Fischer W.B. Viral Membrane Proteins: Structure, Function, and Drug Design
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DANA 259, 260
depth of insertion 73
Dipolar Waves 152
dissociation constant 272, 273, 274, 275,
277, 279
DMA {5-[N,N_-dimethyl]amiloride} 214–216
docking approach 188, 189, 199
DRM 119ff.
drug-binding site 189
drug design 200
dynamin 125
E1 glycoprotein 86
Ebola virus GP 84
E. coli 119, 123
endocytosis 10, 11, 12
endoplasmic reticulum (ER) 3, 4, 5, 7, 8, 9, 12
entry inhibitors 40, 41
envelope protein 35, 37
epitope 257, 259
essential dynamics 193
EsV-1 22
evolution 26
Ewald sums 198
exchange (fast, slow, intermediate) 277, 289
explicite proton transmport simulation 134
Filipin 121
Flaviviruses 216
fluorescence 273, 274, 275, 277
Fourier Transform Infrared Spectroscopy (FTIR) 91
fusion
coronavirus 53
glycoproteins 84
peptide 36, 84, 85
Gag protein 210, 214, 215
Glutathione-S-Transferase (GST) 211,
224, 225
glycoprotein(s) 233, 238, 240, 241, 270
glycoprotein NSP4 85
Goldman-Hodgkin Katz equation 209, 212
Golgi 12
Golgi apparatus 104
Gottschalk, Alfred 247
gramicidin A 190
Great Barrier Reef 257
GRID 259
Grotthuss mechanism 135
guanidinium group 193, 194
␣-helices 210, 228
haemagglutinin 102, 107, 248, 256, 263
haemocoel 10, 11, 12
hepatitis C 208
HCV, hepatitis C virus 86, 87, 189
heat shock protein 70 homolog 8
hedgehog protein 120
HEK293 cells 25
HeLa cells 214, 215
5-helix peptide 188
helical content 70
Herpesvirus saimiri 278
heterologous expression system 25
Hirst, George 247
his-tag 121
HIV-1 35, 147, 207–211, 214–216
HIV-1 gp41 35, 85, 87, 113, 120, 123, 124
HIV-1 gp120 35, 87
HIV-1 integrase 190
HIV-1 protease 187
HMA {5-[N,N_-hexamethylene]amiloride}
214–216
HMMTOP 4
hook-shaped conformation 69
human immunodeficiency virus 269
hydrophobicity
interfacial 122, 123
plot (Kyte and Doolittle) 123
tests 234
hygromycin B test 80, 82, 238
influenza virus 248–249
Type A 102–105, 107, 109, 131, 188, 207,
208, 215, 222, 223, 226–228, 248,
249, 259
Type B 102, 105, 107, 109, 199, 207–209,
222–228, 248, 259
insect transmission 10
internalization motif Yxx ⌽ 120, 123
intrinsic activity 102, 104
ion channel 86, 87, 207, 208
activity 154, 189, 238
cation-selectivity 240
selectivity 119
ionophore 114, 115
iminosugars 199
derivatives 87
inner helix 23
6K 207–209, 216–222
6K interfacial sequences 234
K
channel 22
function of 22
structure of 22
topology 22
KcsA 23
Kcv 21, 83
MA-1D 26
phycodnavirus 83
“30K” superfamily of movement proteins
Kim, Choung 261
KirBac1.1 23
Kyte-Doolittle hydrophaty index scales 235
288 Index
leafhoppers 11
Lentivirus lytic peptide 85
liposomes 114, 121
M1 protein 120ff
M2 83, 86, 96, 131, 188, 207, 208, 215,
222, 223, 226–228
activation pH 132
architecture 132
closed conformation 134, 136
conditional-lethal transgene 119
cytotoxicity 119, 120
E. coli-expressed 119, 121
gating mechanism 133, 134, 136, 142
H
96
helix tilt angle 132
heterologous expression 113, 119
insect cell-expressed 114, 121
low-pH gating 133
open conformation 139
orthomyxovirus 83
post-TM sequence 123
proton selectivity 133
roles in viral life cycle 132
shuttle mechansim 133
M2-TMP 132
helix rotational angle 133
helix tilt angle 133
main protease M
pro
187
membrane
-active protein 234
bodies 7
depolarization 26
destabilization 83, 84
fission (pinching off) 124f
microdomains 119f
oriented 178, 182
permeability 79, 80, 82, 84, 85, 86, 233, 234, 240
thickness 72
membrane fusion 35
coronavirus spikes 51–54
coiled-coils 53
syncytia 51
membrane potential, dissipation of 241, 242
molecular dynamics (MD) simulations 134, 188,
190, 192, 194, 186, 199
steered 198
molecular mechanics calculations 190
morphogenesis 120f
multistate empirical-valence bond (MS-EVB) 134
myristoyl 269
Na
/H
exchanger 197
Na
/Ca
2
exchanger 197
XIP region 124
NADH-dependent quinacrine fluorescence quenching
assay 227
NB 118, 199, 207–209, 222, 223, 225,
227, 228
neuraminidase 102, 107, 187, 188
neuraminidase
active site 254
antibody complexes 257, 258
antigenic properties 257
conserved amino acids 254
crystals 254
crystal structure 253, 263, 264
drug resistant mutants 262–265
epitope structure 257–259
escape mutants 257–259
function 255–259
haemagglutinating 255
heads 250, 251
inactive 255
inhibitors 259–262
monomer 254
mutants 256, 265
N1 to N9 subtypes 253, 257
polypeptide 252
rosettes 250
stalks 250, 252
stubbies 250, 251
tetramer 252, 253
NHR-CHR 36
nicotinic acetylcholine receptor 198
Ni-NTA chromatography 118
N-methyl-D-glucamine 115
NMR spectroscopy 147, 188
solid-state 177, 178, 181, 182, 184
studies 68
Noddy tern 257
non-cell-autonomously replicating proteins 8
N terminus 22, 24
1-octyl-ß-D-glucopyranoside 114
outer helix 23
p7
HCV 87, 189, 199, 208
flavivirus 83
p10, reovirus 83
p56
lcp
119
Palese, Peter 259
palmitate 124
palmitoylation 114, 120, 122
pandemic 265
paramyxovirus SH 83
PBV-1 21
peripheral raft binding 124, 125
peptide synthesis 178, 182
peptide T20 87
permeabilization 79, 82, 84,
phosphorylation 24
Picornavirus 2B and 3A 83
Index 289
PISA 151
PISEMA 151
plant cell wall 3, 10
plant rhabdoviruses 11
planthoppers 11
plant virus 21
plasmodesmata 3, 4, 5, 7, 8
plasmodiophorid 12
polyclonal antibodies 220, 226
pore
activity 241
helix 23
domain 22
module 22
principle component analysis 193
PRODRUG 190
pronase 252
propidium iodide 82
proteoliposomes 115
protonation state 66
proton selectivity 105, 115, 119
translocation assay 115
permeability, unitary 118
pyranine 113, 115
pyrazine ring 193, 194
QX-222, QX-314 198
raft targeting 113, 120
rafts 119f
rational drug design 199
relenza 259
relenza dimer 261
reovirus p10 83
residual dipolar coupling 152
reversal potential 209, 212, 219, 224–226, 232
rhabdovirus alpha 10p 83
rimantadine 199
rimantadine 117, 207, 249
root mean square deviation 193
ross river virus (RRV) 217
rotavirus VP7 85
SARS 187
SARS coronavirus 58, 59
Genetic variation 58
S. cerevisiae 119
secretory pathway 104
selectivity 25, 207–209, 213, 228
selectivity filter 22, 23
Sendai virus, F protein 120
SH3 domain 271, 278, 279, 280, 282
SH, paramixovirus 83
sialic acid 255, 259
sialidase 249
Sindbis virus (SV) 236
site-specific infrared dichroism (SSID) 91
SIV 123
six-helix bundle 38
slide helix 23
sodium dodecyl suplphate 251
solvation of the amino group 71
spectroscopy
CD 188, 189
FTIR 188, 189
NMR 188, 189
X-ray 197
sphingolipid 119
steered MD simulations 190
structural diffusion mechanism 134
structure 178, 184
of fusion peptides 67
of Vpu 155
symbionin 11
SV replicons 237, 240
tamiflu 261
T-cells 119
TGB 6, 7, 8
thrips 11, 12
2TM 22
TM, transmembrane 207–209, 218
TM1 23
TM2 23
TMHMM 4
TMPRED 4, 6, 7, 9, 11, 12, 14
topology 177, 183
TopPred 2, 4
trans 208, 209, 212–214, 219, 220,
224–227
transmembrane 270, 272, 273
transmembrane domain (TMD) 234
transmission by vectors 10
treehoppers 11
Trichoplusia ni 113, 121
triple gene block 6
Triton X-100 121
trypan blue 82
turret 22
uncoating 102–104, 107, 109
urine 197
valinomycin 114, 115
vesicles 213, 221, 227, 228
viral
entry 113
glycoproteins 84
maturation 113
replication 26
virion 102, 103, 107, 109
viroporin 79, 83, 84, 238, 242
inhibitors 79, 80, 82
290 Index
virus
budding 83, 84, 113, 122f, 125
morphology, filamentous 113, 125, 126
morphology, spherical 113, 125, 126
uncoating 118, 122
viruses
Abutilon mosaic virus 5, 12
African cassava mosaic virus 11
Alfalfa mosaic virus 5, 9
Allexivirus 7
Banana bunchy top virus 8
Barley yellow dwarf virus 10
Beet curly top virus 11
Beet necrotic yellow vein virus 12
Beet western yellows virus 10
Beet yellows virus 8
Begomovirus 5, 11
Benyvirus 7, 12
Brome mosaic virus 9
Bromoviridae 5, 9
Buchnera 11
Bymovirus 12
Capillovirus 5
Carlavirus 7
Carmovirus 7
Carnation Italian ringspot virus 9
Carnation mottle virus 7
Closterovirus 8
Comoviridae 5, 9
Comovirus 5, 9
Cowpea mosaic virus 5
Cymbidium ringspot virus 9
Dianthovirus 5
Fabavirus 9
Fiji disease virus 14
Foveavirus 7
Furovirus 5, 12
Geminiviridae 5, 8, 11, 12
Grapevine fanleaf virus 9
Grapevine virus A 5
Grapevine virus B 5
Luteoviridae
Hordeivirus 7
Idaeovirus 5
Luteoviridae 10, 14
Luteovirus,14
Maize streak virus 8
Marafivirus 11
Melon necrotic spot virus 7
Necrovirus 7
Nepovirus 9
viruses Contd.
Nilaparvarta lugens reovirus 14
Nucleorhabdovirus 5
Oat sterile dwarf virus 14
Peanut clump virus 10
Pecluvirus 7, 10
Phycodnaviridae 21
Pomovirus 7, 12
Potato leafroll virus 11
Potato virus A 10
Potexvirus 7
Potyviridae 10
Potyvirus 10
Rice black streaked dwarf virus 14
Rice dwarf virus 11
Rice ragged stunt virus 11
Sida golden mosaic virus 12
Southern cowpea mosaic virus 13
Tenuivirus 11
Tobacco etch virus 10
Tobacco mosaic virus (TMV) 5, 6, 8
Tobamovirus 5, 10
Tobravirus 5
Tomato bushy stunt virus 5, 9
Tomato mosaic virus 10
Tomato ringspot virus 9
Tomato spotted wilt virus 8, 11
Tomato yellow leaf curl Sardinia virus 12
Tombusviridae 5, 9
Tombusvirus 5, 9
Tospovirus 5, 8, 11
Trichovirus 5
Tymovirus 8
Umbravirus 5
virus
budding 234, 240, 241
particle release 154
release 177, 178
VLP (virus-like particles) 214, 215
voltage dependency 25
von Itzstein, Mark 259
Vpr 208, 210
Vpu 83, 85, 86, 96, 124, 147, 177ff, 188, 207–216
structure 167ff
phosphorylation 167ff
whiteflies 11, 12
Wu, Wen Yang 259
WW hydrophobicity scales 234
Xenopus oocytes 24, 25
Index 291