Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Protein Structure Calculation from NMR 279 Table 3 The Most Commonly Used Karplus Relations, 3J(θ) = Acos2θ + Bcosθ + C, for Proteins to Obtain a Torsion Angle θ from the Corresponding 3J Coupling Constant Offset Angle Coupling A(Hz) B(Hz) C(Hz) (degree) a Ref. φ HN –Hα 6.98 –1.38 1.72 –60 47 HN –C' 4.32 0.84 0.00 180 47 HN –Cβ 3.39 –0.94 0.07 60 47 ψ Hα χ1 –Ni+1 H –0.88 –0.61 –0.27 –120 48 α –Hβ 9.5 –160 1.80 –120/0 49 N–Hβ –4.40 1.20 0.10 120/–120 50 C'–Hβ 7.20 –2.04 0.60 0/120 51 a Difference between θ and the standard torsion angle φ, ψ, and χ 1 . of which have been documented elsewhere (3). Recently, the chemical shifts of C α , C β , C', and H α are also being routinely used for identifying local backbone conformation in proteins (52,53). The C α and C' nuclei show an upfield shift in β-strand and a downfield shift in helical structures relative to random coil shifts. Both C β and H α nuclei exhibit the opposite correlation of a downfield shift in β-strands and an upfield shift in helices. Various methods are available for identifying secondary structure elements from the chemical shifts, such as the chemical shift index (CSI) (54). We routinely employ Metzler’s method (55) that uses a combination of C α and C β chemical shifts of i – 1, i, and i + 1 residues. Information about the secondary structure elements in a protein helps with the structural determination process in two ways. First, it allows deduction of dihedral angle restraints based on regular secondary structures. To this end, a new method called TALOS has recently been developed to extract φ and ψ angle restraints by searching a database for chemical shift and sequence homology (56). Second, hydrogen-bonding restraints may be added to regions assigned to a regular secondary structure, although caution must be taken to ensure that the amide exchange rate data concur with the secondary structure already deduced from the NOEs, 3 J-coupling constants, and chemical shifts. Any discrepancy implies a distortion of the regular structure or the presence of flexible regions. Acknowledgments This work is supported by a grant from the Medical Research Council of Canada (MRCC) and National Cancer Institute of Canada (NCIC) to M. I. and by OCI/Amgen Fellowship and NCIC to T. K. Mal and M. Ikura are MRCC Scientist and Howard Hughes Medical Institute of International Research Scholars. We thank Tao Yuan, Hong Qian, and Antonio Pineda-Lucena for useful discussions.
280 Mal et al. References 1. Drenth, J. (1994) Principles of Protein X-ray Crystallography. Springer, New York. 2. Abragam, A. (1961) Principles of Nuclear Magnetism. Clarendon, Oxford. 3. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley, New York. 4. Arseniev, A. S., Kondakov, V. I., Maiorov, V. N., and Bystrov, V. F. and Ovchinnikov, I. A. (1983) Conformation NMR Annalysis of the spatial structure of Butkus eupeus insectotoxin 15A. Bioeng. Rhim. 9, 1667–1689. 5. Braun, W., Bosch, C., Brown, L. R., Gö, N., and Wüthrich, K. (1981) Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon. Biochim. Biophys. Acta 667, 377–396. 6. Clore, G. M., Brünger, A. T., Karplus, M., and Gronenborn, A. M. (1986) Application of molecular dynamics with interproton distance restraints to three dimensional protein structure determination: a model study of crambin. J. Mol. Biol. 191, 523–551. 7. Williamson, M. P., Havel, T. F., and Wüthrich, K. (1985) Solution conformation of proteinase inhibitor IIa from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry. J. Mol. Biol. 182, 295–315. 8. Zuiderweg, E. R. P., Billeter, M., Boelens, R., Scheek, R. M., Wüthrich, K., and Kaptein, R. (1984) Spatial arrangement of the three a helices in a solution structure of E. coli lac repressor DNA-binding domain. FEBS Lett. 174, 243–247. 9. Havel, T. F. and Wüthrich, K. (1984) A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular 1H– 1H proximities in solution. Bull. Math. Biol. 46, 673–698. 10. Braun, W. and Gö, N. (1985) Calculation of protein conformation by proton-proton distance constraints: a new efficient algorithm. J. Mol. Biol. 186, 611–626. 11. Brünger, A. T. (1992) X-PLOR, Version 3. 1. A System for X-Ray Crystallography and NMR. Yale University Press, New Haven, Connecticut. 12. Nilges, M. (1995) Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J. Mol. Biol. 245, 645–660. 13. Nilges, M., Macias, M., O’Donoghue, S. I., and Oschkinat, H. (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β spectrin. J. Mol. Biol. 269, 408–422. 14. Güntert, P., Mumenthaler, C., and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283–298. 15. Güntert P. (1998) Structure calculation of biological macromolecules from NMR data. Quart. Rev. Biophys. 31, 145–237. 16. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690.
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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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Page 267 and 268: 248 Weljie and Heringa ment require
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Page 275 and 276: 256 Li et al. In order for these ex
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Page 279 and 280: 260 Li et al. 3. When the 45% D 2O/
Page 281 and 282: 262 Li et al. sion system works eff
Page 283 and 284: 264 Li et al. reliably produce high
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Page 289 and 290: 270 Mal et al. Table 1 Simulated An
Page 291 and 292: 272 Mal et al. 3.1.2.1. AMBIGUOUS D
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 301 and 302: 282 Mal et al. 33. Jeener, J., Meie
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Page 305 and 306: 286 Werner et al. Our research has
Page 307 and 308: 288 Fig. 1. (A) T 1, T 2 and the he
Page 309 and 310: 290 Werner et al. tion, using gradi
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Page 317 and 318: 298 Werner et al. 9. Reinhardt, D.
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Page 321 and 322: 302 Boyd et al. utilize residual di
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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
Page 339 and 340: 320 Yap et al. modified EF-hand is
Page 341 and 342: 322 Table 1 Angle and Distance Outp
Page 343 and 344: 324 Yap et al. 2. Ikura, M. (1995)
Page 345 and 346: 326 Kobayashi that S-100A1 and S-10
Page 347 and 348: 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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