Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Index 411 Citrulline assay, see Calmodulin, backbone relaxation, 290–296 assays, NOS structure, 301–303, 310 Cleavage of proteins, see Proteases EGTA, see Calcium, chelation Confocal imaging, see Fluorescence, and decontamination imaging Electron paramagnetic resonance, Cromolyn, see Calmodulin, agonists see ESR Cyclic nucleotide Electron spin resonance, see ESR 3':5'-phosphodiesterase, Electroporation, 355–357, see Calmodulin, assays, PDE 358–359, 360–361, 385, Cytochrome c reduction assay, see Calmodulin, assays, NOS 393–397, see also β-Galactosidase, Luciferase D 2D, see NMR, isotope labeling DG, of unfolding, 117 DDG , of calcium-binding, 23 DANSYL, see Fluorescence, FRET Differential scanning calorimetry, see Calorimetry, DSC Dipolar couplings, see NMR, dipolar couplings Enthalpy or protein unfolding, 113, 117 Epidermial growth factor domains, see EGF domains EPR, see ESR ESR, 195–203 Eukaryotic protein expression, 373–374 Evolutionary relationships, see Multiple sequence alignments, phylogentic analysis Dynamics, see NMR, F backbone relaxation Fluorescein dichlorotriazine E (5-DTAF), 384, 385–388 EDTA, see Calcium, chelation and decontamination EF-hand proteins, calcium-binding sequence, 231–233, 242–244, see also Multiple sequence alignment conformational changes on calcium-binding, see Vector geometry mapping Fluorescence, analysis of calcium-binding proteins, 83–85, 89–90, 95–98 Ca fragments of, 183–185 interhelical angles, see Vector geometry mapping synthetic, 175–176 EGF domains, 285–286 2+ on-rates, 95, 100 calcium-binding dyes, 15–17, 90, 97–98, 99–100, 372 dissociation constants, 92–94, 98–100 FRET, 365–366 imaging, 398–402 inner-filter effects, 96 instrumentation, 79–80, 81, 83 scattering effects, 97
412 Index Stern-Volmer plot, 78, 81–83 terbium, 84–85, 101 tryptophan and tyrosine, 75–79 Flow dialysis, 3–5, 9–11 Fluorescence resonance energy transfer, see Fluorescence, FRET Fluorescent CaM indicator proteins, 365–366, 376–379 bacterial expression and purification, 367–370 eukaryotic expression, 373–374 quantitation, 374–375 Fourier Transform Infrared Spectroscopy, see FTIR spectroscopy Free energy, see DG FTIR spectroscopy, 57–72 data processing, 65–69 deuterium shifting, 62–63, 71 instrumentation, 57–60 isotope-edited, 69–70 time-resolved, 71 G Gadolinium, 201 Green Fluorescent Protein, 366, 367–368, 383, see also Fluorescent CaM indicator proteins H Heat capacity,117–118 change on binding (DCp), 121 partial C p(T) of protein, 116 High performance liquid chromotography, see HPLC High pressure liquid chromotography, see HPLC Hill coefficient, see Calcium, binding to proteins, stoichiometry determination HPLC, reverse-phase, 177, 179–180, 330 –332, 384, 386, 388 –392 I Infrared Spectroscopy, see FTIR spectroscopy Interhelical angles, see Vector geometry mapping Isothermal scanning calorimetry, see Calorimetry, ISC K, L Kinetics, see Protein-protein interactions, and Calcium, binding to proteins Lead, see NMR, lead-207 Ligand binding curves, see Calcium, binding to proteins Light scattering, 127–131 Luciferase assay, 356, 357–358, 360 M Mammalian cells, transfection of; see Electroporation Manganese, 200 Mass spectrometry, electrospray ionization (ESI), 162–165, 386–392 Matrilysin, 165 Microinjection, 385, 397–398 Minimal media, see NMR, isotope labeling MLCK, 150–153, see also Calmodulin, assays, MLCK calmodulin-binding domain, 148–150, 167–170
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Methods in Molecular BiologyTM Biol
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M E T H O D S I N M O L E C U L A R
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© 2002 Humana Press Inc. 999 River
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Preface Calcium plays an important
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Contents Dedication ...............
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Contents xi 26 Enzymatic Assays to
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xiv Contents of Companion Volume 15
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xvi Contributors LESLIE D. HICKS
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20 Dean, Kelsey, and Re
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2 Yazawa
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4 Yazawa Fig. 1. Schematic represen
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6 Yazawa Fig. 2. Shop drawing for t
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8 Yazawa DuPont-NEN and the molar c
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10 Yazawa Fig. 4. Examples of the C
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12 Yazawa 5. Plot the calculated Ca
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14 Yazawa 12. Starovasnik, M. A., D
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16 Fig. 1. Molecular structures and
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18 Linse 7. 0.1 M EDTA. Dissolve 37
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20 Linse iterate the other paramete
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22 Linse tive to small alterations
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24 Linse References 1. Tsien, R. Y.
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26 Haiech and Kilhoffer to use the
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28 Haiech and Kilhoffer where γ is
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30 Haiech and Kilhoffer reporter gr
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32 Haiech and Kilhoffer tein with i
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34 Haiech and Kilhoffer Calmodulin
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36 Haiech and Kilhoffer Fig. 3. Mec
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38 Haiech and Kilhoffer We may sugg
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40 Haiech and Kilhoffer 29. Stewart
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42 Haiech and Kilhoffer 62. Becking
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44 Martin and Bayley Fig. 1. Absorp
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46 Martin and Bayley evaporation. C
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48 Martin and Bayley 4. Set the tem
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50 Martin and Bayley Fig. 2. Near-U
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52 Martin and Bayley discussed by M
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54 Martin and Bayley References 1.
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20 Dean, Kelsey, and Reik
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58 Fabian and Vogel are equipped wi
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60 Fabian and Vogel The penetration
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62 Fabian and Vogel perature, ionic
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64 Fabian and Vogel Fig. 3. IR spec
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66 Fabian and Vogel Fig. 4. Lower t
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68 Fabian and Vogel These correlati
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70 Fabian and Vogel Fig. 5. Amide I
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72 Fabian and Vogel 4. ATR-FTIR spe
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74 Fabian and Vogel 25. Georg, H.,
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76 Weljie and Vogel Fig. 1. Simplif
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78 Weljie and Vogel Fig. 3. Steady-
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80 Weljie and Vogel VIS spectrophot
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82 Weljie and Vogel 4. A series of
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84 Table 1 Advanced Fluorescence Me
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86 Weljie and Vogel References 1. L
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90 Johnson and Tikunova is removed
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92 Johnson and Tikunova function of
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94 Johnson and Tikunova Fig. 2. Rat
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96 Johnson and Tikunova Fig. 3. Rat
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98 Johnson and Tikunova Fig. 4. Ca
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100 Johnson and Tikunova cence inte
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102 Johnson and Tikunova 6. Johnson
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104 Julenius Fig. 1. Under conditio
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106 Julenius 3. Mix 50 µL of NHS s
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108 Julenius Fig. 3. A typical sens
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110 Julenius (2), is used in the Ia
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114 Lopez and Makhatadze Fig. 1. Th
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116 Lopez and Makhatadze 6. Buffers
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118 Lopez and Makhatadze The excess
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122 Lopez and Makhatadze Fig. 1. Is
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124 Lopez and Makhatadze 2.5 mL are
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126 Lopez and Makhatadze pendence o
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128 Hicks et al. equipped with a pu
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130 Hicks et al. Fig. 2. Debye plot
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132 Hicks et al. and 1.0 mg/mL for
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134 Hicks et al. Fig. 3. Sedimentat
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136 Hicks et al. 5. Hayes, D. B. (M
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138 Trewhella and Krueger This chap
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140 Trewhella and Krueger of the sc
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142 Trewhella and Krueger Table 1 C
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144 Trewhella and Krueger beam, or
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146 Trewhella and Krueger At very l
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148 Trewhella and Krueger analytica
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150 Trewhella and Krueger collapsed
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152 Trewhella and Krueger P(r) func
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154 Trewhella and Krueger Fig. 3. S
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156 Trewhella and Krueger concentra
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158 Trewhella and Krueger by a Nati
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162 Doherty-Kirby and Lajoie metal
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164 Doherty-Kirby and Lajoie two Ca
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166 Doherty-Kirby and Lajoie 7. Pep
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168 Doherty-Kirby and Lajoie Fig. 1
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170 Doherty-Kirby and Lajoie Fig. 2
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172 Doherty-Kirby and Lajoie 5. Alt
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174 Doherty-Kirby and Lajoie phosph
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176 Shaw Fig. 1. Ribbon drawing of
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178 Shaw 2.3. Other 1. Chemicals fo
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180 Shaw 3.3.3. Purification 1. Con
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182 Shaw 10. Hodges, R. S., Semchuk
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184 Brokx and Vogel Table 1 An Over
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186 Brokx and Vogel Fig. 1. UV abso
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188 Brokx and Vogel Fig. 2. 20% SDS
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190 Brokx and Vogel it through an a
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192 Brokx and Vogel 8. Weljie, A. M
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196 Berliner Fig. 1. Aqueous X-band
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198 Berliner in the Bruker instrume
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200 Berliner Fig. 3. ESR spectra of
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202 Berliner Fig. 5. Low-temperatur
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204 Berliner 14. Musci, G., Reed, G
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206 Clarke and Vogel cal calcium-bi
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208 Clarke and Vogel Fig. 1. 113 Cd
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214 Clarke and Vogel The linewidth
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218 Drakenberg sands, of Hertz broa
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220 Drakenberg 1. Bloch equations m
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222 Drakenberg Fig. 2. Measurement
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224 Drakenberg Fig. 3. (A) 43 Ca NM
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226 Drakenberg Fig. 5. 43 Ca NMR sp
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228 Drakenberg NMR at sub-mM concen
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230 Drakenberg 30. Shimizu, T., Hat
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232 Weljie and Heringa Table 1 Amin
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234 Weljie and Heringa Table 2 Webs
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236 Weljie and Heringa diction meth
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238 Weljie and Heringa these databa
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240 Weljie and Heringa lineages. Th
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242 Weljie and Heringa compared, an
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244 Weljie and Heringa sequences as
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246 Weljie and Heringa much larger
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248 Weljie and Heringa ment require
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250 Weljie and Heringa 10. Kawasaki
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252 Weljie and Heringa 44. Thompson
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254 Weljie and Heringa
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256 Li et al. In order for these ex
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258 Li et al. 7. Mineral Mixture (s
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260 Li et al. 3. When the 45% D 2O/
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262 Li et al. sion system works eff
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264 Li et al. reliably produce high
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268 Mal et al. NMR data, X-PLOR (11
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270 Mal et al. Table 1 Simulated An
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272 Mal et al. 3.1.2.1. AMBIGUOUS D
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274 Mal et al. molecular dynamics a
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276 Mal et al. Assuming a rigid bod
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278 Mal et al. assign (segid A and
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280 Mal et al. References 1. Drenth
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282 Mal et al. 33. Jeener, J., Meie
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286 Werner et al. Our research has
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288 Fig. 1. (A) T 1, T 2 and the he
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290 Werner et al. tion, using gradi
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292 Werner et al. Fig. 3. (A) Rotat
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294 Werner et al. Fig. 4. (A) Line-
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296 Werner et al. Table 2 Models of
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298 Werner et al. 9. Reinhardt, D.
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300 Werner et al. 39. Press, W. H.,
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302 Boyd et al. utilize residual di
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304 Boyd et al. Fig. 1. (A) The sol
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306 Boyd et al. or significant peak
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308 Boyd et al. Fig. 3. Histogram o
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310 Boyd et al. total and NOE energ
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312 Boyd et al. 2. When studying mu
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314 Boyd et al. 4. Downing, A. K.,
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316 Boyd et al. 35. Schulte-Herbrug
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318 Yap et al. image representation
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320 Yap et al. modified EF-hand is
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322 Table 1 Angle and Distance Outp
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324 Yap et al. 2. Ikura, M. (1995)
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326 Kobayashi that S-100A1 and S-10
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328 Kobayashi 3.2. Coupling of Crom
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330 Kobayashi Fig. 2. Tricine/SDS/P
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332 Kobayashi 0.1% TFA at a flow ra
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334 Kobayashi Both recombinant S-10
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336 Kobayashi Fig. 6. Affinity chro
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340 Walsh et al. verts CaM from an
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342 Walsh et al. 11. Bovine serum a
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344 Walsh et al. Fig. 1. CaM-depend
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348 Walsh et al. 3.5. NOS Reduction
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354 Walsh et al. 3. Cho, M. J., Vag
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356 Hughes et al. The electroporati
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358 Hughes et al. 4. 1 M Na 2CO 3.
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Page 385 and 386: 366 Persechini of the different CaM
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Page 433 and 434: 414 Index Phenothiazines, see Calmo
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