Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Vector Geometry Mapping 323 Fig. 2. Example of VGM output for calmodulin (1DMO, 1OSA) as displayed by Molscript (11). Domains (i.e., an interacting pair of EF-hands) of Ca 2+ -free calmodulin are of the closed conformation; the exiting helices of these EFhands are labeled “–Ca 2+ .” Exiting helices of Ca 2+ -bound, open domain EF-hands are labeled “+Ca 2+ .” EF-hands are numbered as they appear in the sequence. Apocalmodulin EF1 is used as the reference in this figure. 3. ω is not a necessarily useful parameter for describing a particular conformation; however, it becomes relevant when the value is compared between two EF-hands that are similarly positioned — either a single EF-hand that undergoes small conformational change (e.g., calpain) or several EF-hands in the same protein (e.g., calmodulin and troponin C). A decrease in ω (negative ∆ω) between an EF-hand in the Ca 2+ -bound state and in the Ca 2+ -free state indicates that upon binding Ca 2+ , the exiting helix undergoes a clockwise rotation about the helix axis, relative to the position of the entering helix. 4. Alignment by structure rather than sequence alone will yield a more accurate result. Some EF-hands, particularly those situated at the N-terminus of the protein, often have a partially unravelled exiting helix. This is the primary reason for superimposing all EF-hands using the entering helix, which is less prone to structural variation. 5. Cylinder representation in Molscript considers only the structural coordinates of the backbone C α atoms, compared to the VGM method of averaging the N, C α, and C' atom coordinates to establish vector endpoints. As a result, an entering helix vector calculated by vgm may not lie precisely along the z-axis in the Molscript representation. Acknowledgements This work was supported by a grant from the Medical Research Council of Canada (M. Ikura) and the NIH grant EY-12347 (JBA). M. Ikura is a Howard Hughes Medical Institute Research Scholar and a MRCC Scientist. References 1. Kawasaki, H., Nakayama, S., and Kretsinger, R. H. (1998) Classification and evolution of EF-hand proteins. Biometals 11, 277–295.
324 Yap et al. 2. Ikura, M. (1995) Calcium binding and conformational response in EF-hand proteins. Trends Biochem. Sci. 21, 14–17. 3. Nelson, M. R. and Chazin, W. J. (1998) Structures of EF-hand Ca 2+ -binding proteins: diversity in the organization, packing and response to Ca 2+ binding. Biometals 11, 297–318. 4. Gagné, S. M., Li, M. X, McKay, R. T., and Sykes, B. D. (1998) The NMR angle on troponin C. Biochem. Cell Biol. 76, 302–312. 5. Szebenyi, D. M., Obendorf, S. K., and Moffat, K. (1981) Structure of vitamin D-dependent calcium-binding protein from bovine intestine. Nature 294, 327–332. 6. Herzberg, O. and James, M. N. (1985) Structure of the calcium regulatory muscle protein troponin-C at 2.8 Å resolution. Nature 313, 653–659. 7. Babu, Y. S., Sack, J. S., Greenhough, T. J., Bugg, C. E., Means, A. R., and Cook, W. J. (1985) Three-dimensional structure of calmodulin. Nature 315, 37–40. 8. Zhang, M., Tanaka, T., and Ikura, M. (1995) Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nat. Struct. Biol. 2, 758–767. 9. Mäler, L. M., Potts, B. C. M., and Chazin, W. J. (1999) High resolution solution structure of apo calcyclin and structural variations in the S100 family of calciumbinding proteins. J. Biomol. NMR 13, 233–247. 10. Nelson, M. R. and Chazin, W. J. (1998) An interaction-based analysis of calciuminduced conformational changes in Ca 2+ sensor proteins. Protein Sci. 7, 270–282. 11. Yap, K. L., Ames, J. B., Swindells, M. B., and Ikura, M. (1999) Diversity of conformational states and changes within the EF-hand protein superfamily. Proteins 37, 499–507. 12. Kraulis, P. J. (1991) MOLSCRIPT: a program to produce detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950. 13. Kuboniwa, H., Tjandra, N., Grzesiek, S., Ren, H., Klee, C. B., and Bax, A. (1995) Solution structure of calcium-free calmodulin. Nat. Struct. Biol. 2, 768–776. 14. Rao, S. T., Wu, S., Satyshur, K. A., Ling, K. Y., Kung, C., and Sundaralingam, M. (1993) Structure of Paramecium tetraurelia calmodulin at 1.8 Å resolution. Protein Sci. 2, 436–447. 15. Drohat, A. C., Amburgey, J. C., Abildgaard, F., Starich, M. R., Baldisseri, D., and Weber, D. J. (1996) Solution structure of rat apo-S100B(bb) as determined by NMR spectroscopy. Biochemistry 35, 11,577–11,588. 16. Finn, B. E., Evenäs, J., Drakenberg, T., Waltho, J. P., Thulin, E., and Forsén, S. (1995) Calcium-induced structural changes and domain autonomy in calmodulin. Nat. Struct. Biol. 2, 777–783. 17. Gagné, S. M., Tsuda, S., Li, M. X., Smillie, L. B., and Sykes, B. D. (1995) Structures of the troponin C regulatory domain in the apo and calcium-saturated states. Nat. Struct. Biol. 2, 784–789.
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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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Page 293 and 294: 274 Mal et al. molecular dynamics a
Page 295 and 296: 276 Mal et al. Assuming a rigid bod
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Page 299 and 300: 280 Mal et al. References 1. Drenth
Page 301 and 302: 282 Mal et al. 33. Jeener, J., Meie
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Page 307 and 308: 288 Fig. 1. (A) T 1, T 2 and the he
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Page 317 and 318: 298 Werner et al. 9. Reinhardt, D.
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Page 329 and 330: 310 Boyd et al. total and NOE energ
Page 331 and 332: 312 Boyd et al. 2. When studying mu
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Page 337 and 338: 318 Yap et al. image representation
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Page 347 and 348: 328 Kobayashi 3.2. Coupling of Crom
Page 349 and 350: 330 Kobayashi Fig. 2. Tricine/SDS/P
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Page 353 and 354: 334 Kobayashi Both recombinant S-10
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Page 367 and 368: 348 Walsh et al. 3.5. NOS Reduction
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Page 375 and 376: 356 Hughes et al. The electroporati
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Page 379 and 380: 360 Hughes et al. range, repeat ste
Page 381 and 382: 362 Hughes et al. Table 1 Examples
Page 385 and 386: 366 Persechini of the different CaM
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Page 389 and 390: 370 Persechini 2. 1 L of Terrific b
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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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