Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Ca 2+ -Binding Proteins Using ESI-MS 173 7. Lafitte, D., Capony, J. P., Grassy, G., Haiech, J., and Calas, B. (1995) Electrospray ionization mass spectrometric study of calcium binding to calmodulin in the presence of magnesium and terbium. J. Mass Spectrom. Rapid Commun. Mass Spectrom. S192–S196. 8. Johnson, K. L., Veenstra, T. D., and Tomlinson, A. J. (1997) Determination of noncovalent metal ion/protein interactions using a microflow electrospray ionization mass spectrometry interface. Rapid Commun. Mass Spectrom. 11, 939–942. 9. Veenstra, T. D., Johnson, K. L., Tomlinson, A. J., Naylor, S., and Kumar, R. (1997) Determination of calcium-binding sites in rat brain calbindin D 28K by electrospray ionization mass spectrometry. Biochemistry 36, 3535–3542. 10. Troxler, H., Kuster, T., Rhyner, J. A., Gehrig, P., and Heizmann, C. W. (1999) Electrospray ionization mass spectrometry:analysis of the Ca 2+ -binding properties of human recombinant α-parvalbumin and nine mutant proteins. Anal. Biochem. 268, 64–71. 11. Hu, P., Buckel, S. D., Whitton, M. M., and Loo, J. A. Calcium binding properties and sequence of frog (Rana tegrinka) parvalbumin as determined by electrospray ionization-mass spectrometry. (1996) Eur. Mass Spectrom. 2, 69–76. 12. Feng, R., Castelhano, A. L., Billedeau, R., and Yuan, Z. (1995) Study of non-covalent enzyme-inhibitor complexes and metal binding stoichiometry of matrilysisn by electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 6, 1105–1111. 13. Chazin, W. and Veenstra, T. D. (1999) Determination of the metal-binding cooperativity of wild-type and mutant calbindin D 9K by electrospray ionization mass spectrometry. Rapid Commun. Mass Spectrom. 13, 548–555. 14. Veenstra, T. D., Johnson, K. L., Tomlinson, A. J., Naylor, S., and Kumar, R. (1997) Electrospray ionization mass spectrometry temperature effects on metal ion: protein stoichiometries and metal induced conformational changes in calmodulin. Eur. Mass Spectrom. 3, 453–459. 15. Veenstra, T. D., Johnson, K. L., Tomlinson, A. J., Kumar, R., and Naylor, S. (1998) Correlation of fluorescence and circular dichroism spectroscopy with electrospray ionization mass spectrometry in the determination of tertiary conformational changes in calcium-binding proteins. Rapid Commun. Mass Spectrom. 12, 613–619. 16. Neubert, T. A., Walsh, K. A., Hurley, J. B., and Johnson, R. S. (1997) Monitoring calcium-induced conformational changes in recoverin by electrospray mass spectrometry. Protein Sci. 6, 843–850. 17. Johnson, R. S. and Walsh, K. A. (1994) Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin. Protein Sci. 3, 2411–2418. 18. Wang, F., Blanchard, J. S., and Tang, X. J. (1997) Hydrogen exchange/electrospray ionization mass spectrometry studies of substrate and inhibitor binding and conformational changes of Escherichia coli dihydrodipicolinate reductase. Biochemistry 36, 3755–3759. 19. Wang, F., Li, W., Emmett, M. R., Hendrickson, C. L., Marshall, A. G., Zhang, Y. L., et al. (1998) Conformational and dynamic changes of Yersinia protein tyrosine
174 Doherty-Kirby and Lajoie phosphatase induced by ligand binding and active site mutation and revealed by H/D exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Biochemistry 37, 15,289–15,299. 20. Wang, F., Scapin, G., Blanchard, J. S., and Angeletti, R. H. (1998) Substrate binding and conformational changes of Clostridium glutamicum diaminopimelate dehydrogenase revealed by hydrogen/deuterium exchange and electrospray mass spectrometry. Protein Sci. 7, 293–299. 21. Zhang, Z., Li, W., Logan. T. M., Li, M., and Marshall, A. G. (1997) Human recombinant [C22A]FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. Protein Sci. 6, 2203–2217. 22. Maier, C., Kim, O. H., and Deinzer, M. L. (1997) Conformational properties of the A-state of cytochrome c studied by hydrogen/deuterium exchange and electrospray mass spectrometry. Anal. Biochem. 252, 127–135. 23. Lafitte, D., Benezech, V., Bompart, J., Laurent, F., Bonnet, P. A., Chapat, J. P., et al. (1997) Characterization of low affinity complexes between calmodulin and pyrazine derivatives by electrospray ionization mass spectrometry. J. Mass Spectrom. 32, 87–93. 24. Nemirovskiy, O. V., Ramanathan, R., and Gross, M. L. (1997) Investigation of calcium-induced, noncovalent association of calmodulin with melittin by electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 8, 809–812. 25. Veenstra, T. D., Tomlinson, A. J., Benson, L., Kumar, R., and Naylor, S. (1998) Low temperature aqueous electrospray ionization mass spectrometry of noncovalent complexes. J. Am. Soc. Mass Spectrom. 9, 580–584. 26. Raferty, M. J. and Geczy, C. L. (1998) Identification of noncovalent dimeric complexes of the recombinant murine S100 protein CP10 by electrospray ionization mass spectrometry and chemical cross-linking. J. Am. Soc. Mass Spectrom. 9, 533–539. 27. Lafitte, D., Heck, A. J. R., Hill, T. J., Jumel, K., Harding, S. E., and Derrick, P. J. (1999) Evidence of noncovalent dimerization of calmodulin. Eur. J. Biochem. 261, 337–344. 28. Ferrige, A. G., Seddon, M. J., Green, B. N., Jarvis, S. A., and Ski lling, J. (1992) Disentangling electrospray spectra with maximum entropy. Rapid Commun. Mass Spectrom. 6, 707–711. 29. Ohki, S., Ikura, M., and Zhang, M. (1997) Identification of Mg 2+ -binding sites and the role of Mg 2+ on target recognition by calmodulin. Biochemistry 36, 4309–4316. 30. Persechini, A., McMillan, K., and Leakey, P. (1994) Activation of myosin light chain kinase and nitric oxide synthase activities by calmodulin fragments. J. Biol. Chem. 269, 16,148–16,154.
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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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Page 141 and 142: 122 Lopez and Makhatadze Fig. 1. Is
Page 143 and 144: 124 Lopez and Makhatadze 2.5 mL are
Page 145 and 146: 126 Lopez and Makhatadze pendence o
Page 147 and 148: 128 Hicks et al. equipped with a pu
Page 149 and 150: 130 Hicks et al. Fig. 2. Debye plot
Page 151 and 152: 132 Hicks et al. and 1.0 mg/mL for
Page 153 and 154: 134 Hicks et al. Fig. 3. Sedimentat
Page 155 and 156: 136 Hicks et al. 5. Hayes, D. B. (M
Page 157 and 158: 138 Trewhella and Krueger This chap
Page 159 and 160: 140 Trewhella and Krueger of the sc
Page 161 and 162: 142 Trewhella and Krueger Table 1 C
Page 163 and 164: 144 Trewhella and Krueger beam, or
Page 165 and 166: 146 Trewhella and Krueger At very l
Page 167 and 168: 148 Trewhella and Krueger analytica
Page 169 and 170: 150 Trewhella and Krueger collapsed
Page 171 and 172: 152 Trewhella and Krueger P(r) func
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Page 175 and 176: 156 Trewhella and Krueger concentra
Page 177 and 178: 158 Trewhella and Krueger by a Nati
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Page 181 and 182: 162 Doherty-Kirby and Lajoie metal
Page 183 and 184: 164 Doherty-Kirby and Lajoie two Ca
Page 185 and 186: 166 Doherty-Kirby and Lajoie 7. Pep
Page 187 and 188: 168 Doherty-Kirby and Lajoie Fig. 1
Page 189 and 190: 170 Doherty-Kirby and Lajoie Fig. 2
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Page 195 and 196: 176 Shaw Fig. 1. Ribbon drawing of
Page 197 and 198: 178 Shaw 2.3. Other 1. Chemicals fo
Page 199 and 200: 180 Shaw 3.3.3. Purification 1. Con
Page 201 and 202: 182 Shaw 10. Hodges, R. S., Semchuk
Page 203 and 204: 184 Brokx and Vogel Table 1 An Over
Page 205 and 206: 186 Brokx and Vogel Fig. 1. UV abso
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
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
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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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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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