Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Shape and Dynamics of Calcium-Binding Proteins 299 pretation of N–15 nuclear magnetic-relaxation of proteins. J. Am. Chem. Soc. 112, 4989–4991. 24. Johnson, B. A. and Blevins, R. A. (1994) NMR View — a computer-program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614. 25. Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–60. 26. Palmer, A. G., Rance, M., and Wright, P. E. (1991) Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance C-12 heteronuclear NMR-spectroscopy. J. Am. Chem. Soc. 113, 4371–4380. 27. Mandel, A. M., Akke, M., and Palmer, A. G. (1995) Backbone dynamics of Escherichia-coli ribonuclease HI- correlations with structure and function in an active enzyme. J. Mol. Biol. 246, 144–163. 28. Kay, L. E., Torchia, D. A., and Bax, A. (1989) Backbone dynamics of proteins as studied by N–15 inverse detected heteronuclear NMR-spectroscopy — application to staphylococcal nuclease. Biochemistry 28, 8972–8979. 29. Farrow, N. A., Zhang, O. W., Formankay, J. D., and Kay, L. E. (1994) A heteronuclear correlation experiment for simultaneous determination of N–15 longitudinal decay and chemical-exchange rates of systems in slow equilibrium. J. Biomol. NMR 4, 727–734. 30. Vold, R. R. and Vold, R. L. (1976) Transverse relaxation in heteronuclear coupled spin systems: AX, AX2, AX3, and AXY. J. Chem. Phys. 64, 320–332. 31. Boyd, J., Hommel, U., and Campbell, I. D. (1990) Influence of cross-correlation between dipolar and anisotropic chemical-shift relaxation mechanisms upon longitudinal relaxation rates of N–15 in macromolecules. Chem. Phys. Lett. 175, 477– 482. 32. Kay, L. E., Nicholson, L. K., Delaglio, F., Bax, A., and Torchia, D. A. (1992) Pulse sequences for removal of the effects of cross-correlation between dipolar and chemical-shift anisotropy relaxation mechanism on the measurement of heteronuclear T1 and T2 values in proteins. J. Mag. Reson. 97, 359–375. 33. Wang, A. C. and Bax, A. (1993) Minimizing the effects of radiofrequency heating in multidimensional NMR experiments. J. Biomol. NMR 3, 715–720. 34. Noggle, J. H. and Shirmer, R. E. (1971) The Nuclear Overhasuer Effect: Chemical Applications. Academic, New York. 35. Grzesiek, S. and Bax, A. (1993) The importance of not saturating H2O in protein NMR — application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115, 12,593–12,594. 36. Kay, L. E. (1995) Field gradient techniques in NMR-spectroscopy. Curr. Opin. Struct. Biol. 5, 674–681. 37. Skelton, N. J., Palmer, A. G., Akke, M., Kordel, J., Rance, M., and Chazin, W. J. (1993) Practical aspects of 2-dimensional proton-detected N-15 spin relaxation measurements. J. Mag. Reson. Ser. B 102, 253–264. 38. Zhu, G. and Bax, A. (1992) Improved linear prediction of damped NMR signals using modified forward backward linear prediction. J. Mag. Reson. 100, 202–207.
300 Werner et al. 39. Press, W. H., Flannery, B. P., Teukosky, S. A., and Vetterling, W. T. (1990) Numerical Recipes. Cambridge University Press, New York. 40. Downing, A. K., Knott, V., Werner, J. M., Cardy, C. M., Campbell, I. D., and Handford, P. A. (1996) Solution structure of a pair of calcium-binding epidermal growth factor-like domains: implications for the Marfan syndrome and other genetic disorders. Cell 85, 597–605. 41. Copie, V., Tomita, Y., Akiyama, S. K., Aota, S., Yamada, K. M., Venable, R. M., et al. (1998) Solution structure and dynamics of linked cell attachment modules of mouse fibronectin containing the RGD and synergy regions: comparison with the human fibronectin crystal structure. J. Mol. Biol. 277, 663–682. 42. Knott, V., Downing, A. K., Cardy, C. M., and Handford, P. (1996) Calcium binding properties of an epidermal growth factor-like domain pair. J. Mol. Biol. 255, 22–27. 43. Luz, L. and Meiboom, S. (1963) Nuclear magneic resonance study of the protolysis of trimethylammonium ion in aqueous solution — order of reaction with respect to solvent. J. Chem. Phys. 39, 366–370. 44. Loria, J. P., Rance, M., and Palmer, A. G. (1999) A relaxation-compensated Carr- Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J. Am. Chem. Soc. 121, 2331–2332. 45. Deverell, C., Morgan, R. E., and Strange, J. H. (1970) Studies of chemical exchange by nuclear magnetic relaxation in the rotating frame. Mol. Phys. 18, 553–559. 46. Akke, M. and Palmer, A. G. (1996) Monitoring macromolecular motions on microsecond to millisecond time scales by R1ρ-R1 constant relaxation-time NMR-spectroscopy. J. Am. Chem. Soc. 118, 911–912. 47. Fushman, D., Tjandra, N., and Cowburn, D. (1998) Direct measurement of N–15 chemical shift anisotropy in solution. J. Am. Chem. Soc. 120, 10,947–10,952. 48. Fushman, D., Tjandra, N., and Cowburn, D. (1999) An approach to direct determination of protein dynamics from N-15 NMR relaxation at multiple fields, independent of variable N-15 chemical shift anisotropy and chemical exchange contributions. J. Am. Chem. Soc. 121, 8577–8582. 49. Kroenke, C. D., Rance, M., and Palmer, A. G. (1999) Variability of the N–15 chemical shift anisotropy in Escherichia coli ribonuclease H in solution. J. Am. Chem. Soc. 121, 10,119–10,125. 50. Tjandra, N., Szabo, A., and Bax, A. (1996) Protein backbone dynamics and N-15 chemical-shift anisotropy from quantitative measurement of relaxation interference effects. J. Am. Chem. Soc. 118, 6986–6991. 51. Clore, G. M., Gronenborn, A. M., Szabo, A., and Tjandra, N. (1998) Determining the magnitude of the fully asymmetric diffusion tensor from heteronuclear relaxation data in the absence of structural information. J. Am. Chem. Soc. 120, 4889–4890.
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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
Page 267 and 268: 248 Weljie and Heringa ment require
Page 269 and 270: 250 Weljie and Heringa 10. Kawasaki
Page 271 and 272: 252 Weljie and Heringa 44. Thompson
Page 273 and 274: 254 Weljie and Heringa
Page 275 and 276: 256 Li et al. In order for these ex
Page 277 and 278: 258 Li et al. 7. Mineral Mixture (s
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 287 and 288: 268 Mal et al. NMR data, X-PLOR (11
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
Page 297 and 298: 278 Mal et al. assign (segid A and
Page 299 and 300: 280 Mal et al. References 1. Drenth
Page 301 and 302: 282 Mal et al. 33. Jeener, J., Meie
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
Page 311 and 312: 292 Werner et al. Fig. 3. (A) Rotat
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Page 317: 298 Werner et al. 9. Reinhardt, D.
Page 321 and 322: 302 Boyd et al. utilize residual di
Page 323 and 324: 304 Boyd et al. Fig. 1. (A) The sol
Page 325 and 326: 306 Boyd et al. or significant peak
Page 327 and 328: 308 Boyd et al. Fig. 3. Histogram o
Page 329 and 330: 310 Boyd et al. total and NOE energ
Page 331 and 332: 312 Boyd et al. 2. When studying mu
Page 333 and 334: 314 Boyd et al. 4. Downing, A. K.,
Page 335 and 336: 316 Boyd et al. 35. Schulte-Herbrug
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
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
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 365 and 366: 346 Walsh et al. Fig. 3. CaM-depend
Page 367 and 368: 348 Walsh et al. 3.5. NOS Reduction
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350 Walsh et al. Fig. 4. CaM-depend
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352 Walsh et al. Fig. 6. CaM-depend
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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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