Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Calcium-43 NMR 229 15. Andersson, T., Drakenberg, T., Forsén, S., Wieloch, T., and Lindsröm, M. (1981) Calcium binding to porcine pancreatic phospholipase A 2 studied by 43 Ca NMR. FEBS Lett. 123, 115–117. 16. Andersson, T., Drakenberg, T., Forsén, S. and Thulin, E. (1981) A 43 Ca NMR and 25 Mg NMR Study of Rabbit Skeletal Muscle Troponin C. FEBS Lett. 125, 39–43. 17. Drakenberg, T., Andersson, T., Forsén, S. and Wieloch, T. (1984) Calcium ion binding to pancreatic phospholipase A 2 and its zymogen: a 43 Ca NMR study. Biochemistry 23, 2387–2392. 18. Chiancone, E., Drakenberg, T., Teleman, O., and Forsén, S. (1985) Dynamic and structural properties of the calcium binding site of bovine serine proteases and their zymogens. J. Mol. Biol. 185, 201–207. 19. Svärd, M., Drakenberg, T., Andersson, T., and Fernlund, P. (1986) Calcium binding to bone γ-carboxyglutamic acid protein from calf studied by 43 Ca NMR. Eur. J. Biochem. 158, 373–378. 20. Teleman, A., Drakenberg, T., and Forsén, S. (1986) Kinetics of Ca 2+ binding to calmodulin and its tryptic fragments studied by 43 Ca–NMR. Biochim. Biophys. Acta 873, 204–213. 21. Linse, S., Brodin, P., Drakenberg, T., Thulin, E., Sellers, P., Elmdén, K., et al. (1987) Structure-function relationships in EF-hand Ca 2+ -binding proteins. Protein engineering and biophysical studies of calbindin D 9k. Biochemistry 26, 6723–6735. 22. Brodin, P., Johansson, C., Forsén, S., Drakenberg, T., and Grundström, T. (1990) Functional properties of calbindin D 9k mutants with exchanged Ca 2+ binding sites. J. Biol. Chem. 265, 11,125–11,130. 23. Johansson, C., Brodin, P., Grundström, T., Thulin, E., Forsén, S., and Drakenberg, T. (1990) Biophysical studies of engineered mutant proteins based on calbindin D 9k modified in the pseudo EF-hand. Eur. J. Biochem. 187, 455–460. 24. Johansson, C., Brodin, P., Grundström, T., Forsén, S., and Drakenberg, T. (1991) Mutation of the pseudo-EF-hand of calbindin D 9k into a normal EF-hand. Biophysical studies. Eur. J. Biochem. 202, 1283–1290. 25. Malmendal, A., Linse, S., Evenäs, J., Forsén, S., and Drakenberg, T. (1999) The battle for the EF-hand: magnesium-calcium interference in calmodulin. Biochemistry 38, 11,884–11,850. 26. Westlund, P.-O. and Wennerström, H. (1982) NMR line shapes of I = 5/2 and I = 7/2 nuclei. Chemical exchange effects and dynamic shift. J. Magn. Reson. 50, 451– 466. 27. Andersson, T., Drakenberg, T., Forsén, S., and Thulin, E. (1982) Characterization of the Ca 2+ binding sites of calmodulin from bovine testis using 43 Ca and 113 Cd NMR. Eur. J. Biochem. 126, 501–505. 28. Drakenberg, T., Forsén, S., and Lilja, H. (1982) 43 Ca NMR studies of calcium binding to proteins: interpretation of experimental data by bandshape analysis. J. Magn. Reson. 53, 412–422. 29. Vogel, H. J., Andersson, T., Braunlin, W. H., Drakenberg, T., and Forsén, S. (1984) Trifluoperazine binding to calmodulin: a shift reagent 43 Ca NMR study. Biochem. Biophys. Res. Commun. 122, 1350–1356.
230 Drakenberg 30. Shimizu, T., Hatano, M., Nagao, S., and Nozawa, Y. (1982) 43Ca NMR studies of Ca2+ -tetrahymena calmodulin complexes. Biochem. Biophys. Res. Commun. 106, 1112–1118. 31. Shimizu, T. and Hatano, M. (1988) 43Ca nuclear magnetic resonance of Ca2+ -calmodulin solutions: effects of trifluoperazine and peptides. Inorg. Chim. Acta 152, 257–260. 32. Vogel, H. J., Drakenberg, T., and Forsén, S. (1985) Structural differences in the two calcium binding sites of the porcine intestinal calcium binding protein: a multinuclear NMR study. Biochemistry 24, 3870–3876. 33. Ogoma, Y., Shimizu, T., Hatano, M., Fujii, T., Hachimori, A., and Kondo, Y. (1988) 43Ca nuclear magnetic resonance spectra of Ca2+ -S100 protein solutions. Inorg. Chem. 27, 1853–1855. 34. Ogoma, Y., Kobayashi, H., Fujii, T., Kondo, Y., Hachimori, A., Shimizu, T., and Hatano, M. (1992) Binding study of metal ions to S100 proteins: 43Ca, 25Mg, 67Zn and 39K n.m.r. Int. J. Biol. Macromol. 14, 279–286. 35. Braunlin, W. H., Vogel, H. J., Drakenberg, T., and Bennick, A. (1986) A calcium-43 NMR study of calcium binding to an acidic proline-rich phosphoprotein from human saliva. Biochemistry 25, 584–589. 36. Wahlgren, M., Dejmek, P., and Drakenberg, T. (1990) A 43Ca and 31P NMR study of the calcium and phosphate equilibria in heated milk solutions. J. Dairy Res. 57, 355–364. 37. Wahlgren, M., Dejmek, P. and Drakenberg, T. (1993) Binding of Mg2+ and Ca2+ to β-casein A1 . A multinuclear magnetic resonance study. J. Dairy Res. 60, 65–78.
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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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Page 203 and 204: 184 Brokx and Vogel Table 1 An Over
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Page 207 and 208: 188 Brokx and Vogel Fig. 2. 20% SDS
Page 209 and 210: 190 Brokx and Vogel it through an a
Page 211 and 212: 192 Brokx and Vogel 8. Weljie, A. M
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Page 215 and 216: 196 Berliner Fig. 1. Aqueous X-band
Page 217 and 218: 198 Berliner in the Bruker instrume
Page 219 and 220: 200 Berliner Fig. 3. ESR spectra of
Page 221 and 222: 202 Berliner Fig. 5. Low-temperatur
Page 223 and 224: 204 Berliner 14. Musci, G., Reed, G
Page 225 and 226: 206 Clarke and Vogel cal calcium-bi
Page 227 and 228: 208 Clarke and Vogel Fig. 1. 113 Cd
Page 233 and 234: 214 Clarke and Vogel The linewidth
Page 237 and 238: 218 Drakenberg sands, of Hertz broa
Page 239 and 240: 220 Drakenberg 1. Bloch equations m
Page 241 and 242: 222 Drakenberg Fig. 2. Measurement
Page 243 and 244: 224 Drakenberg Fig. 3. (A) 43 Ca NM
Page 245 and 246: 226 Drakenberg Fig. 5. 43 Ca NMR sp
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Page 251 and 252: 232 Weljie and Heringa Table 1 Amin
Page 253 and 254: 234 Weljie and Heringa Table 2 Webs
Page 255 and 256: 236 Weljie and Heringa diction meth
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Page 259 and 260: 240 Weljie and Heringa lineages. Th
Page 261 and 262: 242 Weljie and Heringa compared, an
Page 263 and 264: 244 Weljie and Heringa sequences as
Page 265 and 266: 246 Weljie and Heringa much larger
Page 267 and 268: 248 Weljie and Heringa ment require
Page 269 and 270: 250 Weljie and Heringa 10. Kawasaki
Page 271 and 272: 252 Weljie and Heringa 44. Thompson
Page 273 and 274: 254 Weljie and Heringa
Page 275 and 276: 256 Li et al. In order for these ex
Page 277 and 278: 258 Li et al. 7. Mineral Mixture (s
Page 279 and 280: 260 Li et al. 3. When the 45% D 2O/
Page 281 and 282: 262 Li et al. sion system works eff
Page 283 and 284: 264 Li et al. reliably produce high
Page 287 and 288: 268 Mal et al. NMR data, X-PLOR (11
Page 289 and 290: 270 Mal et al. Table 1 Simulated An
Page 291 and 292: 272 Mal et al. 3.1.2.1. AMBIGUOUS D
Page 293 and 294: 274 Mal et al. molecular dynamics a
Page 295 and 296: 276 Mal et al. Assuming a rigid bod
Page 297 and 298: 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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362 Hughes et al. Table 1 Examples
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366 Persechini of the different CaM
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368 Persechini Fig. 1. Schematic re
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370 Persechini 2. 1 L of Terrific b
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372 Persechini Fig. 4. Titration wi
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374 Persechini Table 1 Parameters f
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376 Persechini Fig. 6. The [Ca 2+ -
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378 Persechini determined if the di
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380 Persechini relatively insensiti
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382 Persechini 18. Chafouleas, J. G
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384 Török et al. actions in the c
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386 Török et al. 3. The reaction
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388 Török et al. Fig. 2. Electros
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390 Török et al. Fig. 3. Peptides
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392 Török et al. Table 1 Peptide
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394 Török et al. Fig. 7. Nanospra
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396 Török et al. Fig. 9. Nanospra
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398 Török et al. Fig. 11. Electro
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400 Török et al. 3 µM FL-calmodu
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402 Török et al. Fig. 14. Localiz
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404 Török et al. Fig. 16. Indicat
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406 Török et al. the significantl
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408 Török et al.
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410 Index substitutes, see Fluoresc
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412 Index Stern-Volmer plot, 78, 81
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414 Index Phenothiazines, see Calmo
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