248 index [link.springer.com]978-1-59259-266-1/1.pdf · index absorbance. see ... computations, 216...
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Index
Absorbance. see Ultraviolet-visiblespectroscopy
ADR, see Adrenodoxin reductaseAdrenodoxin reductase (ADR), circular
dichroism analysis, 120, 121Analogs, see Flavin analogs
B
Basis set, see Quantum chemicalcomputations
Bond order, quantum chemicalcomputations, 216
7a-Bromo-acetyl-10-methyl-isoallloxazine,
molecular maquette, concept, 195,196
peptide flavination,flavination reaction and product
isolation, 202-204materials, 197peptide synthesis, 200, 202
synthesis,7-acetyl-10-methyl-isoalloxazine
preparation, 198-200, 204bromination reaction, 200, 204,
2054-chtoro-3-nitro-acetophenone
preparation, 197, 1984-methylamino- 3 -nitro-
acetophenone preparation,198
materials, 196, 197, 204
CD, see Circular dichroism
Charge distribution, quantum chemicalcomputations, 216, 223—225
Circular dichroism (CD),adrenodoxin reductase, 120, 121data presentation and analysis, 115,
116electron transferring fiavoprotein,
119flavocytochrome P-450 BM3, 118,
119guidelines for successful
flavoprotein analysis, 121information available from
flavoprotein experiments, 112—115
instrumentation, 114, 115lipoamide dehydrogenase, 118, 120nitrate reductase, 120sample preparation, 115sensitivity and sample requirements,
116, 117theory, 111, 112
Computation, see Quantum chemicalcomputations
Covalent flavoproteins,catalysis of flavinylation, 181, 182identification of flavoproteins, 183,
1S9linkage analysis,
aminoacyl flavin isolation, 185,189, 190
6-S-cysteinyl flavin absorptionspectra, 186, 187
8a-5-cysteinyl riboilavins,fluorescence analysis, 188,190
247
248 Index
histidine-linked flavinfluorescence spectra, 187,190
mass spectrometry, 186materials, 182, 183peptide isolation, 184, 185, 189standards, 188, 189strategy, 184tyrosine-linked flavin,
absorption spectra, 187fluorescence spectra, 188, 190
linkage types, 181, 182Cysteine-linked flavins, see Covalent
flavoproteins
D
5-Deaza-5-carbafiavins, mechanismstudies of flavoenzymes,166-169
Disulfide reductase, see Lipoamidedehydrogenase
freeze quench studies, see Freezequench
theory, 99, 100Electron transferring flavoprotein
(ETF), circular dichroismanalysis, 119
Erythrocyte glutathione reductaseactivation coefficient (EGRAC),
chemotherapy patients, 237determination,
calculations, 232confounding factors, 235, 236materials, 230principle, 231,232
field studies, 235premature infants, 236
ESR, see Electron spin resonanceETF, see Electron transferring
flavoproteinExtinction coefficient see Ultraviolet-
visible spectroscopy
E
EGRAC, see Erythrocyte glutathionereductase activation coefficient
Electron spin resonance (ESR),flavin semiquinone analysis,
catalysis studies,catalytic competence of flavin
semiquinones, 107, 108semiquinone formation, 107
data acquisition, 101, 102g-factor, J03, 104glucose oxidase semiquinones,
102linewidth, 102, 103overview, 97-99quantitative analysis, 105sample preparation, 100, 101signal saturation, 105, 106
FAD, see Flavin adenine dinucleotideFlavin adenine dinucleotide (FAD),
affinity for flavoproteins, 149analogs in flavoprotein analysis,
advantages over other approaches,157,158
isoalloxazine ring systemaccessibility studies,
pyrazine ring, 162, 163pyrimidine ring, 1608-substituted flavins, 165, 166substitution sites in analogs,
160-162xylene ring, 163, 164
mechanistic probing,5-deaza-5-carbaftavins, 166-
1698-substituted flavins, 168, 169
oxidation-reduction potentials.
Index 249
Hammett s value correlation,172-174
mechanistic implications, 174,175
modification by proteininteractions, 169, 170,173, 174
pyrimidine substitutionsensitivity, 172, 173
values, 170-172rationale, 160
biosynthesis, 1chemical synthesis, 158, 159fluorescence assays,
apoflavodoxin quenching assay,35-37,41
fluorescence properties ofcofactors and fiavoproteins,overview, 26—28
pH-dependent assay, 38, 41,42phosphodiesterase-based assay,
calibration and linearity test,12,22
data acquisition, 12, 13, 22data analysis, 13—16denaturation of protein, 13—15materials, 10, 11principle, 11, 12
fluorescence properties of cofactorand flavoproteins, overview,26-28
forms in catalysis, 207, 208identification and quantification in
flavoproteins,high-performance liquid
chromatography assay,calibration curve construction,
20data analysis, 20, 22principle, 18, 20sample preparation, 20
materials, 10,11overview, 9, 10
ultraviolet-visible spectroscopyassay,
heat denaturation, 17, 22iron-sulfur flavoproteins, 18phosphodiesterase treatment,
17sodium dodecyisulfate
treatment of simpleflavoproteins, 16, 17, 22
redox potential, 49, 50removal from flavoproteins,
overview of techniques, 149semiquinone properties, 97, 98structure, 139, 140, 159
Flavin analogs, see also 7a-Bromo-acetyl-10-methyl-isoallloxazine,
advantages over other flavoproteinanalysis approaches, 157, 158
isoalloxazine ring systemaccessibility studies,
pyrazine ring, 162, 163pyrimidine ring, 1608-substituted flavins, 165, 166substitution sites in analogs. 160—
162xylene ring, 163, 164
mechanistic probing,5-deaza-5-carbaflavins, 166-169^substituted flavins, 168, 169
oxidation-reduction potentials,Hammett s value correlation,
172—174mechanistic implications, 174,
175modification by protein
interactions, 169, 170, 173,174
pyrimidine substitutionsensitivity, 172,173
values, 170-172rationale for flavoprotein analysis,
160Flavin mononucleotide (FMN),
250 Index
affinity for flavoproteins, 149, 150analogs in flavoprotein analysis,
advantages over other approaches,157, 158
rationale,160
isoalloxazine ring systemaccessibility studies,
pyrazine ring, 162, 163pyrimidine ring, 3608-substituted flavins, 165, 166substitution sites in analogs,
160-162xylene ring, 163, 164
mechanistic probing,5-deaza-5-carbaflavins, 166—
1698-substituted flavins, 168, 169
oxidation-reduction potentials,Hammett a value correlation,
172-174mechanistic implications, 174,
175modification by protein
interactions, 169, 170,173,174
pyrimidine substitutionsensitivity, 172, 173
values, 170-172biosynthesis, 1chemical synthesis, 158, 159fluorescence assays,
apoflavodoxin quenching assay,35-41
fluorescence properties ofcofactors and flavoproteins,overview, 26-28
pH-dependent assay, 38, 41,42pb osp hod iesterase-based assay,
calibration and linearity test,12,22
data acquisition, 12, 13, 22data analysis, 13-16
denaturation of protein, 13—15materials, 10,11principle, 11,12
forms in catalysis, 207, 208identification and quantification in
flavoproteins,high-performance liquid
chromatography assay,calibration curve construction,
20data analysis, 20, 22principle, 18, 20sample preparation, 20
materials, 10,11overview, 9,10ultraviolet-visible spectroscopy
assay,heat denaturation, 17,22iron-sulfur flavoproteins, 18phosphodiesterase treatment,
17sodium dodecylsulfate
treatment of simpleflavoproteins, 16, 17,22j
reconstitution in flavoproteins,apoenzyme stability, 152, 153flavin incubation, 152, 154materials, 151yield determination, 152—154
retiox potential, 49, 50removal from flavoproteins,
materials, 150, 151overview of techniques, 149, 150pheny) Sepbarose
chromatography, 151—153semiquinone properties, 97, 98structure, 139, 140, 159
Flavocytochrome b2
dissociation constants for flavinmononucleotide, 150
flavin moTionucleotidereconstitution,
Index 251
apoenzyme stability, 152, 153flavin incubation, 152, 154materials, 151yield determination, 152-154
flavin monoiiucleotide removal,materials, 150, 151overview of techniques, 149, 150phenyl Sepharose
chromatography, 151-153freeze quench studies, 88
Flavocytochrome P-450 BM3circular dichroism analysis, 118, 119Raman spectroscopy, 134, 135
Flavoprotein mono oxygen a ses, see also/5-Hydroxyben^oate hydroxylase,
classification, 67general reaction, 67quantum mechanical calculations of
nudeophilic reactivity andactivation barriers, 220, 221,223
Flavoprotein oxidases, see alsoVanillyl-alcohol oxidase,
general reaction, 63half-reactions, 64, 65rate-limiting step, 63
Fluorescence spectroscopy,cuvets, 29denaturation studies of flavoproteins,
32-34emission spectra, collection for
flavoproteins, 31, 32,41,43excitation spectra, collection for
flavoproteins, 29-31,41, 43,44
flavin cofactor identification andquantification,
apoflavodoxin quenching assay,35-37,41
fluorescence properties ofcofactors and flavoproteins,overview, 26—28
pH-deptmdent assay, 38,41, 42
phosphodiesterase-based assay,calibration and linearity test,
12, 22data acquisition, 12, 13, 22data analysis, 13-16denaturation of protein, 13—15materials, 10, IIprinciple, 11, 12
inner filter effect, 43instrumentation, 28, 29, 44lifetimes, 26, 39,42linkage identification in covalent
flavoproteins,8a-S-cysteinylriboflavins, 188,
190standards, 188, 189tyrosine-linked flavins, 188, 190
polarization of flavin fluorescence,39,42
quantum yield, 26quenching studies of flavoproteins,
39,40, 42reduced flavoproteins, 40, 41renaturation studies of flavoproteins,
32, 34, 35reproducibility, 44temperature sensitivity, 43,44theory, 25, 26
FMN, see Flavin mononueleotideFreeze quench,
aging and spraying into cold solvent,91,92
flavocytochrome b2, 88materials and apparatus, 89-91, 93nonflavin enzymes, 88, 89principles, 87, 88ram control, 90spectroscopic analysis, 87-89stopping the reaction, 92temperature control, 90temperature dependence of electron
transfer reactions,92,93
252 index
g-Factor, see Electron spin resonanceGeometry, optimization with quantum
chemical computations, 216, 218,219
Glucose oxidase, electron spinresonance of flavin semiquinones,102
Glucose-6-phosphate dehydrogenasedeficiency, erythrocyteglutathione reductase activationcoefficient in patients, 235
Glutathione reductase (GR),erythrocyte glutathione reductase
activation coefficientdetermination,
calculations, 232confounding factors, 235, 236materials, 230principle, 231, 232
nitric oxide donor modification,applications, 240crystallization of modified
protein, 234, 239, 240materials, 230physiological significance, 239,
240reaction conditions, 233
reversible denaturation assay fordrug testing,
denaturadon reaction, 234materials, 230, 231peptidomimetic inhibitors, 240,
241rationale, 234, 240renaturation and assay, 234, 235
GR, see Glutathione reductase
H
Hammett s value, oxidation-reductionpotential correlation, 172—174
Heat of formation, quantum chemicalcomputations, 216
High-performance liquidchromatography (HPLC), flavincofactor identification andquantification,
calibration curve construction, 20data analysis, 20, 22materials, 10, 11principle, 18,20sample preparation, 20
Highest occupied molecular orbital(HOMO), quantum chemicalcomputations,
nucleophilic reactivity and activationbarriers in flavoproteinmonooxygenases, 220, 221,223
orbital energy and distribution, 216Histidine-linked flavins, see Covalent
flavoproteinsHOMO, see Highest occupied
molecular orbitalHPLC, see High-performance liquid
chromatography^-Hydroxybenzoate hydroxylase
(PHBH),activity assay and steady-state
kinetics, 68, 70,77,78,81quantum chemical computation,
nucleophilic reactivity andactivation barriers, 220, 221,223
reaction catalyzed, 68substrate specificity, 68transient kinetic studies,
overview, 68-70oxidative half-reaction, 79-81reductive half-reaction, 78, 79, 81
Hypothyroidism, diagnosis witherythrocyte glutathione reductaseactivation coefficient, 236
Index 253
l
Infrared spectroscopy, protein studies,126
Inner filter effect, fluorescence,43
Lipoamide dehydrogenase,absorbance spectroscopy, 63activity assays,
materials, 70, 80overview, 62standard assay, 71steady-state kinetics, 71, 72, 80
circular dichroism analysis, 118, 120reaction catalyzed, 62transient kinetic studies,
NADH reduction of oxidizedenzyme, 73, 74, 80
overview, 62, 63, 74oxidative half-react ion, 73, 80reductive half-reaction, 72, 73, 80
Lowest unoccupied moJecular orbital(LUMO),
oxidation-reduction potential, lineardependence of energy, 172
quantum chemical computations,charge effects, 223, 224nucleophilic reactivity and
activation barriers inflavo proteinmonooxygenases, 220,221,223
orbital energy and distribution,216
redox potential calculation foTsubstituted flavins, 220, 221
LUMO, see Lowest unoccupiedmolecular orbital
M
Molecular maquette,
definition, 195flavin analog for synthesis, see 7a-
Bromo-acety i -10-methyl-isoalloxazine,
flavin binding site design,195, 196
N
Nitrate reductase, circular dichroismanalysis, 120
Nitric oxide (NO), modification ofglutathione reductase,
applications, 240crystallization of modified protein,
234,239, 240materials, 230physiological significance, 239, 240reaction conditions, 233
NMR, see Nuclear magnetic resonanceNO, see Nitric oxideNuciear magnetic resonance (NMR),
instrumentation, 142isotope enrichment, 144one-dimensional experiments, 142,
143paramagnetic effects, 140, 141, 146phosphorous-31 resonance
experiments, 144pTOtoi) resonance experiments, 143,
144sample preparation, 139-142sensitivity and sample requirements,
139, 140, 144shimming/field homogeneity/peak
overlap, 145three-dimensional experiments, 142,
143tubes, 145
OOxidation-reduction potential,
flavin analogs,
254 Index
Hammctt o value correlation.172-174
mechanistic implications,174,175
modification by proteininteractions, 169,170,173,174
pyrimidine substitutionsensitivity, 172, 173
values, 170-172flavin cofactors, 49, 50flavoproteins,
factors affecting redox values, 50,98,99
measurement techniques,overview, 50, 51
spectreiectrochemicalmeasurement,
assembly of apparatus, 57cuvet preparation, 56, 58data acquisition and analysis,
57, 58materials, 52, 54—56overview, 51, 52sodium dithionite preparation,
56, 57lowest unoccupied molecular orbital,
linear dependence, 172reference solutions in measurement,
49,51
PDE, see PhosphodiesterasePeptide flavination, see 7a-Bromo-
acetyl-10-methyl-isoallloxazinePHBH, see p-Hydroxybenzoate
hydro xylasePhosphodiesterase (PDE), assays for
flavin cofactor identification,fluorescence,
11-16ultraviolet-visible spectroscopy, 17,
18
Photochemical reduction, seeUltraviolet-visible spectroscopy
Polarization, see Fluorescencespectroscopy
Presteady-state kinetics, see Freezequench; Stopped-flowspectroscopy
Protein-energy malnutrition, effect onerythrocyte ghitathione reductaseactivation coefficient, 235, 236
Quantum chemical computations,ab initio methods, 209, 210, 213,
214,218,225,226failures and troubleshooting, 217,
218geometry, optimization, 216, 218,
219hardware, 209, 210nucleophilic reactivity and activation
barriers in flavoproteinmonooxygenases, 220, 221,223
redox potential calculation forsubstituted flavins, 220, 221
software, 207-209steps in analysis,
calculation model selectionfactors,
basis sets, 214, 215,226charge of system, 211, 212,
224, 225, 227computation time, 214, 215environmental effects, 212,
213initial geometry, 211quantum mechanical method,
213,214,225,226output parameters, defining and
selection, 215,216
Index 255
running of job, 217starting geometry, defining, 210,
211validation and analysis, 217, 227
R
Raman spectroscopy,applications, 125fluorescence quenching, 135interpretation of flavoprotein
spectra, 132-135resonance Raman spectroscopy,
data acquisition, 128materials, 126, 127sample preparation, 128
semiquinone formation for studies,127,128, 131, 132
surface enhanced resonance Ramanscattering,
coIJoidal silver preparation, 127,129-131,135,136
materials, 127sample preparation, 127, 131
theory, 126Rapid-reaction kinetics, see Freeze
quench; Stopped-flowspectroscopy
Redox potential, see Oxidation-reduction potential
Riboflavin,clinical interventions,deficiency correction, 237
disease treatment and prevention,237, 238
medication compliancemonitoring with high doses,238
precautions with riboflavinsolutions, 233
premature infants, 236tissue glue application, 238
deficiency monitoring, seeErythrocyte glutathionereductase activation coefficient
Riboflavin,redox potential, 49, 50structure, 1, 2, 139, 140,159
s, see Hammett cr valueSemiquinone,
electron spin resonance analysis,catalysis studies,
catalytic competence of flavinsemiquinones, 107, 108
semiquinone formation, 107g-factor, 103, 104glucose oxidase semiquinones,
102linewidth, 102, 103overview, 97-99quantitative analysis, 105sample preparation, 100, 101signal saturation, 105, 106
formation for Raman spectroscopystudies, 127, 128,131, 132
properties, overview, 97, 98ultraviolet-visible spectroscopy, 3,
98SERRS, see Surface enhanced
resonance Raman scatteringSpin distribution, quantum chemical
computations, 216Stopped-flow spectroscopy,
lipoamide dehydrogenase,NADH reduction of oxidized
enzyme, 73, 74, 80overview, 62, 63, 74oxidative half-reaction, 73, 80reductive half-reaction, 72, 73, 80
/j-hydroxybenzoatc hydroxylase,overview, 68—70oxidative half-reaction, 79-81
256 Index
reductive half-reaction, 78, 79, 81vanillyl-alcohol oxidase,
oxidative ha if-reaction, 76, 77, 81reductive half-reaction, 66, 67,
75,76,80,81Surface enhanced resonance Raman
scattering (SERRS), see Ramanspectroscopy
Thioredoxin reductase (TrxR),reversible denaturation assay fordrug testing,
denaturation reaction, 234materials, 230, 231peptidomhnetic inhibitors, 240, 241rationale, 234, 240renaturation and assay, 234, 235
Transient kinetics, see Freeze quench;Stopped-flow spectroscopy
TrxR, see Thioredoxin reductaseTyrosine-iinked flavins, see Covalent
flavoproteins
Ultraviolet-visible spectroscopy, seealso Stopped-flow spectroscopy,
applications with flavoproteins,overview, 3, 4
extinction coefficient, determinationfor flavins,
calculations, 5materials, 4precipitation of protein!! 5, 6
flavin analog accessibility s udies inflavoproteins, 165, 166
flavin cofactor identification ,mdquantification,
heat denaturation, 17, 22iron-suifur flavoproteins, 18materials, 10, 11phosphodiesterase treatment, 17sodium dodecylsulfate treatment
of simple flavoproteins, 16,17,22
flavin semiquinones, 3, 98hydroquinorte versus semiquinone
flavins, 3linkage identification in covalent
flavoproteins,6-5-cysteinyl flavins, 186, 187tyrosine-iinked flavins, 187
oxidized versus reduced flavincofactors, 1,2,4,27,28
photochemical reduction offlavoproteins,
catalysts, 6irradiation of sample, 5, 6materials, 5overview, 4
Vanillyi-alcohol oxidase,assay and steady-state kinetic
analysis, 74, 75rate-limiting step, 64, 65, 67reaction catalyzed, 65structure, 65transient kinetic studies,
oxidative half-reaction, 76,77,81
reductive half-reaction, 66, 67,75,76,80,81
Vibrational spectroscopy, see Infraredspectroscopy;
Raman spectroscopyVinca alkyloids, riboflavin inactivation,
229,233