gel phase .................................................................. 449
transition........................................193, 449, 450, 456
Phenyl alanine ...................................................... 453, 458
Phosphate (Pi)...................................................... 289–315
release....................................................................... 298
binding..................................................................... 295
contamination ................................................ 292, 293
Pi biosensor ............................................................. 289
Pi mop ..................................................................... 293
release......................................................294, 303–311
Phosphate contamination ............................................. 293
Phosphatidylinositol (3,4,5)-triphosphate (PIP3) ...... 467
Photobleaching .........................109, 113, 117, 118, 169,
172, 179
Photomultiplier tube (PMT) ..................... 399, 418, 461
voltage...................................................................... 128
Polarization ............................... 111, 135, 231–245, 323,
450–453, 457, 459, 461, 462
Polarized light .......................................14, 232, 234, 450
Polyacrylamide gel electrophoresis (PAGE) ....... 325, 327
Coomassie Blue ..................................... 178, 325, 328
densitometry................................................... 328, 329
native PAGE ........................................................7, 332
Orange G .......................................324, 327, 332, 336
SDS-PAGE ..........................6, 23, 24, 257, 324, 403,
410, 414, 430
silver staining ............................................................. 42
Tris-glycine ................................................................ 24
Tris-tricine ................................................................. 24
Polymerase activity ............................................... 342, 398
Protein
alkaline phosphatase................................................ 312
avidin........................................................................ 185
bovine serum albumin (BSA) ..............................9, 21,
179, 358, 385, 409, 412, 415, 416
calmodulin (CaM)...............................................83, 88
CaM-dependent protein kinase I (CamKI) .......88, 96
carbonic anhydrase isoform II (CAII) .......... 165, 170
Chd1 ........................................................................ 298
chromodomain helicase DNA binding protein
(Chd1) ................................................ 295, 313
C-terminal domain of the Hendra virus nucleoprotein
(Ntail)........................................................... 119
α-chymotrypsin (α-CT) ................................. 163, 164
exopolyphosphatase (PPX1)................................... 312
Fe-S cluster complex (SufBC) ................................ 305
FUSE binding interacting repressor
(FIR) ................ 383, 385, 386, 390, 391, 394
heparin ............................................................ 186, 187
HIV-1 restriction factor.......................................... 311
human papilloma virus E7 (HPV E7) ................... 124
IGF2 mRNA-binding protein 1
(IMP1/ZBP1).................................... 360, 362
lysozyme
hen egg white (HEWL) ............ 47, 48, 66, 72–74
mouse double minute oncogene/E3 ubiquitin ligase
(MDM2) ...................................................... 121
neuromodulin (NMp) ........................................ 89–94
phosphatases ............................................................ 289
phosphohydrolases .................................................. 289
pleckstrin homology (PH) domain ........................ 466
prenyltransferases .................................................... 312
purine nucleoside phosphorylase
(PNPase) ............................................. 291, 294
pyrophosphatase (PPase) ........................................ 312
RNA-binding proteins (RBP) ...................... 423, 427,
431, 434, 440
RNases ......................... 330, 331, 425, 427, 430, 440
RT domain ............................................ 383, 390, 394
soybean trypsin inhibitor (SBTI) .................. 164, 170
streptavidin ....................................185, 187, 353, 369
SufBC.............................................................. 305–311
T4 polynucleotide kinase ........................................ 312
X domain (XD) ....................................................... 119
Protein concentration
absorbance ........................4, 31, 32, 36, 43, 140, 334
Bradford................................................................... 334
Protein Data Bank (PDB) ......................... 119, 291, 424,
429, 437, 439, 443, 449, 479
Proximity sensing ................................342, 344, 348, 349
Q
Quartz crystal microbalance......................................... 184
Quench flow .................................................305–307, 310
R
Radioactive label ........................................................... 325
Rapid mixing
continuous-flow ...................................................... 108
quenched-flow......................................................... 108
stopped-flow............................................................ 108
Rate
apparent .......................................................... 280, 286
exchange ................................................ 465, 466, 471
Rayleigh interference .................................................... 398
Reaction
endothermic ............................................................ 138
exothermic ............................................................... 138
first-order reaction ..............................................85, 86
second-order reaction ............................................. 281
Reference
biosensors .............................................. 352, 353, 358
flow cells ......................................................... 372, 377
layers ............................................................... 352, 353
samples........................ 14, 33, 38, 77, 261, 398, 399,
412, 472, 476
Refractive index increment (dn/dc) ...........................382,
390, 393, 394
Regeneration ............ 343, 345, 366, 370, 372, 373, 377
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index 491
transition........................................193, 449, 450, 456
Phenyl alanine ...................................................... 453, 458
Phosphate (Pi)...................................................... 289–315
release....................................................................... 298
binding..................................................................... 295
contamination ................................................ 292, 293
Pi biosensor ............................................................. 289
Pi mop ..................................................................... 293
release......................................................294, 303–311
Phosphate contamination ............................................. 293
Phosphatidylinositol (3,4,5)-triphosphate (PIP3) ...... 467
Photobleaching .........................109, 113, 117, 118, 169,
172, 179
Photomultiplier tube (PMT) ..................... 399, 418, 461
voltage...................................................................... 128
Polarization ............................... 111, 135, 231–245, 323,
450–453, 457, 459, 461, 462
Polarized light .......................................14, 232, 234, 450
Polyacrylamide gel electrophoresis (PAGE) ....... 325, 327
Coomassie Blue ..................................... 178, 325, 328
densitometry................................................... 328, 329
native PAGE ........................................................7, 332
Orange G .......................................324, 327, 332, 336
SDS-PAGE ..........................6, 23, 24, 257, 324, 403,
410, 414, 430
silver staining ............................................................. 42
Tris-glycine ................................................................ 24
Tris-tricine ................................................................. 24
Polymerase activity ............................................... 342, 398
Protein
alkaline phosphatase................................................ 312
avidin........................................................................ 185
bovine serum albumin (BSA) ..............................9, 21,
179, 358, 385, 409, 412, 415, 416
calmodulin (CaM)...............................................83, 88
CaM-dependent protein kinase I (CamKI) .......88, 96
carbonic anhydrase isoform II (CAII) .......... 165, 170
Chd1 ........................................................................ 298
chromodomain helicase DNA binding protein
(Chd1) ................................................ 295, 313
C-terminal domain of the Hendra virus nucleoprotein
(Ntail)........................................................... 119
α-chymotrypsin (α-CT) ................................. 163, 164
exopolyphosphatase (PPX1)................................... 312
Fe-S cluster complex (SufBC) ................................ 305
FUSE binding interacting repressor
(FIR) ................ 383, 385, 386, 390, 391, 394
heparin ............................................................ 186, 187
HIV-1 restriction factor.......................................... 311
human papilloma virus E7 (HPV E7) ................... 124
IGF2 mRNA-binding protein 1
(IMP1/ZBP1).................................... 360, 362
lysozyme
hen egg white (HEWL) ............ 47, 48, 66, 72–74
mouse double minute oncogene/E3 ubiquitin ligase
(MDM2) ...................................................... 121
neuromodulin (NMp) ........................................ 89–94
phosphatases ............................................................ 289
phosphohydrolases .................................................. 289
pleckstrin homology (PH) domain ........................ 466
prenyltransferases .................................................... 312
purine nucleoside phosphorylase
(PNPase) ............................................. 291, 294
pyrophosphatase (PPase) ........................................ 312
RNA-binding proteins (RBP) ...................... 423, 427,
431, 434, 440
RNases ......................... 330, 331, 425, 427, 430, 440
RT domain ............................................ 383, 390, 394
soybean trypsin inhibitor (SBTI) .................. 164, 170
streptavidin ....................................185, 187, 353, 369
SufBC.............................................................. 305–311
T4 polynucleotide kinase ........................................ 312
X domain (XD) ....................................................... 119
Protein concentration
absorbance ........................4, 31, 32, 36, 43, 140, 334
Bradford................................................................... 334
Protein Data Bank (PDB) ......................... 119, 291, 424,
429, 437, 439, 443, 449, 479
Proximity sensing ................................342, 344, 348, 349
Q
Quartz crystal microbalance......................................... 184
Quench flow .................................................305–307, 310
R
Radioactive label ........................................................... 325
Rapid mixing
continuous-flow ...................................................... 108
quenched-flow......................................................... 108
stopped-flow............................................................ 108
Rate
apparent .......................................................... 280, 286
exchange ................................................ 465, 466, 471
Rayleigh interference .................................................... 398
Reaction
endothermic ............................................................ 138
exothermic ............................................................... 138
first-order reaction ..............................................85, 86
second-order reaction ............................................. 281
Reference
biosensors .............................................. 352, 353, 358
flow cells ......................................................... 372, 377
layers ............................................................... 352, 353
samples........................ 14, 33, 38, 77, 261, 398, 399,
412, 472, 476
Refractive index increment (dn/dc) ...........................382,
390, 393, 394
Regeneration ............ 343, 345, 366, 370, 372, 373, 377
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index 491