Index. deuterium oxide as a solvent, 140, 152 isotope exchange induced shifts, 152 secondary structure contributions, 140 Amino acid analysis,

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1 Index A Absorbance, 93 problems with measurement, 95 relation to optical density, 93 Accessible surface area, 13, 14, 17, 23 apolar hydrogen, 24 correlations, 14 hydrogen bond, 25 renormalization, 25 Activation energy, see Protein folding and unfolding Aggregation, 150, 151 Amide I absorption region of peptide bonds, amino acid side change contributions, 139, 140 deuterium oxide as a solvent, 137, 142, 148, 152 isotope exchange induced shifts, 152 isotope replacement induced shifts, 150 protein spectra as examples, 145, 146 hepatitis B surface antigen, 146 IgG monoclonal antibody, 146 Pseudomonas exotoxin, 146 secondary structure assignments, 138, 139 trifluoroacetate interference, 149 water interference, 148, 149 Amide II absorption region of peptide bonds, 138, 140 deuterium oxide as a solvent, 140, 152 isotope exchange induced shifts, 152 secondary structure contributions, 140 Amino acid analysis, B Beer-Lambert law, 93 deviations from, 93 first derivative of, 98 C Carbamylation of protein amino groups, effects on protein stability, 56, 57 alpha crystallin, 56 mechanism, 56 isocynate ion, 56 urea, 56 Chain entropy, 15, 16 Chaperones, 357, Chaperonin(s), Chemical modification amino groups, by cyanate, 56, 117, 178 Chromatography, see Ion exchange and HPLC Circular dichroism (CD), 115 kinetics, 118 stopped-flow, 80, 115, 356 Cold denaturation, see Denaturation, by cold Configurational entropy, 3, 4, 8, 16, 18,

2 370 Index amino acid composition, 4 Conformational entropy, 177 Conformational phase diagrams, 351 Conformational stability, 177 Co-solvents, 253 classes, 253 destabilizers, 253 reference states, 254 solvents of given composition, 254, 262, 263 water, 259, 261 stabilization/destabilization by, 261 stabilizers, 253 Cyclic dipeptides, 12, 19 dissolution, 19 hydrogen bonding, 19 van der Waals interactions, 19 Cystine destruction, beta elimination mechanism, 45, 46 dehydroalanine formation, 45, 46 lysinoalanine formation, 45, 46 insulin, 46 kinetics of reaction, 45, 46 Cysteine residues, alkylation, see Thiol groups, trapping counting, 223 destruction, see Cysteine destruction oxidation, see Oxidation of cysteine residues reactivity, see Thiol groups, reactivity D Deamidation of asparagine residues, detection methods, capillary zone electrophoresis, 41 isoelectric focusing, 40, 58, 59 mass spectroscopy, 41 effects on protein refolding, 40 effects on protein stability, 39, 40 hirudin, 41 human growth hormone, 41 ribonuclease A, 39, 40 intramolecular mechanism, 38, 39 isoaspartate, succinimide, tertiary structure effects, 39 kinetics of reaction, Degrees of freedom rotors, 29 translational, 16 Denaturation, see also Protein folding and unfolding by cold, ,213 by guanidine hydrochloride, 117, , 344 by heat, ,213,281 reversibility, influence of chaperones, 361 problems caused by free sulfhydryls, 182 by urea, 117, , 263, 281, 344 Denaturation curves, urea and guanidine hydrochloride, 72, 115, 183 analysis of, determination of, 183, 184, 263 Differential scanning calorimetry (DSC), 6, cell compartment, 192 information gained from, 191 measurement, baseline determination, 198 experimental design, 193 sample preparation, 193 two-dimensional DSC, apo-myoglobin, 212 protonation effects, 212 ribonuclease A, 213 Disulfide bonds,

3 Index 371 counting, 223, 225, 227, 247 formation and breakage, 220, 221, ,238, 239, 245,246 identifying, 222, 227 in protein folding, 219, 221,229, 239 in protein stability, 219, 222, 229, 237, 238 kinetic analysis of formation and breakage intermolecular reagents, , 234, 235 interpretation, 223, , 239 methods, mixed-disulfide formation, 221, , 235, 236 pathways of formation, 238, 239 rearrangement, 221,223, 234, 239 trapping, see Thiol groups, trapping Dithiothreitol, in disulfide formation and reduction, 221,234, 235, 245 in kinetic analysis, 234, 235 purification, 242 quantification, 242, 243 E Effective concentration, 236, 237 Electrostatic interactions, 4, 272 Ellman's reaction, 242, 243,249 Enzymatic digestion of proteins, in SDS polyacrylamide gels, ,169, 170 in solution, 159, , Equilibrium constants, for denaturation, 186, 255 effect of co-solvents, 255 for disulfide bond formation, , , 248 Excess heat capacity function, see Heat capacity, excess heat capacity function Extinction coefficient, 94, 95 biological chromaphores, 99 calculation of, 95 F Fluorescence, anisotropy, 68, 69, 76 rotational correlation time, 69 emission energy (wavelength), 67, 72, 73 average, 67, 72, 73, 75 decay associated spectra, 81, 82 extrinsic probes, 65, 84 ANS, 80, 348, 350, 356, 362 DNS, 76 use in gathering structural information, 84 intrinsic fluorescence, polarization, 68,349 quantum yields, 66 native vs. denatured states, 66 quenching, 66, 67, 75 red shift on unfolding, 67, 68 steady state measurements, 72 time-resolved measurements, 80 double kinetics, 85 Folding, see Protein folding and unfolding Folding intermediates, see Protein folding and unfolding, intermediates Folding kinetics, see Protein folding and unfolding, kinetics Folding mechanism, see Protein folding and unfolding, folding mechanism Fourier transform infrared spectroscopy (FTIR), 137 Free energy, of calcium binding to subtilisin BPN', 277 of disulfide bonds, 219, 237, 238 of folded state, 177, 238, 272

4 372 Index FTIR data analysis, calculation of derivatives, 145 curve fitting methods, 145 Fourier self-deconvolution, bandwidth, 145 resolution enhancement, 145 pattern recognition methods, 147 protein stability analysis, 148, 149 FTIR instrumentation, detectors, 141 microscopy, 144 sampling geometry, attenuated total reflectance, 142, 143 diffuse reflectance, 143 photoacoustic spectroscopy, 144 transmission, 141,142 Fundamental forces, contributions of, 27 G Gel electrophoresis, densitometry, 248 high ph gels, 240,241,245,249 low ph gels, 240, 241,244, 245, 249 separating disulfide bonded species, 223, ,234, 246, 249 staining, 241,246, 247 Glutathione, in disulfide formation and breakage, see Disulfide bonds, kinetic analysis of formation and breakage, intermolecular reagents quantification, 242, 243 Glycation of protein amino groups, effects on protein stability, alpha crystallin, mechanism, 55, 56 AGEs, 55 glucose, 55, 56 maillard reaction, 55 Guanidine hydrochloride, denaturation by, see Denaturation, by guanidine hydrochloride formation of molten globules, 345, preparation of stock solutions by refractive index, 178 by weight, 178 H Heat capacity, 195 difference, 5, 196 of buffer solutions, 194 excess heat capacity function, 197, 198 deconvolution of, deconvolution theory, 202 statistical thermodynamic definition, of the folded state, 195, 196 of the unfolded state, 195 Heat denaturation, see Denaturation, by heat HPLC, desalting of proteins, 247, 249 of disulfide bonded species, , 248, 249 reverse phase, 160, 165 reproducibility, 170 resolution, 172 sensitivity, 173 of thiol and disulfide reagents, 224, 242, 248 Hydrogen bonding, 3, 9, 15, 17, 28, 29, 272, 298, 301 amide, 29 cooperativity, 29 enthalpy change, 13 Hydrogen/deuterium exchange, ,349

5 Index 373 acquisition of NMR data, D vs 2D, 293 acquisition time, 293 protein concentration, 293 analysis of NMR data, 296, 297 equilibrium studies, data interpretation, 301,302 protection factor, 298 two-state model, 301,302 identification of secondary structure by, 301,305, 308 inverse-detected heteronuclear experiments, 295 kinetic studies of protein folding, competition method, data interpretation, experimental design, 303,304 pulsed methods, model compounds, 297 Hydrogen/tritium exchange, 293 Hydrolysis of peptide bonds, aspartic acid residues, kinetics, 42, 43 mechanism at low ph, 42 detection methods, mass spectroscopy, 44 SDS-PAGE, 44 sequence determination, 44 effects on protein stability, 43, 44 ribonuclease A, 43 subtilisin BPN, 44 tissue plasminogen activator (t-pa), 44 proteolysis, 43, 44 succinimide formation, 43 Hydration, 5, 14, 16 enthalpy change, 14 entropy change, 14, 15 Hydrophobic effect, 2, 5, 8, 10, 28 Hydrophobic probes, 76, 80, 348, 356, 362 Hydrophobicity, 6, 7, 8 I enthalpy change, 13 scales, 12 Intermediates, see Protein folding and unfolding Iodoacetamide, preparation of, 241 trapping cysteine residues, 222, 223,225, 227, 240, 246, 247 Iodoacetic acid, blocking cysteine residues, 222, 223, 225, 227, 240, 246, 247 preparation of, 241 Ion exchange chromatography, disulfide bonded species, 223, 224 K Kinetics, of cysteine destruction, see Cysteine destruction, kinetics of deamidation, see Deamidation of asparigine residues, kinetics of disulfide bonds, see Disulfide bonds, kinetics of peptide bond hydrolysis, see Hydrolysis of peptide bonds, kinetics of protein folding, see Protein folding and unfolding, kinetics L Linkage relationships, 237 Liquid hydrocarbon model, 17 Liquid transfer studies, 12 M Mass spectrometry, electrospray (ESMS), 157, 158 laser desorption(ldms), 158

6 374 Index Mechanism, see Protein folding and unfolding, folding mechanism Minimizing degradative covalent reactions, 59 Mixed-disulfides, identification, , 234, 247 kinetics of formation, see Disulfide bonds, kinetic analysis of formation and breakage, mixed-disulfide formation Model compound studies, 11 hydrogen/deuterium exchange, 297 model compounds, 17, 19 Molar absorptivity (see extinction coefficient) Molten globules, 130, 131, , 362, 363 classes, 343 detection by absorption spectroscopy, 109 detection by FT1R, 150 experimental conditions to generate, 350 a-lactalbumin, 352 apomyoglobin, 353 [~-lactamase, 352 carbonic anhydrase, 356 cytochrome c, 352 DnaK, 352 staphylococcal nuclease, 353 ubiquitin, 354 models, structural, 355 theoretical, 346 physiological role, 357 properties, MPG plot, enthalpy, 6 entropy, 7 O Optical density, 93 correction for light scattering, 95, 96 Oxidation of cysteine residues, mechanism, 48, 49 cysteic acid formation, 49 disulfide formation, 48, 49 sulfenic acid formation, effects on protein stability, acidic fibroblast growth factor, 49, 50 alpha amylase, 50, 51 T4 lysozyme, 50, 51 Oxidation of methionine residues, effects on protein stability, 51, 52 subtilisin, 52 mechanism, 51, 52 hydrogen peroxide, 51, 52 methionine sulfoxide, 51 methionine sulfone, 51 P Packing, 10 densities, 19 density, 10 protein interior, 20 side chains, 20 volumes, 19 Partition function, see Protein folding and unfolding, partition function Phenylalanine, 93, 94 second derivative UV peak, 104 Photodegradation of proteins, effects on protein stability, immunoglobulin, 54 ribonuclease T1, 54 mechanism, 52, 53 kynurenine (Kyn), 53, 54 N-formylkynurenine (NFK), 53, 54 tryptophan residues, 53, 54 UV radiation, 52-55, 57 optical measurements, precautions, 55 Posttranslational modification in proteins, 157

7 Index 375 detection by comparative HPLC mapping, 174 Preferential interactions, 256, 257, 259 measurements, densimetry, preferential binding, 257 preferential exclusion, 257 preferential hydration, 257 preferential interaction parameter, 257 Proline Isomerization, 314, 315, 319, 320 activation energy of, 314, 328 detection of, influence on folding rates, rates of, 328 Prolyl isomerase, 327 Protein folding and unfolding, acid-unfolded state, 351 conversion to molten globule, 351 activation energy 283,326, 327 decrease in subtilisin sitedirected mutant, 283 negative, 327 cooperative unfolding, 27 denatured state, 345 residual structure, 27 disulfide bonds, folding pathways, see Disulfide bonds, pathways of formation kinetics, see Disulfide bonds, kinetic analysis of formation and breakage role of, see Disulfide bonds energetics, 23, 191 calculating from crystal structures, 23 parameterization, 23 folding mechanism, kinetic determination of, 78, 125, Q three-state, 131,347 two-state, 65, 103, 115, 128, 131,185, ,206, 211,272, 337,338, 347 intermediates, 65, 80, 117, 344, 356 detection of, off pathway, 318 kinetics, 21, of o~-lactalbumin, 119 analysis of, of dihydrofolate reductase, 124 double jump experiments, jump experiments, of lysozyme, 119 refolding kinetics, of ribonulcease A, 314, 319, 338 of ribonuclease T1,325, 326, , 338 unfolding kinetics, partition function, 200 experimental evaluation of, 202, 203 reference states, gas, 14 liquid, 17 solid, 18 Quasinative states, 239, 246, 250 R Redox potential, 237 Refolding, analysis of, chaparonin assisted, intermediates during, 117, stability of, kinetic CD, 117 S Salt Bridges, see Electrostatic interactions

8 376 Index SDS-PAGE, 44, 159, 160, 274 Secondary structure, 109, 115, 124, 138, 298 assignment by infrared spectroscopy, formation of, 126, 348 identification of by hydrogen/ deuterium exchange, 301, 305, 308 molten globules, 350, 355 Site-directed mutagenesis, 9, 84, subtilisin BPN', 44, 273 inactivation, 277 removal of calcium binding site, 279, 280 Solid transfer studies, 12 State function, 201 Stopped-flow CD apparatus, 123, 124 dead time, 119,124 mixing artifacts in, 123, 124 mixing efficiency, 123, 124 Structural thermodynamics, 217 T Tertiary structure, 109, 116, 125, 182 molten globules, 348, 350, 355 Thiol groups, air oxidation, 243,249 pk values, 220, 229, 236 quantification, 243 reactivity, 220, 222,228, 23 I, 236 trapping, acidification, 222, 239, 248 alkylation, see Iodoacetamide and iodoacetic acid Thiol-disulfide interchange, 44 /18,220 effects on protein stability, 47, 48 bovine serum albumin, 48 gamma crystallin, 47, 48 porcine ribonuclease inhibitor, 48 kinetics, mechanism, 46, 47,220, 221,228 thiolate ion, 46 mixed disulfide formation, 47, 48 ph dependence, 220, 222, 249 quenching, see Thiol groups, trapping Titration calorimetry, 274, 275 Transition-state theory, , 337, 339 Tryptophan, 93 extinction coefficient, 99 Two-state model, see Protein folding and unfolding, folding mechanism, two state Tyrosine, 93 extinction coefficient, 99 ionization state, 103 U Ultraviolet spectroscopy, advantages, 111, 112 data analysis, 110, 111 difference spectroscopy, used to monitor protein unfolding, 103, 104 extrinsic chromaphores, 109, 110 far UV, first derivative, 98 instrumental considerations, 95, 110, lll metal ions, 109 near UV range, 93 second derivative, analysis of mixtures by, 98 measurement of amino acid content of proteins, 98 use in the presence of light scattering, unfolding monitored by, Unfolding, see Protein folding and unfolding Unfolded state, 10, 29 heat capacity of, 195 Urea, denaturation by, see Denaturation, by urea

9 Index 377 preparation of stock solutions, by refractive index, 117, 178 by weight, 178 V van der Waals interactions, 3, 10, 15, 19, 20, 28,272 van't Hoff analysis, W Water, role of 5, 30 X X-ray crystallography, 275,281