Membrane proteins (cont.)
biosynthesis of outer membrane proteins, 49
bitopic integral MPs, 15
crystallization, 498–508
destabilization by detergents, 70–72, 76
detergent extraction, 65–68
detergent-induced conformational alterations, 80–81
detergent intrusion into MP structures, 79
engineering water-soluble versions, 88
extrinsic, 15
functional dynamics of TM regions, 32–47
functions, 8–12
integral ¼ intrinsic, 15
modes of association with the membrane, 13–15
monotopic integral MPs, 15
MP/detergent complexes, 68–69
overexpression (overview), 50–51
polytopic integral MPs, 15
posttranslational insertion, 48
protocol for APol-assisted folding (Protocol 6.1),
354–356
protocol for transfer from APol to NDs (Protocol 5.3),
319–322
protocol for transfer from detergent to APol (Protocol
5.1), 311–314
role of positive-inside rule in biosynthesis, 49
structure, 13–22
deposited in the Protein Data Bank, 13
of TM regions, 15–22
two-stage model of folding of α-helical MPs, 48, 50
Membrane protein/SMA complexes
SEC and EM characterization, 260
SV-AUC analysis, 425, 427
Membrane protein stabilization by APols
comparative studies, 294
Membrane protein structures
deposited in the Protein Data Bank, 499
Membrane scaffold proteins (MSPs), 107
variants, 107, 108
Metabolon, 261
MexB
as a target for αRep selection using BAPol, 605
as a target for αRep selection using BNAPol, 605
Mhp1
ESI-MS analyses of Mhp1/A8-35 complexes, 638
Micelles, 5, 62
shape and dynamics, 64
Michel, H., 13, 501, 604
Minard, P., 605
Mini-nanodiscs, 134
Mitochondria, 4, 6
cristae, 4
intermembrane space, 6
matrix, 6
Mitochondrial supercomplex B, see Respirasome
Mitochondrial uncoupler UCP2
detergent-induced conformational alteration, 80
Moiseenkova-Bell, V.Y., 555
Molecular crowding, 25
Molecular dynamics simulations of MP/APol
complexes, 303
MOMP, see Major outer membrane protein (MOMP)
from C. trachomatis
Mono-olein
chemical structure, 506
cubic phase, 506
phase diagram of the mono-olein/water system, 507
Monotopic integral MPs, 15
Motor nerve terminals, 8
MP, see Membrane proteins
MS, see Mass spectrometry
MS/MS, see Tandem mass spectrometry
MsbA
stabilization by octyl-grafted peptides, 119
MscL, see Mechanosensitive channel, large pore (E. coli)
(MscL)
Multidrug resistance pumps, 10
Muscle contraction, 10
N
Na
+ ,K
+ -ATPase, 10
inactivation by detergents, 76
inhibition by membrane-dissolved detergent, 67
nAChR, see Nicotinic acetylcholine receptor (nAChR)
NADH:ubiquinone oxidoreductase, see Complex I
NADPH-dependent cytochrome P450
oxidoreductase, 261
Nanodisc-based investigations of MPs
overview, 115, 116
Nanodisc-forming amphipathic peptides, 119
Nanodiscs (NDs), 134
alternatives to MSPs, 109
dynamics of trapped MPs, 112
empty, MD simulation, 109
empty, organization, 109
empty, state of the lipids, 110
empty, structure of MSPs, 110
as hosts for MP folding, 115
as hosts for MPs during CFE, 115
MP-containing, deformation, 113
MP-containing, lipid content, 112, 113
MP-containing, MD simulation, 113
MP-containing, overview, 111–115
MP-containing, preparation, 111
overview, 105
overview of applications, 115, 116
peptide-based, 127
preparation, 107
prospects for MP crystallization, 117
relative sizes of guest MP and ND, 112, 113
stabilization of trapped MPs, 112
transfer of ND-trapped BR to a lipidic
mesophase, 118
use to control MP lipid environment, 116
use to control MP oligomerization, 116
Nano-ESI, 626
Nanomaterials, use of APols in, 238
Naphthalene-labeled A8-75, 397
700
Index
biosynthesis of outer membrane proteins, 49
bitopic integral MPs, 15
crystallization, 498–508
destabilization by detergents, 70–72, 76
detergent extraction, 65–68
detergent-induced conformational alterations, 80–81
detergent intrusion into MP structures, 79
engineering water-soluble versions, 88
extrinsic, 15
functional dynamics of TM regions, 32–47
functions, 8–12
integral ¼ intrinsic, 15
modes of association with the membrane, 13–15
monotopic integral MPs, 15
MP/detergent complexes, 68–69
overexpression (overview), 50–51
polytopic integral MPs, 15
posttranslational insertion, 48
protocol for APol-assisted folding (Protocol 6.1),
354–356
protocol for transfer from APol to NDs (Protocol 5.3),
319–322
protocol for transfer from detergent to APol (Protocol
5.1), 311–314
role of positive-inside rule in biosynthesis, 49
structure, 13–22
deposited in the Protein Data Bank, 13
of TM regions, 15–22
two-stage model of folding of α-helical MPs, 48, 50
Membrane protein/SMA complexes
SEC and EM characterization, 260
SV-AUC analysis, 425, 427
Membrane protein stabilization by APols
comparative studies, 294
Membrane protein structures
deposited in the Protein Data Bank, 499
Membrane scaffold proteins (MSPs), 107
variants, 107, 108
Metabolon, 261
MexB
as a target for αRep selection using BAPol, 605
as a target for αRep selection using BNAPol, 605
Mhp1
ESI-MS analyses of Mhp1/A8-35 complexes, 638
Micelles, 5, 62
shape and dynamics, 64
Michel, H., 13, 501, 604
Minard, P., 605
Mini-nanodiscs, 134
Mitochondria, 4, 6
cristae, 4
intermembrane space, 6
matrix, 6
Mitochondrial supercomplex B, see Respirasome
Mitochondrial uncoupler UCP2
detergent-induced conformational alteration, 80
Moiseenkova-Bell, V.Y., 555
Molecular crowding, 25
Molecular dynamics simulations of MP/APol
complexes, 303
MOMP, see Major outer membrane protein (MOMP)
from C. trachomatis
Mono-olein
chemical structure, 506
cubic phase, 506
phase diagram of the mono-olein/water system, 507
Monotopic integral MPs, 15
Motor nerve terminals, 8
MP, see Membrane proteins
MS, see Mass spectrometry
MS/MS, see Tandem mass spectrometry
MsbA
stabilization by octyl-grafted peptides, 119
MscL, see Mechanosensitive channel, large pore (E. coli)
(MscL)
Multidrug resistance pumps, 10
Muscle contraction, 10
N
Na
+ ,K
+ -ATPase, 10
inactivation by detergents, 76
inhibition by membrane-dissolved detergent, 67
nAChR, see Nicotinic acetylcholine receptor (nAChR)
NADH:ubiquinone oxidoreductase, see Complex I
NADPH-dependent cytochrome P450
oxidoreductase, 261
Nanodisc-based investigations of MPs
overview, 115, 116
Nanodisc-forming amphipathic peptides, 119
Nanodiscs (NDs), 134
alternatives to MSPs, 109
dynamics of trapped MPs, 112
empty, MD simulation, 109
empty, organization, 109
empty, state of the lipids, 110
empty, structure of MSPs, 110
as hosts for MP folding, 115
as hosts for MPs during CFE, 115
MP-containing, deformation, 113
MP-containing, lipid content, 112, 113
MP-containing, MD simulation, 113
MP-containing, overview, 111–115
MP-containing, preparation, 111
overview, 105
overview of applications, 115, 116
peptide-based, 127
preparation, 107
prospects for MP crystallization, 117
relative sizes of guest MP and ND, 112, 113
stabilization of trapped MPs, 112
transfer of ND-trapped BR to a lipidic
mesophase, 118
use to control MP lipid environment, 116
use to control MP oligomerization, 116
Nano-ESI, 626
Nanomaterials, use of APols in, 238
Naphthalene-labeled A8-75, 397
700
Index