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Deconvolution of Calcium-Binding Curves 41 45. Forsen, S., Thulin, E., Drakenberg, T., Krebs, J., and Seamon, K. (1980) A 113Cd NMR study of calmodulin and its interaction with calcium, magnesium and trifluoperazine. FEBS Lett. 117, 189–194. 46. Seamon, K. (1980) NMR studies on tyrosine-138 of calmodulin. Ann. NY Acad. Sci. 356, 433–434. 47. Krebs, J., Carafoli, E., Thulin, E., and Forsen, S. (1980) 1H- and 113Cd-NMR studies of calmodulin. Ann. NY Acad. Sci. 356, 397–398. 48. Andersson, T., Drakenberg, T., Forsen, S., and Thulin, E. (1982) Characterization of the Ca 2+ binding sites of calmodulin from bovine testis using 43Ca and 113Cd NMR. Eur. J. Biochem. 126, 501–505. 49. Teleman, A., Drakenberg, T., and Forsen, S. (1986) Kinetics of Ca 2+ binding to calmodulin and its tryptic fragments studied by 43Ca-NMR. Biochim. Biophys. Acta. 873, 204–213. 50. Yazawa, M., Kawamura, E., Minowa, O., Yagi, K., Ikura, M., and Hikichi, K. (1984) N-terminal region (domain 1) of calmodulin is the low affinity site for Ca 2+ . A 13C NMR study of S-cyanocalmodulin. J. Biochem. (Tokyo) 95, 443–446. 51. Drabikowski, W., Kuznicki, J., and Grabarek, Z. (1977) Similarity in Ca2+-induced changes between troponic-C and protein activator of 3':5'-cyclic nucleotide phosphodiesterase and their tryptic fragments. Biochim. Biophys. Acta. 485, 124–133. 52. Klee, C. B. (1977) Conformational transition accompanying the binding of Ca 2+ to the protein activator of 3',5'-cyclic adenosine monophosphate phosphodiesterase. Biochemistry 16, 1017–1024. 53. Richman, P. G. and Klee, C. B. (1979) Specific perturbation by Ca 2+ of tyrosyl residue 138 of calmodulin. J. Biol. Chem. 254, 5372–5376. 54. Drabikowski, W., Brzeska, H., Kuznicki, J., and Grabarek, Z. (1980) Studies on structure and function of calmodulin. Ann. NY Acad. Sci. 356, 374–375. 55. Kilhoffer, M. C., Demaille, J. G., and Gerard, D. (1981) Tyrosine fluorescence of ram testis and octopus calmodulins. Effects of calcium, magnesium, and ionic strength. Biochemistry 20, 4407–4414. 56. Wang, C. L. (1985) A note on Ca 2+ binding to calmodulin. Biochem. Biophys. Res. Commun. 130, 426–430. 57. Drabikowski, W., Brzeska, H., and Venyaminov, S. (1982) Tryptic fragments of calmodulin. Ca 2+ - and Mg 2+ -induced conformational changes. J. Biol. Chem. 257, 11,584–11,590. 58. Minowa, O. and Yagi, K. (1984) Calcium binding to tryptic fragments of calmodulin. J. Biochem. (Tokyo) 96, 1175–1182. 59. Dalgarno, D. C., Klevit, R. E., Levine, B. A., Williams, R. J., Dobrowolski, Z., and Drabikowski, W. (1984) 1H NMR studies of calmodulin. Resonance assignments by use of tryptic fragments. Eur. J. Biochem. 138, 281–289. 60. Aulabaugh, A., Niemczura, W. P., and Gibbons, W. A. (1984) High field proton NMR studies of tryptic fragments of calmodulin: a comparison with the native protein. Biochem. Biophys. Res. Commun. 118, 225–232. 61. Maune, J. F., Klee, C. B., and Beckingham, K. (1992) Ca 2+ binding and conformational change in two series of point mutations to the individual Ca (2+) -binding sites of calmodulin. J. Biol. Chem. 267, 5286–5295.
42 Haiech and Kilhoffer 62. Beckingham, K. (1991) Use of site-directed mutations in the individual Ca 2(+) - binding sites of calmodulin to examine Ca 2(+) -induced conformational changes. J. Biol. Chem. 266, 6027–6030. 63. Kilhoffer, M. C., Roberts, D. M., Adibi, A. O., Watterson, D. M., and Haiech, J. (1988) Investigation of the mechanism of calcium binding to calmodulin. Use of an isofunctional mutant with a tryptophan introduced by site-directed mutagenesis. J. Biol. Chem. 263, 17,023–17,029. 64. Kilhoffer, M. C., Kubina, M., Travers, F., and Haiech, J. (1992) Use of engineered proteins with internal tryptophan reporter groups and pertubation techniques to probe the mechanism of ligand-protein interactions: investigation of the mechanism of calcium binding to calmodulin. Biochemistry 31, 8098–8106. 65. Pedigo, S. and Shea, M. A. (1995) Discontinuous equilibrium titrations of cooperative calcium binding to calmodulin monitored by 1-D 1H-nuclear magnetic resonance spectroscopy. Biochemistry 34, 10,676–10,689. 66. Pedigo, S. and Shea, M. A. (1995) Quantitative endoproteinase GluC footprinting of cooperative Ca2+ binding to calmodulin: proteolytic susceptibility of E31 and E87 indicates interdomain interactions. Biochemistry 34, 1179–1196. 67. Shea, M. A., Verhoeven, A. S., and Pedigo, S. (1996) Calcium-induced interactions of calmodulin domains revealed by quantitative thrombin footprinting of Arg37 and Arg106. Biochemistry 35, 2943–2957. 68. Sorensen, B. R. and Shea, M. A. (1998) Interactions between domains of apo calmodulin alter calcium binding and stability. Biochemistry 37, 4244–4253. 69. Kilhoffer, M. C., Roberts, D. M., Adibi, A., Watterson, D. M., and Haiech, J. (1989) Fluorescence characterization of VU-9 calmodulin, an engineered calmodulin with one tryptophan in calcium binding domain III. Biochemistry 28, 6086–6092. 70. Haiech, J., Kilhoffer, M. C., Craig, T. A., Lukas, T. J., Wilson, E., Guerra-Santos, L., and Watterson, D. M. (1990) Mutant analysis approaches to understanding calcium signal transduction through calmodulin and calmodulin regulated enzymes. Adv. Exp. Med. Biol. 269, 43–56. 71. Haiech, J., Derancourt, J., Pechere, J. F., and Demaille, J. G. (1979) Magnesium and calcium binding to parvalbumins: evidence for differences between parvalbumins and an explanation of their relaxing function. Biochemistry 18, 2752–2758. 72. Lafitte, D., Capony, J. P., Grassy, G., Haiech, J., and Calas, B. (1995) Analysis of the ion binding sites of calmodulin by electrospray ionization mass spectrometry. Biochemistry 34, 13,825–13,832. 73. Heizmann, C. W. and Cox, J. A. (1998) New perspectives on S100 proteins: a multi-functional Ca (2+) -, Zn (2+) - and Cu (2+) -binding protein family. Biometals 11, 383–397. 74. Declercq, J. P., Tinant, B., Parello, J., and Rambaud, J. (1991) Ionic interactions with parvalbumins. Crystal structure determination of pike 4. 10 parvalbumin in four different ionic environments. J. Mol. Biol. 220, 1017–1039. 75. Gilli, R., Lafitte, D., Lopez, C., Kilhoffer, M., Makarov, A., Briand, C., and Haiech, J. (1998) Thermodynamic analysis of calcium and magnesium binding to calmodulin. Biochemistry 37, 5450–5456.
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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
Page 10 and 11: Contents Dedication ...............
Page 12: Contents xi 26 Enzymatic Assays to
Page 15 and 16: xiv Contents of Companion Volume 15
Page 17 and 18: xvi Contributors LESLIE D. HICKS
Page 19 and 20: 20 Dean, Kelsey, and Re
Page 21 and 22: 2 Yazawa
Page 23 and 24: 4 Yazawa Fig. 1. Schematic represen
Page 25 and 26: 6 Yazawa Fig. 2. Shop drawing for t
Page 27 and 28: 8 Yazawa DuPont-NEN and the molar c
Page 29 and 30: 10 Yazawa Fig. 4. Examples of the C
Page 31 and 32: 12 Yazawa 5. Plot the calculated Ca
Page 33 and 34: 14 Yazawa 12. Starovasnik, M. A., D
Page 35 and 36: 16 Fig. 1. Molecular structures and
Page 37 and 38: 18 Linse 7. 0.1 M EDTA. Dissolve 37
Page 39 and 40: 20 Linse iterate the other paramete
Page 41 and 42: 22 Linse tive to small alterations
Page 43 and 44: 24 Linse References 1. Tsien, R. Y.
Page 45 and 46: 26 Haiech and Kilhoffer to use the
Page 47 and 48: 28 Haiech and Kilhoffer where γ is
Page 49 and 50: 30 Haiech and Kilhoffer reporter gr
Page 51 and 52: 32 Haiech and Kilhoffer tein with i
Page 53 and 54: 34 Haiech and Kilhoffer Calmodulin
Page 55 and 56: 36 Haiech and Kilhoffer Fig. 3. Mec
Page 57 and 58: 38 Haiech and Kilhoffer We may sugg
Page 59: 40 Haiech and Kilhoffer 29. Stewart
Page 63 and 64: 44 Martin and Bayley Fig. 1. Absorp
Page 65 and 66: 46 Martin and Bayley evaporation. C
Page 67 and 68: 48 Martin and Bayley 4. Set the tem
Page 69 and 70: 50 Martin and Bayley Fig. 2. Near-U
Page 71 and 72: 52 Martin and Bayley discussed by M
Page 73 and 74: 54 Martin and Bayley References 1.
Page 75 and 76: 20 Dean, Kelsey, and Reik
Page 77 and 78: 58 Fabian and Vogel are equipped wi
Page 79 and 80: 60 Fabian and Vogel The penetration
Page 81 and 82: 62 Fabian and Vogel perature, ionic
Page 83 and 84: 64 Fabian and Vogel Fig. 3. IR spec
Page 85 and 86: 66 Fabian and Vogel Fig. 4. Lower t
Page 87 and 88: 68 Fabian and Vogel These correlati
Page 89 and 90: 70 Fabian and Vogel Fig. 5. Amide I
Page 91 and 92: 72 Fabian and Vogel 4. ATR-FTIR spe
Page 93 and 94: 74 Fabian and Vogel 25. Georg, H.,
Page 95 and 96: 76 Weljie and Vogel Fig. 1. Simplif
Page 97 and 98: 78 Weljie and Vogel Fig. 3. Steady-
Page 99 and 100: 80 Weljie and Vogel VIS spectrophot
Page 101 and 102: 82 Weljie and Vogel 4. A series of
Page 103 and 104: 84 Table 1 Advanced Fluorescence Me
Page 105 and 106: 86 Weljie and Vogel References 1. L
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Page 109 and 110: 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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20 Dean, Kelsey, and Reik
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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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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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