Response times ................32, 43, 86, 290, 292, 312, 457
Ribosomes ....................................................304, 341–349
RNA–protein interaction ....................352, 424, 426–433
S
Sample
batch to batch consistency....................................3, 20
flash-freezing ............................................................. 19
homogeneity..................................3, 7, 8, 19, 26, 267
lyophilization ............................................................. 19
qualities.....................................................73, 266, 432
storage conditions .................................................4, 16
Scan
emission scans................................................. 277, 282
Screening
19F observed........................................................... 251
Second virial coefficient (A2) ....................................... 382
Sedimentation
sedimentation coefficients .............................. 76, 398,
405–408, 413, 415, 419
sedimentation velocity 397, 398, 403, 405, 406, 408,
411, 412, 418
Signal-to-noise ratio.................................... 173, 274, 413
Single-stranded DNA-binding protein ........................ 398
Software
ASTRA................................................... 388, 390, 391
crystallographic ....................................................... 443
GraphPad Prism .................................... 294, 329, 478
GUSSI.................................................... 165, 177, 410
ImageJ...................................................................... 329
MARS ............................................................. 294, 314
Microsoft Excel ....................................................... 294
Rcrane ...................................................................... 440
RNA 3D MOTIF ATLAS ...................................... 426
SEDFIT ................................................................... 410
SEDPHAT............................................................... 410
Solvation .........................................................49, 149, 156
Spectrometer
wavelengths ................................................21, 31, 454
Spectroscopy
absorbance spectroscopy....................... 4, 41, 48, 144
circular dichroism (CD) spectroscopy ..................... 12
linear dichroism (LD) spectroscopy....................... 450
UV spectroscopy
absorbance ................................... 5, 410, 454, 458
extinction coefficients ......................365, 410, 411
tryptophan ........................................................... 48
Stoichiometry ..............................8, 55, 59, 74, 136, 143,
144, 148, 245, 321, 329, 330, 374, 378, 386,
390, 397
Stopped-flow ........... 106, 108, 109, 119, 127, 292–294,
304–306, 309, 310, 314, 315
Structure
phase problem ......................................................... 437
Supershift assays ................................................... 323, 329
Surface plasmon resonance (SPR)...............................135,
153, 186, 274
sensor chip ............................................................... 432
Surfaces .......................20, 37, 48–50, 53, 61, 67–71, 74,
108, 149, 150, 153, 168, 179, 183, 185, 191,
195, 224, 332, 352, 366, 398, 402, 415, 466
T
Ternary complexes ...................................... 202, 357, 359
Test compounds ........................203, 206, 222, 227, 238,
240, 241, 243, 244
Thermal shift assay (TSA).......................... 49, 53, 55–56,
71, 72, 201, 202, 213
Thermal stabilisation..................................................... 202
Thermodynamics........................... 15, 16, 18, 34, 35, 39,
83, 355, 360, 361
Thermostability .............................. 16, 19, 33, 35, 38, 40
Titration curve .............................................................. 283
Titrations ................................ 92, 93, 96, 110, 120, 238,
249, 259, 264, 278, 283, 285, 286, 329, 337,
402, 405–408
Tool compounds ........................................ 202–204, 209,
210, 212–214, 243, 255, 258–260
Total ion current (TIC) ....................................... 475, 483
Transition states .......................................... 110, 125, 126
Triphosphates .................... 274, 275, 293, 297, 304, 312
Tryptophan.......................... 4, 36, 49, 73, 305, 334, 453
Turnover
multiple.................................................................... 295
single ...................................................... 232, 310, 311
Tyrosine ....................................................... 4, 49, 73, 453
U
Unimolecular processes .................................................. 85
V
Vesicle
small unilamellar (SUV) ......................................... 455
unilamellar ............................................................... 193
Viscoelasticity/viscoelastic............................................ 184
heparin ..................................................................... 186
modeling.................................................................. 190
Viscosity........................................................................... 97
W
Western blotting..................................................... 43, 323
X
X-ray crystallography ..................... 48, 83, 252, 264, 341
Z
Zimm plot ..................................................................... 382
492
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index
Ribosomes ....................................................304, 341–349
RNA–protein interaction ....................352, 424, 426–433
S
Sample
batch to batch consistency....................................3, 20
flash-freezing ............................................................. 19
homogeneity..................................3, 7, 8, 19, 26, 267
lyophilization ............................................................. 19
qualities.....................................................73, 266, 432
storage conditions .................................................4, 16
Scan
emission scans................................................. 277, 282
Screening
19F observed........................................................... 251
Second virial coefficient (A2) ....................................... 382
Sedimentation
sedimentation coefficients .............................. 76, 398,
405–408, 413, 415, 419
sedimentation velocity 397, 398, 403, 405, 406, 408,
411, 412, 418
Signal-to-noise ratio.................................... 173, 274, 413
Single-stranded DNA-binding protein ........................ 398
Software
ASTRA................................................... 388, 390, 391
crystallographic ....................................................... 443
GraphPad Prism .................................... 294, 329, 478
GUSSI.................................................... 165, 177, 410
ImageJ...................................................................... 329
MARS ............................................................. 294, 314
Microsoft Excel ....................................................... 294
Rcrane ...................................................................... 440
RNA 3D MOTIF ATLAS ...................................... 426
SEDFIT ................................................................... 410
SEDPHAT............................................................... 410
Solvation .........................................................49, 149, 156
Spectrometer
wavelengths ................................................21, 31, 454
Spectroscopy
absorbance spectroscopy....................... 4, 41, 48, 144
circular dichroism (CD) spectroscopy ..................... 12
linear dichroism (LD) spectroscopy....................... 450
UV spectroscopy
absorbance ................................... 5, 410, 454, 458
extinction coefficients ......................365, 410, 411
tryptophan ........................................................... 48
Stoichiometry ..............................8, 55, 59, 74, 136, 143,
144, 148, 245, 321, 329, 330, 374, 378, 386,
390, 397
Stopped-flow ........... 106, 108, 109, 119, 127, 292–294,
304–306, 309, 310, 314, 315
Structure
phase problem ......................................................... 437
Supershift assays ................................................... 323, 329
Surface plasmon resonance (SPR)...............................135,
153, 186, 274
sensor chip ............................................................... 432
Surfaces .......................20, 37, 48–50, 53, 61, 67–71, 74,
108, 149, 150, 153, 168, 179, 183, 185, 191,
195, 224, 332, 352, 366, 398, 402, 415, 466
T
Ternary complexes ...................................... 202, 357, 359
Test compounds ........................203, 206, 222, 227, 238,
240, 241, 243, 244
Thermal shift assay (TSA).......................... 49, 53, 55–56,
71, 72, 201, 202, 213
Thermal stabilisation..................................................... 202
Thermodynamics........................... 15, 16, 18, 34, 35, 39,
83, 355, 360, 361
Thermostability .............................. 16, 19, 33, 35, 38, 40
Titration curve .............................................................. 283
Titrations ................................ 92, 93, 96, 110, 120, 238,
249, 259, 264, 278, 283, 285, 286, 329, 337,
402, 405–408
Tool compounds ........................................ 202–204, 209,
210, 212–214, 243, 255, 258–260
Total ion current (TIC) ....................................... 475, 483
Transition states .......................................... 110, 125, 126
Triphosphates .................... 274, 275, 293, 297, 304, 312
Tryptophan.......................... 4, 36, 49, 73, 305, 334, 453
Turnover
multiple.................................................................... 295
single ...................................................... 232, 310, 311
Tyrosine ....................................................... 4, 49, 73, 453
U
Unimolecular processes .................................................. 85
V
Vesicle
small unilamellar (SUV) ......................................... 455
unilamellar ............................................................... 193
Viscoelasticity/viscoelastic............................................ 184
heparin ..................................................................... 186
modeling.................................................................. 190
Viscosity........................................................................... 97
W
Western blotting..................................................... 43, 323
X
X-ray crystallography ..................... 48, 83, 252, 264, 341
Z
Zimm plot ..................................................................... 382
492
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index
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