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Monitoring Ca 2+ -Calmodulin Concentration 381 approx 20-fold less. The 45 nMK d indicator appears to represent a good balance between maximizing the indicator response to a typical [Ca 2+ –CaM] i transient and minimizing perturbation of the CaM system. References 1. Nairn, A. C. and Picciotto, M. R. (1994) Calcium/calmodulin-dependent protein kinases. Semin. Cancer Biol. 5, 295–303. 2. Gallagher, P. J., Herring, B. P., and Stull, J. T. (1997) Myosin light chain kinases. J. Muscle Res. Cell Motil., 18, 1–16. 3. Bredt, D. S. and Snyder, S. H. (1990) Isolation of nitric oxide synthetase, a calmodulin-requiring enzyme. Proc. Natl. Acad. Sci. USA 87, 682–685. 4. Stemmer, P. M. and Klee, C. B. (1994) Dual calcium ion regulation of calcineurin by calmodulin and calcineurin B. Biochemistry 33, 6859–6866. 5. Cooper, D. M., Mons, N., and Karpen, J. W. (1995) Adenylyl cyclases and the interaction between calcium and cAMP signalling. Nature 374, 421–424. 6. Cox, J. A., Malnoe, A., and Stein, E. A. (1981) Regulation of brain cyclic nucleotide phosphodiesterase by calmodulin. J. Biol. Chem. 256, 3218–3222. 7. Manalan, A. S. and Klee, C. B. (1984) Calmodulin. Adv. Cycl. Nuc. Prot. Phos. Res. 18, 227–278. 8. Vogel, H. J. and Zhang, M. J. (1995) Protein engineering and NMR studies of Calmodulin. Mol. Cell Biochem. 149, 3–15. 9. Apel, E. D. and Storm, D. R. (1992) Functional domains of neuromodulin (GAP-43). Perspect. Dev. Neurobiol. 1, 3–11. 10. Coluccio, L. M. (1997) Myosin I. Am. J. Physiol. 273, C347–359. 11. Whittaker, M. and Milligan, R. A. (1997) Conformational changes due to calciuminduced calmodulin dissociation in brush border myosin I-decorated F-actin revealed by cryoelectron microscopy and image analysis. J. Mol. Biol. 269, 548–557. 12. Cho, H. J., Xie, Q. W., Calaycay, J., Mumford, R. A., Swiderek, K. M., Lee, T. D., and Nathan, C. (1992) Calmodulin is a subunit of nitric oxide synthase from macrophages. J. Exp. Med. 176, 599–604. 13. Shenolikar, S., Cohen, P. T., Cohen, P., Nairn, A. C., and Perry, S. V. (1979) The role of calmodulin in the structure and regulation of phosphorylase kinase from rabbit skeletal muscle. Eur. J. Biochem. 100, 329–337. 14. Xia, X. M., Fakler, B., Rivard, A., Wayman, G., Johnson-Pais, T., Keen, J. E., et al. (1998) Mechanism of calcium gating in small-conductance calcium-activated potassium channels. Nature 395, 503–507. 15. Shoshan-Barmatz, V. and Ashley, R. H. (1998) The structure, function, and cellular regulation of ryanodine-sensitive Ca2+ release channels. Int. Rev. Cytol. 183, 185–270. 16. Deisseroth, K., Heist, E. K., and Tsien, R. W. (1998) Translocation of calmodulin to the nucleus supports CREB phosphorylation in hippocampal neurons. Nature 392, 198–202. 17. Luby-Phelps, K., Hori, M., Phelps, J. M., and Won, D. (1995) Ca (2+) -regulated dynamic compartmentalization of calmodulin in living smooth muscle cells. J. Biol. Chem. 270, 21,532–21,538.
382 Persechini 18. Chafouleas, J. G., Bolton, W. E., Hidaka, H., Boyd, A. E. D., and Means, A. R. (1982) Calmodulin and the cell cycle: involvement in regulation of cell-cycle progression. Cell 28, 41–50. 19. Kakiuchi, S., Yasuda, S., Yamazaki, R., Teshima, Y., Kanda, K., Kakiuchi, R., and Sobue K. (1982) Quantitative determinations of calmodulin in the supernatant and particulate fractions of mammalian tissues. J. Biochem. 92, 1041–1048. 20. Vanaman, T. C. and Klee, C. B. (1982) Calmodulin. Adv. Protein Chem. 35, 213–321. 21. Schulman, H., Heist, K., and Srinivasan, M. (1995) Decoding Ca 2+ signals to the nucleus by multifunctional CaM kinase. Prog. Brain Res. 105, 95–104. 22. Beals, C. R., Clipstone, N. A., Ho, S. N., and Crabtree, G. R. (1997) Nuclear localization of NF-ATc by a calcineurin-dependent, cyclosporin-sensitive intramolecular interaction. Genes Devel. 11, 824–834. 23. Romoser, V. A., Hinkle, P. M., and Persechini, A. (1997) Detection in living cells of Ca 2+ -dependent changes in the fluorescence of an indicator composed of two green fluorescent protein variants linked by a calmodulin-binding sequence. A new class of fluorescent indicators. J. Biol. Chem. 272, 13,270–13,274. 24. Persechini, A. and Cronk, B. (1999) The relationship between the free concentrations of Ca 2+ and Ca 2+ -calmodulin in intact cells. J. Biol. Chem. 274, 6827–6830. 25. Persechini, A., Lynch, J. A., and Romoser, V. A. (1997) Novel fluorescent indicator proteins for monitoring free intracellular Ca 2+ . Cell Calcium 22, 209–216. 26. Miyawaki, A., Llopis, J., Heim, R., McCaffery, J. M., Adams, J. A., et al. (1997) Fluorescent indicators for Ca 2+ based on green fluorescent proteins and calmodulin. Nature 388, 882–887. 27. Persechini, A., Blumenthal, D. K., Jarrett, H. W., Klee, C. B., Hardy, D. O., and Kretsinger, R. H. (1989) The effects of deletions in the central helix of calmodulin on enzyme activation and peptide binding. J. Biol. Chem. 264, 8052–8058. 28. Lukas, T. J., Burgess, W. H., Prendergast, F. G., Lau, W., and Watterson, D. M. (1986) Calmodulin binding domains: characterization of a phosphorylation and calmodulin binding site from myosin light chain kinase. Biochemistry 25, 1458–1464. 29. Tsien, R. Y. (1998) The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544. 30. Miyawaki, A., Griesbeck, O., Heim, R., and Tsien, R. Y. (1999) Dynamic and quantitative Ca 2+ measurements using improved cameleons. Proc. Natl. Acad. Sci. USA 96, 2135–2140. 31. Bers, D., Patton, C., and Nuccitelli, R. (1994) A practical guide to the preparation of Ca 2+ buffers. Methods Cell Biol. 40, 3–29. 32. Brozovich, F. V. (1995) PKC regulates agonist-induced force enhancement in single alpha-toxin permeabilized smooth muscle cells. Am. J. Physiol. 268, C1202–C1206. 33. Grynkiewicz, G., Poenie, M., and Tsien, R. (1985) A new generation of Ca 2+ indicators with greatly improved fluorescence properties. J. Biol. Chem. 260, 3440–3450. 34. Blumenthal, D. K. and Stull, J. T. (1980) Activation of skeletal muscle myosin light chain kinase by calcium (2+) and calmodulin. Biochemistry 19, 5608–5614.
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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
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
Page 363 and 364: 344 Walsh et al. Fig. 1. CaM-depend
Page 367 and 368: 348 Walsh et al. 3.5. NOS Reduction
Page 373 and 374: 354 Walsh et al. 3. Cho, M. J., Vag
Page 375 and 376: 356 Hughes et al. The electroporati
Page 377 and 378: 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: 20 Dean, Kelsey, and Reik
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
Page 399: 380 Persechini relatively insensiti
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
Page 415 and 416: 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
Page 423 and 424: 404 Török et al. Fig. 16. Indicat
Page 425 and 426: 406 Török et al. the significantl
Page 427 and 428: 408 Török et al.
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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