Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Index 413 Molecular modeling, 147–148, 157, 236 Multiple sequence alignment, 231–233, 238, 241–249 algorithms and programs, 235, 237, 246–249 analysis, 235–237 phylogenetic analysis, 236–237, 239–241 sequence retrieval, 234–235, 237–238 substitution matrices, 238 Myosin Light Chain Kinase, see MLCK N 15N, see NMR, isotope labeling 15N relaxation, see NMR, backbone relaxation NADPH oxidation assay, see Calmodulin, assays, NOS Nitric oxide synthase, see Calmodulin, assays, NOS NMR spectroscopy, backbone relaxation, 285–293 cadmium-113, 205–214 chemical exchange, 208–209 calcium-43, 217–228 chemical shift anisotropy, see CSA CSA, 213–214 diffusion tensor, 286, 293–295 dipolar couplings, 301–303 alignment additives, 304–305, 312 analysis, 306–308 field effects, 312 structure refinement, 308–310 validation, 310–312 estimation of tc, 290–291 exchange contributions, 286–287, 291–292, 295, 296–297 HN correlation (HSQC) type spectra, 307 isotope labeling, 255–256 13 C/ 15 N, 256–259, 260–262 2 H and 2 H/ 13 C/ 15 N, 258, 259–265 lead-207, 205–214 order parameters, 287, 295 quadrupolar relaxation, 218–220, 221 structure determination, 267–279, see also NMR spectroscopy, dipolar couplings ambiguous restraints, 271–273 calcium restraints, 277–278 NOE and 3 J restraints, 268, 275–279 pseudoatom corrections, 276–277 structure calculation, 269–270, 273–275 validation, 270 NOS, see Calmodulin, assays, NOS Nuclear magnetic resonance spectroscopy, see NMR spectroscopy O Order parameters, see NMR, backbone relaxation Oxyhemoglobin assay, see Calmodulin, assays, NOS P Parvalbumin, 211–212 PDE, see Calmodulin, assays, PDE Peptide synthesis, 176–177, 178–179
414 Index Phenothiazines, see Calmodulin, agonists Phosphodiesterase, see Calmodulin, assays, PDE Phylogenetic trees, see Multiple sequence alignment, phylogenetic analysis Proteases, thrombin, 184–184, 187, 189–190 trypsin, 184–189, 384, 388 Protein aggregation, see Light Scattering; Analytical Ultracentrifugation Protein concentration determination, 46, 52, 80, 83, 118, 124, 155–156 Protein expression, 260, 262–264 antibiotics, 257 Protein folding/unfolding, energies, 113, see also Enthalpy Protein-protein interactions, see also CD spectroscopy, by ESI-MS, 167–168, 172 by SPR, 105–109 thermodynamics, see Calorimetry, ITC Protein purification, see Chromotography and HPLC Protein structure, primary, see Multiple sequence alignment secondary, 50–52, 67–70 prediction, 235–236 tertiary, see Molecular modeling; NMR spectroscopy, structure deterimination; Vector geometry mapping Proteolysis, see Proteases R Radius of gyration (Rg), 145–147 Recoverin, 164 Residual dipolar couplings, see NMR, dipolar couplings S S-100 proteins, see also EFhand proteins purification, 329–336 SAXS, see Small-angle X-ray scattering ScaM, see Calmodulin, soybean Scatchard plot, 28–29 Secondary structure, see Protein structure, secondary Sedimentation equilibrium, 127, 131–135 Small-angle X-ray scattering, 137–138 data analysis, 145–148 facilities and instrumentation, 138–140 theory, 141–143 Soybean calmodulin, see Calmodulin, soybean Spin labeling, paramagnetic, 196–197, 198–199 SPR, 103–104 calcium-dependent interactions, 106–107 instrumentation, 104–105 kinetics, 107–109 Surface Plasmon Resonance, see SPR T T1/T2 relaxation, see NMR spectroscopy, backbone relaxation
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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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360 Hughes et al. range, repeat ste
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Page 385 and 386: 366 Persechini of the different CaM
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Page 429 and 430: 410 Index substitutes, see Fluoresc
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