Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Spatial Distribution of Ca 2+ -Binding Proteins 405 Fig. 17. Indicator of calmodulin activation using TA-calmodulin and FLcalmodulin. Simultaneous use of the activation-sensitive and activation-insensitive derivative allows us to distinguish between activation and local concentration changes of calmodulin. The sequence shows mitotic events from 79–121 min. FL-calmodulin is an inert fluorophore. If the [Ca 2+ ] is changed from 10 nM – 0.1 mM at physiological ionic strength and pH, the fluorescence intensity of FL-calmodulin changes by less than 5%. No further change occurs on peptide target binding. Similar observations were made with Cy5-calmodulin and Texas Red-calmodulin. Thus FL-, Cy5-, and Texas Red-calmodulins report calmodulin localization in the cell. In contrast, if calmodulin is labeled at Lys 75 with the environmentally sensitive TA-Cl probe (11), Ca 2+ -binding results in a 5.5-fold increase of fluorescence intensity and target binding may cause a further twofold increase (12). TA-calmodulin fluorescence thus reports the interactions of calmodulin, as well as its concentration changes in the cell. In order to distinguish between the two events, TA- and FL-calmodulin can both be applied to the same cell and their fluorescence emissions are scanned simultaneously. 5. It is instructive to compare the target binding and enzyme activation properties of fluorescently labeled calmodulin with unlabeled calmodulin. TA-calmodulin and
406 Török et al. the significantly less-bright Lys 75-labeled DANSYL-calmodulin bind to targets with an approx threefold increased dissociation constant and act as an activator of cyclic-AMP phosphodiesterase similar to unmodified calmodulin. Lys 75-modified calmodulins appear to act as a competitive inhibitor of smooth muscle myosin light-chain kinase (13). They do, however, activate calmodulin-dependent protein kinase II auto- and substrate phosphorylation (Török, K. and Fraser, C., unpublished data). It is thus expected that Lys 75-labeled calmodulins are accurate reporters of calmodulin movements and activities in the cell. The inhibitory property can either be taken advantage of or countered by trace-level application of the fluorescent calmodulin in the cell. References 1. Cohen, P. and Klee, C. B., eds. (1988) Calmodulin. Elsevier, New York. 2. Mann, D. and Vanaman, T. C. (1987) Specific chemical modification as a probe of calmodulin function. Methods Enzymol. 139, 417–433. 3. Zhang, M. and Vogel, H. J. (1993) NMR studies of the pKa’s of the lysine sidechains in calmodulin. J. Biol. Chem. 268, 22,420–22,428. 4. Török, K., Lane, A. N., Martin, S. R., Janot, J.-M., and Bayley, P. M. (1992) Effects of calcium binding on the internal dynamic properties of bovine brain calmodulin, studied by NMR and optical spectroscopy. Biochemistry 31, 3452–3462. 5. Giedroc, D. P., Puett, D., Sinha, S. K., and Brew, K. (1987) Calcium effects on calmodulin lysine reactivities. Arch. Biochem. Biophys. 252, 136–144. 6. Selsted, M. E. (1997) HPLC methods for purification of antimicrobial peptides. Methods Mol. Biol. 78, 17–33. 7. Smith, R. D., Loo, J. A., Edmonds, C. G., Barinaga, C. J., and Udseth, H. R. (1990) New developments in biochemical mass spectrometry: electrospray ionisation. Anal. Chem. 62, 882–899. 8. Mann, M. and Wilm, M. (1995) Electrospray mass spectrometry for protein characterization. Trends Biochem. Sci. 20, 219–224. 9. Allen, G. (1989) Sequencing of proteins and peptides. Laboratory techniques in Biochemistry and Molecular Biology (Burdon, R. H. and van Knippenberg, eds.), Elsevier, Amsterdam. 10. Yost, R. A. and Boyd, R. K. (1990) Tandem mass spectrometry: quadrupole and hybrid instruments. Methods Enzymol. 193, 154–200. 11. Cowley, D. J., O’Kane, E., and Todd, R. S. J. (1991) Triazinylaniline derivatives as fluorescence probes. Part 1. Absorption and fluorescence in organic solvents and in aqueous media in relation to twisted intramolecular charge-transfer state formation, H bonding and protic equilibria. J. Chem. Soc. Perkin. Trans. 2, 1495–1500. 12. Török, K. and Trentham, D. R. (1994) Mechanism of 2-chloro-(ε-amino-Lys75)- (6-(4-N,N-diethylamino-phenyl)-1,3,5-triazin-4-yl)-calmodulin interactions with smooth muscle myosin light chain kinase and derived peptides. Biochemistry 33, 12,807–12,820. 13. Török, K., Cowley, D. J., Brandmeier, B. D., Howell, S., Aitken A., and Trentham. D. R. (1998) Inhibition of calmodulin-activated smooth muscle myosin light chain
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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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Page 379 and 380: 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 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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Page 401 and 402: 382 Persechini 18. Chafouleas, J. G
Page 403 and 404: 384 Török et al. actions in the c
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Page 411 and 412: 392 Török et al. Table 1 Peptide
Page 413 and 414: 394 Török et al. Fig. 7. Nanospra
Page 415 and 416: 396 Török et al. Fig. 9. Nanospra
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Page 429 and 430: 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
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