Constant (cont.)
observed first order rate constant (k obs ) ................... 92
rate constants....... 50, 106, 108, 121, 128, 131, 151,
303–307, 310, 311, 314, 335, 354, 355, 366,
403, 432
steady-state rate constant........................................ 307
turnover number (k cat ) ..........................292, 295–303
Control experiments .................102, 111, 117, 118, 163,
180, 264
Cooperativity ........................................................ 146, 148
Coupling ratio ............................................................... 304
Crystal
cryoprotectants............................................... 436, 445
freezing ........................................................... 436, 445
harvesting ................................................................ 436
Curve fitting
global fitting ................................................... 122, 147
residuals ................................................. 114, 115, 130
Cuvettes ............................ 54, 60, 72, 76, 140, 155, 164,
179, 275, 277, 280, 284, 293, 294, 309
D
Data analysis
butterfly plot................................................... 478, 480
coefficient of variance............................ 223, 226, 229
confidence interval .................................59, 62–66, 70
error surface projection (ESP) ................................. 78
simulation ............................................................ 98–99
z-score............................................................. 226, 230
Dead time (mixing time) .....................84, 86, 89, 90, 92,
109, 114, 120, 126, 127, 130, 298, 454
Denaturant
guanidine hydrochloride......................................... 481
Detergent
BRIJ ......................................................................... 243
CHAPS .................................................................... 220
DDM ....................................................................... 220
octyl β-D-glucopyranoside ..................................... 243
sodium dodecyl sulfate (SDS) .................................... 6
Triton X-100 .................................................. 227, 243
Tween 20........................................................ 164, 243
Diethylpyrocarbonate (DEPC) ........................... 323, 324
Differential power ....................................... 52, 65, 66, 77
Differential scanning calorimetry (DSC).......... 16, 18, 38
Differential scanning fluorimetry (DSF) ....................201,
205, 206, 213
extrinsic fluorophores .................................. 16, 37–38
intrinsic fluorophore .............................. 16–18, 36–37
Diffusion coefficient............................................... 97, 398
Dimethyl sulphoxide (DMSO) ......................37, 41, 153,
165, 178, 188, 203, 205–207, 209–211, 222,
224, 228, 238, 245, 249, 252, 256, 261, 264
Dissociation constant .................................................... 136
DNA polymerase III ..................................................... 398
DNA replication ................................................... 321, 398
Dynamic light scattering (DLS)
hydrodynamic radius (R h ) .......................................... 8
E
Effective particle theory................................................ 405
Electrophoretic mobility shift assay
(EMSA) ............ 321, 322, 429, 430, 432, 444
Enthalpy (ΔH) .......................................18, 39, 49, 65, 76
Enthalpy-entropy compensation .................................. 150
Enthalpy of ionization ...................................71, 138, 155
Entropy (ΔS).......................... 18, 49, 136, 149, 150, 163
Enzymes............................ 9, 39, 48, 152, 217–219, 221,
222, 224, 227, 228, 232, 241, 245, 398, 403
Equilibrium .............................27, 50, 68, 106, 108–110,
112, 118, 119, 121, 125, 129, 237, 238, 240,
273–286, 323, 326, 328–330, 335–337,
354–356, 361, 363, 365, 366, 397, 406, 432
Equilibrium binding .....83, 94, 100, 128, 237, 276, 337
Exchange rates............................................. 466, 472, 481
Expression vectors......................................................... 292
F
Filter
bandpass.......................................................... 112, 399
long-pass ............. 112, 128, 280, 283, 284, 294, 308
Flash photolysis .................................................... 292, 304
Flow
cells......................................................... 372, 373, 377
Couette flow......................... 451, 452, 454, 456, 461
orientation ............................................................... 451
Fluorescence
acceptor.................................................. 274, 282, 284
anisotropy ................................................. 76, 231–245
autofluorescence............................................. 241, 244
donor ..................................................... 274, 282, 284
emission .............................17, 38, 51, 53, 73, 76, 88,
111, 128, 162, 234, 243, 245, 274, 278, 282,
284, 290, 291, 328, 399
excitation ..................36, 38, 51, 53, 73, 88, 89, 100,
111, 128, 162, 234, 242, 243, 245, 274, 282,
284, 290, 291, 328, 399, 404, 410
inner filter effects ................. 232, 242, 245, 399, 418
intensities ...................... 17, 119, 167, 201, 212, 225,
232, 234, 235, 242, 244, 245, 277, 278, 282,
283, 290, 291, 296, 300, 399, 417, 418, 432
quenching .................... 111, 126, 237, 238, 274, 402
spectroscopy ..................................................... 16, 106
Fluorescence detection system (FDS)................ 399, 400,
409, 411, 413, 415, 417
Fluorophore
Alexa 488................................................................. 178
Alexa 647................................................................. 236
488
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index
observed first order rate constant (k obs ) ................... 92
rate constants....... 50, 106, 108, 121, 128, 131, 151,
303–307, 310, 311, 314, 335, 354, 355, 366,
403, 432
steady-state rate constant........................................ 307
turnover number (k cat ) ..........................292, 295–303
Control experiments .................102, 111, 117, 118, 163,
180, 264
Cooperativity ........................................................ 146, 148
Coupling ratio ............................................................... 304
Crystal
cryoprotectants............................................... 436, 445
freezing ........................................................... 436, 445
harvesting ................................................................ 436
Curve fitting
global fitting ................................................... 122, 147
residuals ................................................. 114, 115, 130
Cuvettes ............................ 54, 60, 72, 76, 140, 155, 164,
179, 275, 277, 280, 284, 293, 294, 309
D
Data analysis
butterfly plot................................................... 478, 480
coefficient of variance............................ 223, 226, 229
confidence interval .................................59, 62–66, 70
error surface projection (ESP) ................................. 78
simulation ............................................................ 98–99
z-score............................................................. 226, 230
Dead time (mixing time) .....................84, 86, 89, 90, 92,
109, 114, 120, 126, 127, 130, 298, 454
Denaturant
guanidine hydrochloride......................................... 481
Detergent
BRIJ ......................................................................... 243
CHAPS .................................................................... 220
DDM ....................................................................... 220
octyl β-D-glucopyranoside ..................................... 243
sodium dodecyl sulfate (SDS) .................................... 6
Triton X-100 .................................................. 227, 243
Tween 20........................................................ 164, 243
Diethylpyrocarbonate (DEPC) ........................... 323, 324
Differential power ....................................... 52, 65, 66, 77
Differential scanning calorimetry (DSC).......... 16, 18, 38
Differential scanning fluorimetry (DSF) ....................201,
205, 206, 213
extrinsic fluorophores .................................. 16, 37–38
intrinsic fluorophore .............................. 16–18, 36–37
Diffusion coefficient............................................... 97, 398
Dimethyl sulphoxide (DMSO) ......................37, 41, 153,
165, 178, 188, 203, 205–207, 209–211, 222,
224, 228, 238, 245, 249, 252, 256, 261, 264
Dissociation constant .................................................... 136
DNA polymerase III ..................................................... 398
DNA replication ................................................... 321, 398
Dynamic light scattering (DLS)
hydrodynamic radius (R h ) .......................................... 8
E
Effective particle theory................................................ 405
Electrophoretic mobility shift assay
(EMSA) ............ 321, 322, 429, 430, 432, 444
Enthalpy (ΔH) .......................................18, 39, 49, 65, 76
Enthalpy-entropy compensation .................................. 150
Enthalpy of ionization ...................................71, 138, 155
Entropy (ΔS).......................... 18, 49, 136, 149, 150, 163
Enzymes............................ 9, 39, 48, 152, 217–219, 221,
222, 224, 227, 228, 232, 241, 245, 398, 403
Equilibrium .............................27, 50, 68, 106, 108–110,
112, 118, 119, 121, 125, 129, 237, 238, 240,
273–286, 323, 326, 328–330, 335–337,
354–356, 361, 363, 365, 366, 397, 406, 432
Equilibrium binding .....83, 94, 100, 128, 237, 276, 337
Exchange rates............................................. 466, 472, 481
Expression vectors......................................................... 292
F
Filter
bandpass.......................................................... 112, 399
long-pass ............. 112, 128, 280, 283, 284, 294, 308
Flash photolysis .................................................... 292, 304
Flow
cells......................................................... 372, 373, 377
Couette flow......................... 451, 452, 454, 456, 461
orientation ............................................................... 451
Fluorescence
acceptor.................................................. 274, 282, 284
anisotropy ................................................. 76, 231–245
autofluorescence............................................. 241, 244
donor ..................................................... 274, 282, 284
emission .............................17, 38, 51, 53, 73, 76, 88,
111, 128, 162, 234, 243, 245, 274, 278, 282,
284, 290, 291, 328, 399
excitation ..................36, 38, 51, 53, 73, 88, 89, 100,
111, 128, 162, 234, 242, 243, 245, 274, 282,
284, 290, 291, 328, 399, 404, 410
inner filter effects ................. 232, 242, 245, 399, 418
intensities ...................... 17, 119, 167, 201, 212, 225,
232, 234, 235, 242, 244, 245, 277, 278, 282,
283, 290, 291, 296, 300, 399, 417, 418, 432
quenching .................... 111, 126, 237, 238, 274, 402
spectroscopy ..................................................... 16, 106
Fluorescence detection system (FDS)................ 399, 400,
409, 411, 413, 415, 417
Fluorophore
Alexa 488................................................................. 178
Alexa 647................................................................. 236
488
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index