Polycystic Kidney Disease 2 (Pkd2) channel
SP cryo-EM reconstructions in A8-35 vs. NDs, 557
Polycystin
SP cryo-EM reconstruction in A8-35, 569
Polyethyleneglycol (PEG)
effect on solutions of bc 1 /A8-35 complexes, 438
Polyfructose, 169
Polymer mass and dispersity
calibrating SEC columns, 214–216
controlling the average size and dispersity, 218–222
determining the average mass and dispersity, 214
expressing the average mass and dispersity, 213–214
expression of the average degree
of polymerization, 217
how to limit the dispersity, 211
kinetics of conventional radical polymerization
and origin of dispersity, 216–217
origin of dispersity, 210
Polymer topology
how to control it, 222–225
Polystyrene beads
use for removing detergent from MP/detergent/APol
complexes, 253, 256, 312, 321
Polytopic integral MPs, 15
Poly-γ-glutamic acid, hydrophobized, 119
Porin (R. capsulatus), 8
TM structure, 18
Postsynaptic membrane, 36
Potassium channels, 8
PPy, see Polypyrrole
PreserveX™-QML, 152
Prestegard, J.H., 99
Privé, G.G., 120
Protein kinase C, 85
Protein microarrays, 592
Proteomics
use of A8-35, 644
Proteorhodopsin
dynamics in NDs, 114
Protocols
amphipol-assisted folding of MPs (Protocol 6.1),
354–356
APol-mediated immobilization of MPs for SPR
experiments (Protocol 13.1), 617–619
AUC analysis of MP/APol complexes (Protocol 9.1),
440–443
CFE of MPs in the presence of NAPols (Protocol 7.1),
375–376
crystallizing bc 1 /A8 35/detergent complexes
(Protocol 11.1), 523–524
determining the amount of MP-bound APol
(Protocol 5.2), 314–318
electrospray ionization-ion mobility spectrometrymass spectrometry (ESI-IM-MS) of MP/APol
complexes (Protocol 14.1), 648–654
preparation of MP/APol samples for SP cryo-EM
(Protocol 12.1), 579–583
SEC analysis of MP/APol complexes (Protocol 9.2),
444–446
synthesis of A8-35 (Protocol 4.1), 205–210
transferring a MP from APols to nanodiscs
(Protocol 5.3), 319–322
transferring MPs from detergents to APols
(Protocol 5.1), 311–314
PSE-C9-13, 83
chemical structure, 83
P-type ATPases, 44
Pucci, B., 130, 161, 165, 227, 476
Pullulane, 169
Pumps, 10
Purple membrane, 34, 411
absence of solubilization by A8-35, 261
delipidated, 287
delipidation by deoxycholate, 67
extraction of BR by SMA, 260
lipid content, 275
lipid-mediated association of BR trimers, 29
solubilization by OTG, 266, 411
Q
QENS, see Quasi-elastic neutron scattering
Quantum dots, APol-coated, 238
Quasi-elastic neutron scattering (QENS)
by A8-35 particles, 187–189
R
Radford, S.E., 636, 654
Radical polymerization
kinetics and origin of polymer dispersity, 216–217
RAFT, see Reversible addition-fragmentation chain
transfer polymerization (RAFT)
Raman scattering spectroscopies, 395
RC, see Photosynthetic reaction centers (RCs), bacterial
Redox potential
in various compartments, 59
Re-entrant loops, 19, 20, 48
Regulated passive diffusion, 8
Removing free APol from solutions of MP/APol
complexes, 257
Reps, α-, 289, 500, 605
Residence time of a detergent monomer in a micelle, 299
Resonance Raman spectroscopy (RRS), 395, 396
Respirasome, 22, 565
bound cardiolipin, 26
SP cryo-EM reconstruction in A8-35, 569
SP cryo-EM reconstructions in A8-35 vs.
digitonin, 557
SP cryo-EM studies, 562
structural role of lipids, 29
Respiration, 4, 10
Retinal, 10, 32
cofactor of BR, 33
cofactor of rhodopsin, 85
release upon BR denaturation, 34, 292, 334
separation from denatured bacterio-opsin, 292
uptake by APol-trapped bacterio-opsin, 289, 343
Retinol receptor, 280
Reverse micelles, 458
704
Index
SP cryo-EM reconstructions in A8-35 vs. NDs, 557
Polycystin
SP cryo-EM reconstruction in A8-35, 569
Polyethyleneglycol (PEG)
effect on solutions of bc 1 /A8-35 complexes, 438
Polyfructose, 169
Polymer mass and dispersity
calibrating SEC columns, 214–216
controlling the average size and dispersity, 218–222
determining the average mass and dispersity, 214
expressing the average mass and dispersity, 213–214
expression of the average degree
of polymerization, 217
how to limit the dispersity, 211
kinetics of conventional radical polymerization
and origin of dispersity, 216–217
origin of dispersity, 210
Polymer topology
how to control it, 222–225
Polystyrene beads
use for removing detergent from MP/detergent/APol
complexes, 253, 256, 312, 321
Polytopic integral MPs, 15
Poly-γ-glutamic acid, hydrophobized, 119
Porin (R. capsulatus), 8
TM structure, 18
Postsynaptic membrane, 36
Potassium channels, 8
PPy, see Polypyrrole
PreserveX™-QML, 152
Prestegard, J.H., 99
Privé, G.G., 120
Protein kinase C, 85
Protein microarrays, 592
Proteomics
use of A8-35, 644
Proteorhodopsin
dynamics in NDs, 114
Protocols
amphipol-assisted folding of MPs (Protocol 6.1),
354–356
APol-mediated immobilization of MPs for SPR
experiments (Protocol 13.1), 617–619
AUC analysis of MP/APol complexes (Protocol 9.1),
440–443
CFE of MPs in the presence of NAPols (Protocol 7.1),
375–376
crystallizing bc 1 /A8 35/detergent complexes
(Protocol 11.1), 523–524
determining the amount of MP-bound APol
(Protocol 5.2), 314–318
electrospray ionization-ion mobility spectrometrymass spectrometry (ESI-IM-MS) of MP/APol
complexes (Protocol 14.1), 648–654
preparation of MP/APol samples for SP cryo-EM
(Protocol 12.1), 579–583
SEC analysis of MP/APol complexes (Protocol 9.2),
444–446
synthesis of A8-35 (Protocol 4.1), 205–210
transferring a MP from APols to nanodiscs
(Protocol 5.3), 319–322
transferring MPs from detergents to APols
(Protocol 5.1), 311–314
PSE-C9-13, 83
chemical structure, 83
P-type ATPases, 44
Pucci, B., 130, 161, 165, 227, 476
Pullulane, 169
Pumps, 10
Purple membrane, 34, 411
absence of solubilization by A8-35, 261
delipidated, 287
delipidation by deoxycholate, 67
extraction of BR by SMA, 260
lipid content, 275
lipid-mediated association of BR trimers, 29
solubilization by OTG, 266, 411
Q
QENS, see Quasi-elastic neutron scattering
Quantum dots, APol-coated, 238
Quasi-elastic neutron scattering (QENS)
by A8-35 particles, 187–189
R
Radford, S.E., 636, 654
Radical polymerization
kinetics and origin of polymer dispersity, 216–217
RAFT, see Reversible addition-fragmentation chain
transfer polymerization (RAFT)
Raman scattering spectroscopies, 395
RC, see Photosynthetic reaction centers (RCs), bacterial
Redox potential
in various compartments, 59
Re-entrant loops, 19, 20, 48
Regulated passive diffusion, 8
Removing free APol from solutions of MP/APol
complexes, 257
Reps, α-, 289, 500, 605
Residence time of a detergent monomer in a micelle, 299
Resonance Raman spectroscopy (RRS), 395, 396
Respirasome, 22, 565
bound cardiolipin, 26
SP cryo-EM reconstruction in A8-35, 569
SP cryo-EM reconstructions in A8-35 vs.
digitonin, 557
SP cryo-EM studies, 562
structural role of lipids, 29
Respiration, 4, 10
Retinal, 10, 32
cofactor of BR, 33
cofactor of rhodopsin, 85
release upon BR denaturation, 34, 292, 334
separation from denatured bacterio-opsin, 292
uptake by APol-trapped bacterio-opsin, 289, 343
Retinol receptor, 280
Reverse micelles, 458
704
Index