Ligand (cont.)
tri-N-acetylglucosamine (triNAG/NAG3) ............ 47,
52, 139
Light
scattering ............. 8, 9, 25, 101, 135, 232, 234, 242,
334, 416, 456, 460
stray light ................................................................. 461
Linear dichroism ........................................................... 450
Linearly polarized................................................. 234, 450
Lipid
bilayers ......................................................20, 451, 452
1,2-dimyristoyl-sn-glycero-3-phosphocholine
(DMPC)..................................... 450, 454, 455
dipalmitoylphosphatidylcholine
(DPPC) ............................................... 455, 456
monolayers .............................................................. 183
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
(POPC) ...................................... 452, 454, 455
1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine
(POPS)......................................................... 455
tethered bilayers ...................................................... 183
Liposome ...................185, 195, 450–452, 454, 456–462
Liposome degradation .................................................. 457
Local parameter............................................................... 51
Low angle light scattering (LALS) ............................9, 27
M
Mass spectrometers ................ 9, 30, 218, 220, 221, 228,
466, 467, 469, 470, 473, 475, 481, 482
Mass spectrometry (MS)
electrospray ionization (ESI)...............10–12, 29, 484
hydrogen-deuterium exchange mass spectrometry
(HDX-MS) ......................................... 465–484
intact mass .................................................... 12, 29–30
matrix-assisted laser desorption ionization
(MALDI) .................................... 10–12, 29–30
peptide fingerprint .....................................12, 13, 257
Mechanical events ......................................................... 304
Melting temperature (T m ) ...................16, 141, 201, 202,
206, 207, 213
Membrane proteins....................... 5, 7, 9, 20, 22, 28, 36,
37, 212, 466
Membranes ....................... 20, 43, 54, 60, 183, 187–189,
275, 392, 416, 449–454, 460, 465–467,
469–471, 477–479, 481
Michaelis–Menten equation ......................................... 295
Microscale thermophoresis (MST) .................... 161–181,
252, 323
Model
building.................................................. 438, 440, 443
completion...................................................... 438, 443
homology................................................................. 437
refinement....................................................... 438, 440
validation ........................................................ 438, 443
Monochromator.................. 53, 280, 294, 305, 309, 461
Multi-angle light scattering (MALS) ....... 9, 27, 382–394
Multilamellar vesicle ..................................................... 193
N
Nanolevers ....................................................342–344, 349
Noise ............. 9, 30–34, 62, 73, 77, 114, 115, 126, 135,
141, 151, 153, 157, 179, 194, 258, 285, 314,
336, 388, 389, 392, 393, 413, 454, 476
Non-linear regression .........................58, 62, 65, 70, 355
Nuclear magnetic resonance (NMR) .................... 83, 274
Carr-Purcell-Meiboom Gill (CPMG) .................... 266
13 C, 1 H correlation spectra ........................... 250, 268
1 H spectra ................................................................ 268
15 N, 1 H HSQC spectra ................249, 250, 257, 268
relaxation filtered experiments
(T1ρ, T2) ............................................ 250, 258
saturation transfer difference
(STD) ........................ 250, 253, 258, 261, 264
screening
chemical
shift
perturbation
(CSP) ........................ 249, 251, 252, 265, 268
compound mixture ........................................... 251
19 F observed ...................................................... 250
fragment library.........................................252–256
ligand-observed (LO-NMR) ...........248–252, 258
potent competitor ............................................. 261
protein-observed (PO-NMR) ......................... 249,
250, 258, 265
water-ligand observed gradient spectroscopy (waterLOGSY) ............250, 253, 256–258, 262–268
Nucleic acid
DNA ...........312, 378, 390, 394, 416, 428, 437, 438
RNA ............................ 312, 330, 360, 394, 428, 430,
437, 438, 440
topologically associating domain (TAD) ...... 118–120
Nucleotides............................4, 101, 156, 289–316, 361,
371, 376, 377, 398, 401, 403, 405, 406, 409,
411, 416
Numerical integration....................................96, 103, 419
O
Off-rate (k off )..............................136, 151, 250, 335, 349
On-rate (k on ) ................................................................. 335
Orthogonal assays ........................................................... 48
Oscillation............................................................. 184, 342
Oscillation frequency .................................................... 184
P
Passivation ....................................................195, 343–345
Peptide
membrane-inserting....................................... 449, 450
peptide backbone .................................................... 458
unfolded...........................................14, 449, 459, 462
Phase
490
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index
tri-N-acetylglucosamine (triNAG/NAG3) ............ 47,
52, 139
Light
scattering ............. 8, 9, 25, 101, 135, 232, 234, 242,
334, 416, 456, 460
stray light ................................................................. 461
Linear dichroism ........................................................... 450
Linearly polarized................................................. 234, 450
Lipid
bilayers ......................................................20, 451, 452
1,2-dimyristoyl-sn-glycero-3-phosphocholine
(DMPC)..................................... 450, 454, 455
dipalmitoylphosphatidylcholine
(DPPC) ............................................... 455, 456
monolayers .............................................................. 183
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
(POPC) ...................................... 452, 454, 455
1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine
(POPS)......................................................... 455
tethered bilayers ...................................................... 183
Liposome ...................185, 195, 450–452, 454, 456–462
Liposome degradation .................................................. 457
Local parameter............................................................... 51
Low angle light scattering (LALS) ............................9, 27
M
Mass spectrometers ................ 9, 30, 218, 220, 221, 228,
466, 467, 469, 470, 473, 475, 481, 482
Mass spectrometry (MS)
electrospray ionization (ESI)...............10–12, 29, 484
hydrogen-deuterium exchange mass spectrometry
(HDX-MS) ......................................... 465–484
intact mass .................................................... 12, 29–30
matrix-assisted laser desorption ionization
(MALDI) .................................... 10–12, 29–30
peptide fingerprint .....................................12, 13, 257
Mechanical events ......................................................... 304
Melting temperature (T m ) ...................16, 141, 201, 202,
206, 207, 213
Membrane proteins....................... 5, 7, 9, 20, 22, 28, 36,
37, 212, 466
Membranes ....................... 20, 43, 54, 60, 183, 187–189,
275, 392, 416, 449–454, 460, 465–467,
469–471, 477–479, 481
Michaelis–Menten equation ......................................... 295
Microscale thermophoresis (MST) .................... 161–181,
252, 323
Model
building.................................................. 438, 440, 443
completion...................................................... 438, 443
homology................................................................. 437
refinement....................................................... 438, 440
validation ........................................................ 438, 443
Monochromator.................. 53, 280, 294, 305, 309, 461
Multi-angle light scattering (MALS) ....... 9, 27, 382–394
Multilamellar vesicle ..................................................... 193
N
Nanolevers ....................................................342–344, 349
Noise ............. 9, 30–34, 62, 73, 77, 114, 115, 126, 135,
141, 151, 153, 157, 179, 194, 258, 285, 314,
336, 388, 389, 392, 393, 413, 454, 476
Non-linear regression .........................58, 62, 65, 70, 355
Nuclear magnetic resonance (NMR) .................... 83, 274
Carr-Purcell-Meiboom Gill (CPMG) .................... 266
13 C, 1 H correlation spectra ........................... 250, 268
1 H spectra ................................................................ 268
15 N, 1 H HSQC spectra ................249, 250, 257, 268
relaxation filtered experiments
(T1ρ, T2) ............................................ 250, 258
saturation transfer difference
(STD) ........................ 250, 253, 258, 261, 264
screening
chemical
shift
perturbation
(CSP) ........................ 249, 251, 252, 265, 268
compound mixture ........................................... 251
19 F observed ...................................................... 250
fragment library.........................................252–256
ligand-observed (LO-NMR) ...........248–252, 258
potent competitor ............................................. 261
protein-observed (PO-NMR) ......................... 249,
250, 258, 265
water-ligand observed gradient spectroscopy (waterLOGSY) ............250, 253, 256–258, 262–268
Nucleic acid
DNA ...........312, 378, 390, 394, 416, 428, 437, 438
RNA ............................ 312, 330, 360, 394, 428, 430,
437, 438, 440
topologically associating domain (TAD) ...... 118–120
Nucleotides............................4, 101, 156, 289–316, 361,
371, 376, 377, 398, 401, 403, 405, 406, 409,
411, 416
Numerical integration....................................96, 103, 419
O
Off-rate (k off )..............................136, 151, 250, 335, 349
On-rate (k on ) ................................................................. 335
Orthogonal assays ........................................................... 48
Oscillation............................................................. 184, 342
Oscillation frequency .................................................... 184
P
Passivation ....................................................195, 343–345
Peptide
membrane-inserting....................................... 449, 450
peptide backbone .................................................... 458
unfolded...........................................14, 449, 459, 462
Phase
490
PROTEIN-LIGAND INTERACTIONS: METHODS AND APPLICATIONS
Index