon .............................................................. 280, 284
Ligand
adenosine triphosphate (ATP)................................ 274
ADP ......................................................................... 290
GDP ......................................................................... 290
glucose ..................................................................... 290
glutamate ................................................................. 290
GTP ......................................................................... 303
guanosine triphosphate (GTP)............................... 274
Mant-ATP....................................................... 308, 310
Mant-GDPNP ......................................................... 274
Mant-GTP ............................................................... 275
7-methyl guanosine (7-MEG)...................... 291, 293,
294, 305
phosphate ................................................................ 289
phosphatidylinositol (3,4,5)-triphosphate
(PIP 3 ) .......................................................... 467
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index 489
1,8-ANS..................................................................... 37
coumarins ................................................................ 290
CPM......................................................................... 212
Cy ............................................................................. 232
Cyanine-5 ....................................................... 165, 166
DCVJ ....................................................................... 212
6-FAM ..................................................................... 328
fluorescein....................................................... 232, 325
fluorescein isothiocyanate (FITC)......................... 401,
403, 404, 407–412
green fluorescent protein (GFP) ............................ 400
Mant......................................................................... 282
rhodamine ............................................................... 232
SYBR Green II ........................................................ 328
SYBR Safe ....................................................... 328, 336
SYPRO Orange ..................... 37, 201, 203, 205, 206,
212, 213
tryptophan ............................................. 101, 274, 282
tyrosine ........................................................... 274, 282
yellow fluorescent protein (YFP) ........................... 400
Folding ............................. 12, 15, 16, 86, 106, 107, 109,
110, 112, 121, 122, 125, 128, 130, 150, 458
Fo ¨rster resonance energy transfer ................................ 274
Fragment-based lead discovery (FBLD)............. 247, 248
Free energy (ΔG) .............................. 103, 125, 128, 136,
149, 150, 367
G
GTPases ......................................289, 292, 303, 304, 312
Guanosine
triphosphate (GTP)................................................. 293
H
Heat capacity (ΔC p ) ........................................... 16, 18, 77
High-throughput screening ......................................... 217
AMI-MS .................................................................. 222
CETSA HT..................................................... 202, 204
fluorescence polarization ............................... 231–245
Hill slope .............................................................. 241, 245
Homology modelling ................................................... 444
Hybridization .................... 342, 344, 345, 347–349, 371
Hydrogen-deuterium exchange (HDX) ............ 469–473,
475, 479, 481, 482
Hydrophobicity ............................................................. 470
I
Inhibition......... 213, 222, 223, 225, 227, 292, 295, 298
Instrumental response function (instrumental time
constant) ........................................................ 88
Interaction
complexes ................... 105, 107, 119, 124, 161, 322,
329, 335, 337, 361, 362, 397, 398, 402, 403,
406, 408, 418
Intermediates........................ 84, 97, 106, 107, 110, 112,
113, 116, 122, 124, 125, 130, 131, 238, 245,
303, 304, 307, 438
Intrinsically disordered protein (IDP) ............... 106, 107,
110, 118, 119, 121, 122, 124–126
Isomerisation ................................................................... 97
Isothermal titration calorimetry (ITC)........................ 274
baseline .....................................................66, 142, 153
c-value .......................................................67, 143, 144
data analysis ............................................................... 78
heat ...................49, 65–67, 144, 147–149, 151–153,
156–158
heat capacity ............................................................ 150
measurement ..................................... 48, 64, 135, 141
stoichiometry............................................65, 136, 145
Isotherms .......................... 65–68, 70, 76, 120, 143, 337,
406, 407, 410, 413, 415, 419
K
Kinetics
amplitudes .......... 112, 121, 123, 124, 307, 315, 365
Burst phase .............................................................. 307
exponential equations ............................................. 305
Lag phase ............................................... 305, 311, 314
membrane binding.................................................. 454
pre-steady state ........................................................ 292
second order ............................................................ 118
steady state.............50, 292, 295, 297, 303, 305, 307
L
Labelling
fluorescence ...................................................... 76, 243
Lamp
xenon .............................................................. 280, 284
Ligand
adenosine triphosphate (ATP)................................ 274
ADP ......................................................................... 290
GDP ......................................................................... 290
glucose ..................................................................... 290
glutamate ................................................................. 290
GTP ......................................................................... 303
guanosine triphosphate (GTP)............................... 274
Mant-ATP....................................................... 308, 310
Mant-GDPNP ......................................................... 274
Mant-GTP ............................................................... 275
7-methyl guanosine (7-MEG)...................... 291, 293,
294, 305
phosphate ................................................................ 289
phosphatidylinositol (3,4,5)-triphosphate
(PIP 3 ) .......................................................... 467
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index 489