Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Deconvolution of Calcium-Binding Curves 37 As calmodulin belongs to the EF-hand family of intracellular Ca 2+ -binding proteins, we may wonder if this binding mechanism is pertinent to most proteins of the family. Moreover, the number of Ca 2+ -binding sites varies from 2 (parvalbumin) to 6 (for review, see ref. 18). In 1979, we already showed that the same general model applies to parvalbumin (71). As parvalbumin has two EF-hand Ca 2+ -binding sites, the parameters of such a model were easier to describe. Parvalbumin is not very close to calmodulin from an evolutionary point of view. Therefore, a principle of simplicity leads us to suggest that the sequential binding model is probably pertinent to most EF-hand Ca 2+ -binding proteins. 6. Open questions Recent studies on calmodulin using mass spectrometry have shown that calmodulin exhibits more than four binding sites for Ca2+ and for others cations (72). Other Ca2+ -binding proteins exhibit cationic binding sites (Zn2+ or Cu2+ for S100 [73], a third site for Parvalbumin [74]). This suggests that, in addition to the so called EF Ca2+ -binding sites, others cationic sites exist on these proteins. These sites may bind Ca2+ and/or Mg2+ among others cations with low specificity. However, up to now, there are only few studies on the physiological role of these sites. Recently, using microcalorimetry, we have shown that Mg2+ acts through these cationic sites to modulate the Ca2+ -binding affinities of the individual EF hand sites of calmodulin. We also brought evidence that Mg2+ modulates the interaction between the two lobes of calmodulin (75). Other experimental conditions (ionic strength, presence of target structures or peptides such as the RS20 or M13 [the binding domain of myosin light chain kinase of smooth muscle or skeletal muscle, respectively], others cations, ethylene glycol) modify the Ca2+ -binding parameters of the system, but qualitatively the mechanism of Ca2+ -binding to calmodulin seems to remain unchanged. In the cell, the water concentration is likely to be different from the one prevailing in the test tube. The observation that ethylene glycol (which decreases the water concentration) has a strong effect on calmodulin (64), suggests that depending on the localization of calmodulin within the cell, its Ca2+ -binding parameters and, therefore, its Ca2+ -binding kinetics may be different. Monitoring the different calmodulin/Ca2+ complexes directly in the various cellular compartment seems now to be of paramount importance if one has to get deeper insight into how calmodulin plays its multifunctional role in the cell. 7. Conclusions Most of the controversies in the Ca2+ -binding protein field have arisen from a misuse or misunderstanding of the equations governing the interaction between a protein and a ligand, when the protein is a multisite protein.
38 Haiech and Kilhoffer We may suggest the following conjectures: • The set of binding equations probably has mathematical properties that it would be interesting to decipher in order to improve the statistical tests associated with the deconvolution of calcium binding experimental curves; • The use of several experimental techniques (namely, mass spectrometry, equilibrium or flow dialysis, microcalorimetry, spectroscopic techniques, and so on) is needed to cross the possible molecular interpretations; and • With the progress in molecular dynamics, the molecular interpretation of a protein system has to be simulated. New emerging techniques let envisage that in the coming years, the interaction between a protein and its ligands will be performed directly inside the cell and at the level of the single molecule. Such a fantastic development will shed new light on how cells manage Ca 2+ signaling. References 1. Gerke, V., Heizmann, C. W., and Krebs J. (1998) Special Issue. 5th European symposium on calcium binding proteins in normal and transformed cells, in Biochem. Biophys. Acta. Molecular Cell Research, vol. 1148 (2) (Avruch, J., ed.), Elsevier, Amsterdam. 2. Wasserman, R. H., Corradino, R. A., Carafoli, E., Kretsinger, R. H., MacLennan, D. H., and Siegel, F. L. (1977) Calcium — Binding Proteins and Calcium Function, North Holland, New York. 3. Heizmann, C. W. (1991) Novel calcium binding proteins, in Fundamentals and Clinical Implications, Springer-Verlag, Berlin, Heidelberg. 4. Kretsinger, R. H. (1975) Hypothesis: calcium modulated proteins contain EF hands, in Calcium Transport in Contraction and Secretion (Carafoli, E., et al., eds.), Amsterdam, North-Holland, pp. 469–78. 5. Pochet, R., Lawson, D. E. M., and Heizmann, C. W. (1989) Calcium binding proteins in normal and transformed cells, in Advances in Experimental Medicine and Biology, vol. 269, Plenum, New York. 6. Goodman, M., Pechere, J. F., Haiech, J., and Demaille, J. G. (1979) Evolutionary diversification of structure and function in the family of intracellular calcium-binding proteins. J. Mol. Evol. 13, 331–352. 7. Cheung, W. Y. (1970) Cyclic 3',5'-nucleotide phosphodiesterase. Demonstration of an activator. Biochem. Biophys. Res. Commun. 38, 533–538. 8. Cheung, W. Y. (1980) Calmodulin plays a pivotal role in cellular regulation. Science 207, 19–27. 9. Kakiuchi, S. and Yamazaki, R. (1970) Calcium dependent phosphodiesterase activity and its activating factor (PAF) from brain studies on cyclic 3',5'-nucleotide phosphodiesterase (3). Biochem. Biophys. Res. Commun. 41, 1104–1110. 10. Klee, C. B., Crouch, T. H., and Richman, P. G. (1980) Calmodulin. Annu. Rev. Biochem. 49, 489–515. 11. Klee, C. B. and Vanaman, T. C. (1982) Calmodulin. Adv. Prot. Chem. 35, 213–321.
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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
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 and 16: xiv Contents of Companion Volume 15
Page 17 and 18: xvi Contributors LESLIE D. HICKS
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
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Page 27 and 28: 8 Yazawa DuPont-NEN and the molar c
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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: 36 Haiech and Kilhoffer Fig. 3. Mec
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
Page 67 and 68: 48 Martin and Bayley 4. Set the tem
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Page 71 and 72: 52 Martin and Bayley discussed by M
Page 73 and 74: 54 Martin and Bayley References 1.
Page 75 and 76: 20 Dean, Kelsey, and Reik
Page 77 and 78: 58 Fabian and Vogel are equipped wi
Page 79 and 80: 60 Fabian and Vogel The penetration
Page 81 and 82: 62 Fabian and Vogel perature, ionic
Page 83 and 84: 64 Fabian and Vogel Fig. 3. IR spec
Page 85 and 86: 66 Fabian and Vogel Fig. 4. Lower t
Page 87 and 88: 68 Fabian and Vogel These correlati
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Page 91 and 92: 72 Fabian and Vogel 4. ATR-FTIR spe
Page 93 and 94: 74 Fabian and Vogel 25. Georg, H.,
Page 95 and 96: 76 Weljie and Vogel Fig. 1. Simplif
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20 Dean, Kelsey, and Reik
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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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148 Trewhella and Krueger analytica
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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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168 Doherty-Kirby and Lajoie Fig. 1
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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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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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