Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Contributors JEAN-RENÉ ALATTIA • Division of Molecular and Structural Biology, Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada JAMES B. AMES • Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada STEFAN BAGBY • Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada PETER M. BAYLEY • Division of Physical Biochemistry, National Institute for Medical Research, London, UK LAWRENCE J. BERLINER • Department of Chemistry, The Ohio State University, Columbus, OH JONATHAN BOYD • Department of Biochemistry and OCMS, University of Oxford, South Parks Road, Oxford, UK RICHARD D. BROKX • Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada IAIN D. CAMPBELL • Department of Biochemistry and OCMS, University of Oxford, South Parks Road, Oxford, UK TERESA E. CLARKE • Department of Biological Sciences, University of Calgary, Calgary, AB, Canada DAVID C. CORSON • Canadian Institutes of Health Research Group in <strong>Protein</strong> Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada AMANDA L. DOHERTY-KIRBY • Department of Biochemistry, University of Western Ontario, London, ON, Canada A. KRISTINA DOWNING • Department of Biochemistry and OCMS, University of Oxford, South Parks Road, Oxford, UK TORBJÖRN DRAKENBERG • Department of Physical Chemistry 2, Lund University, Lund, Sweden HEINZ FABIAN • Max-Delbrück-Center for Molecular Medicine, Berlin, Germany THOMAS GRUNDSTRÖM • Department of Cell and and Molecular Biology, Umeå University, Umeå, Sweden JACQUES HAIECH • Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg, Illkirch, France JAAP HERINGA • Division of Mathematical Biology, MRC National Institute for Medical Research, London, UK xv
xvi Contributors LESLIE D. HICKS • Department of Biochemistry, University of Alberta, Edmonton, AB, Canada STEVEN HOWELL • National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK KATE HUGHES • Department of Cell and and Molecular Biology, Umeå University, Umeå, Sweden MITSUHIKO IKURA • Division of Medical and Structural Biology, Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada J. DAVID JOHNSON • Department of Molecular and Cellular Biochemistry, The Ohio State University Medical Center, Columbus, OH KARIN JULENIUS • Department of Physical Chemistry, Lund University, Lund, Sweden CYRIL M. KAY • Department of Biochemistry, University of Alberta, Edmonton, AB, Canada MARIE-CLAUDE KILHOFFER • Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg, Illkirch, France RYOJI KOBAYASHI • Department of Chemistry, Kagawa Medical University, Ikenobe, Miki-cho, Kita-gun, Kagawa, Japan RITSU KONDO • Department of Medical Biochemistry, The Ohio State University Medical Center, Columbus, OH JOANNA K. KRUEGER • Chemistry Department, University of North Carolina, Charlotte, NC GILLES A. LAJOIE • Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, Department of Chemistry, University of Waterloo, Waterloo, ON, Canada MONICA X. LI • Canadian Institutes of Health Research Group in <strong>Protein</strong> Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada SARAH LINSE • Department of Physical Chemistry 2, Lund University, Lund, Sweden MARIA M. LOPEZ • Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA GEORGE I. MAKHATADZE • Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA TAPAS K. MAL • Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
Page 1 and 2: Methods in Molecular BiologyTM Biol
Page 3 and 4: M E T H O D S I N M O L E C U L A R
Page 5 and 6: © 2002 Humana Press Inc. 999 River
Page 8 and 9: Preface Calcium plays an important
Page 10 and 11: Contents Dedication ...............
Page 12: Contents xi 26 Enzymatic Assays to
Page 15: xiv Contents of Companion Volume 15
Page 19 and 20: 20 Dean, Kelsey, and Re
Page 21 and 22: 2 Yazawa
Page 23 and 24: 4 Yazawa Fig. 1. Schematic represen
Page 25 and 26: 6 Yazawa Fig. 2. Shop drawing for t
Page 27 and 28: 8 Yazawa DuPont-NEN and the molar c
Page 29 and 30: 10 Yazawa Fig. 4. Examples of the C
Page 31 and 32: 12 Yazawa 5. Plot the calculated Ca
Page 33 and 34: 14 Yazawa 12. Starovasnik, M. A., D
Page 35 and 36: 16 Fig. 1. Molecular structures and
Page 37 and 38: 18 Linse 7. 0.1 M EDTA. Dissolve 37
Page 39 and 40: 20 Linse iterate the other paramete
Page 41 and 42: 22 Linse tive to small alterations
Page 43 and 44: 24 Linse References 1. Tsien, R. Y.
Page 45 and 46: 26 Haiech and Kilhoffer to use the
Page 47 and 48: 28 Haiech and Kilhoffer where γ is
Page 49 and 50: 30 Haiech and Kilhoffer reporter gr
Page 51 and 52: 32 Haiech and Kilhoffer tein with i
Page 53 and 54: 34 Haiech and Kilhoffer Calmodulin
Page 55 and 56: 36 Haiech and Kilhoffer Fig. 3. Mec
Page 57 and 58: 38 Haiech and Kilhoffer We may sugg
Page 59 and 60: 40 Haiech and Kilhoffer 29. Stewart
Page 61 and 62: 42 Haiech and Kilhoffer 62. Becking
Page 63 and 64: 44 Martin and Bayley Fig. 1. Absorp
Page 65 and 66: 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
Page 157 and 158:
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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Page 231 and 232:
Page 233 and 234:
214 Clarke and Vogel The linewidth
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Page 237 and 238:
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
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
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256 Li et al. In order for these ex
Page 277 and 278:
258 Li et al. 7. Mineral Mixture (s
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260 Li et al. 3. When the 45% D 2O/
Page 281 and 282:
262 Li et al. sion system works eff
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264 Li et al. reliably produce high
Page 285 and 286:
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
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274 Mal et al. molecular dynamics a
Page 295 and 296:
276 Mal et al. Assuming a rigid bod
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278 Mal et al. assign (segid A and
Page 299 and 300:
280 Mal et al. References 1. Drenth
Page 301 and 302:
282 Mal et al. 33. Jeener, J., Meie
Page 303 and 304:
Page 305 and 306:
286 Werner et al. Our research has
Page 307 and 308:
288 Fig. 1. (A) T 1, T 2 and the he
Page 309 and 310:
290 Werner et al. tion, using gradi
Page 311 and 312:
292 Werner et al. Fig. 3. (A) Rotat
Page 313 and 314:
294 Werner et al. Fig. 4. (A) Line-
Page 315 and 316:
296 Werner et al. Table 2 Models of
Page 317 and 318:
298 Werner et al. 9. Reinhardt, D.
Page 319 and 320:
300 Werner et al. 39. Press, W. H.,
Page 321 and 322:
302 Boyd et al. utilize residual di
Page 323 and 324:
304 Boyd et al. Fig. 1. (A) The sol
Page 325 and 326:
306 Boyd et al. or significant peak
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308 Boyd et al. Fig. 3. Histogram o
Page 329 and 330:
310 Boyd et al. total and NOE energ
Page 331 and 332:
312 Boyd et al. 2. When studying mu
Page 333 and 334:
314 Boyd et al. 4. Downing, A. K.,
Page 335 and 336:
316 Boyd et al. 35. Schulte-Herbrug
Page 337 and 338:
318 Yap et al. image representation
Page 339 and 340:
320 Yap et al. modified EF-hand is
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322 Table 1 Angle and Distance Outp
Page 343 and 344:
324 Yap et al. 2. Ikura, M. (1995)
Page 345 and 346:
326 Kobayashi that S-100A1 and S-10
Page 347 and 348:
328 Kobayashi 3.2. Coupling of Crom
Page 349 and 350:
330 Kobayashi Fig. 2. Tricine/SDS/P
Page 351 and 352:
332 Kobayashi 0.1% TFA at a flow ra
Page 353 and 354:
334 Kobayashi Both recombinant S-10
Page 355 and 356:
336 Kobayashi Fig. 6. Affinity chro
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Page 359 and 360:
340 Walsh et al. verts CaM from an
Page 361 and 362:
342 Walsh et al. 11. Bovine serum a
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344 Walsh et al. Fig. 1. CaM-depend
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Page 367 and 368:
348 Walsh et al. 3.5. NOS Reduction
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Page 373 and 374:
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.
Page 379 and 380:
360 Hughes et al. range, repeat ste
Page 381 and 382:
362 Hughes et al. Table 1 Examples
Page 383 and 384:
Page 385 and 386:
366 Persechini of the different CaM
Page 387 and 388:
368 Persechini Fig. 1. Schematic re
Page 389 and 390:
370 Persechini 2. 1 L of Terrific b
Page 391 and 392:
372 Persechini Fig. 4. Titration wi
Page 393 and 394:
374 Persechini Table 1 Parameters f
Page 395 and 396:
376 Persechini Fig. 6. The [Ca 2+ -
Page 397 and 398:
378 Persechini determined if the di
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380 Persechini relatively insensiti
Page 401 and 402:
382 Persechini 18. Chafouleas, J. G
Page 403 and 404:
384 Török et al. actions in the c
Page 405 and 406:
386 Török et al. 3. The reaction
Page 407 and 408:
388 Török et al. Fig. 2. Electros
Page 409 and 410:
390 Török et al. Fig. 3. Peptides
Page 411 and 412:
392 Török et al. Table 1 Peptide
Page 413 and 414:
394 Török et al. Fig. 7. Nanospra
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396 Török et al. Fig. 9. Nanospra
Page 417 and 418:
398 Török et al. Fig. 11. Electro
Page 419 and 420:
400 Török et al. 3 µM FL-calmodu
Page 421 and 422:
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
Page 431 and 432:
412 Index Stern-Volmer plot, 78, 81
Page 433 and 434:
414 Index Phenothiazines, see Calmo
Page 435:
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