Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Calcium Binding to Proteins 23 of the chelator. Another problem with waiting too long is that the protein and/or chelator may start to absorb calcium form the cuvet. It is often best to wait 20–60 s until the initial quick changes in absorbance have settled and then note the recording. For a slowly equilibrating system, the cuvet may be put in darkness for equilibration for a few minutes at each titration point. 9. For example, if your absorbance is around 0.2 and you add 5-µL calcium aliquots to 2.5 mL titrand, the dilution will cause the absorbance to drop by 0.0004 at each addition. 10. An in-house computer program that performs the described analysis can be obtained from the author at Sara.Linse@Fkem2.LTH.SE. 11. The initial total calcium concentration in the titrand before any calcium additions are made can be determined by atomic absorption spectroscopy. Another way is to let the titration data specify the initial calcium concentration Ca 0 by fitting the data using several different values of Ca 0, and choosing the one that gives a value of (AMAX-AMIN) that agrees with A 2–A 3, (see Subheading 3.1., step 3). 12. It may be dangerous to use an adjustable factor F if the stoichiometry is not known or if the chelator and/or protein binds calcium with a lower affinity so that the curve does not have a sharp corner at the point of saturation. Using F to correct for protein concentration errors, however, works fine with a set of proteins with high affinity and known stoichiometry, because F is often better determined by the data than by any other method. 13. Such error bars do not include systematic errors because of false values of the calcium affinity for the chelator. Hence, they are a measure of precision rather than accuracy. Because the method is based on competition between the protein and a chelator, the precision is often high, and when the aim is to study the effects of mutations or other modifications, the method can be very useful and reliable. 14. The free energy of interaction between binding events at separate sites ∆∆G cannot be measured by the chelator method because this is a microscopic property. However, the macroscopic binding constants can be used to calculate a lower limit to -∆∆G. For a protein with two sites, this limiting value is RT ln (4K 2/K 1) and equal to the true cooperativity if the two sites have equal affinities. For a more thorough discussion of cooperativity and how it can be measured, see refs. 5, 7, and 8. 15. If the initial calcium concentration is not precisely known, or if it is too high (several µM) the precision in the determined macroscopic-binding constants will be reduced. In such cases, it is especially difficult to quantitate the cooperativity, as points are missing in the beginning of the curve (see Fig. 2C). The initial curvature is not defined and the separation of the total affinity into individual macroscopic binding constants becomes uncertain. Acknowledgments Helpful comments on the manuscript by Eva Thulin, Tord Berggård, and Jonas Fast are gratefully acknowledged.
24 Linse References 1. Tsien, R. Y. (1980) New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis and properties of prototype structures. Biochemistry 19, 2396–2404. 2. Linse, S., Brodin, P., Drakenberg, T., Thulin, E., Sellers, P., Elmdén, K., et al. (1987) Structure-function relationships in EF-hand Ca2+ -binding proteins. Protein engineering and biophysical studies of calbindin D9k. Biochemistry 26, 6723–6735. 3. Haugland, R. (1996) Handbook of fluorescent probes and research chemicals. Molecular Probes, Inc., Eugene, Oregon. 4. Rand, M. D., Lindblom, A., Carlson, J, Villoutreix, B. O., and Stenflo, J. (1997) Calcium binding to tandem repeats of EGF-like modules. Expression and characterization of the EGF-like modules of human Notch-1 implicated in receptor-ligand interactions. Protein Sci. 6, 2059–2071. 5. Linse, S., Sellers, P., and Thulin, E. (1993) Disulfide bonds in homo and heterodimers of EF-hand subdomains of calbindin D9k: stability, calcium binding and NMR studies. Protein Sci. 2, 985–1000. 6. Bylsma, N., Drakenberg, T., Andersson, I., Leadley, P. F., and Forsén, S. (1992) Prokaryotic calcium-binding protein of the calmodulin superfamily. Calcium binding to Saccharopolyspora erythraea 20 kDa protein. FEBS Lett. 299, 44–47. 7. Linse, S., Johansson, C., Brodin, P., Grundström, T., Drakenberg, T., and Forsén, S. (1991). Electrostatic contribution to the binding of Ca2+ in calbindin D9k. Biochemistry 30, 154–162. 8. Forsén, S. and Linse, S. (1995) Cooperativity: over the hill. Tr. Biochem. Sci. 20, 495–497.
Page 1 and 2: Methods in Molecular BiologyTM Biol
Page 3 and 4: M E T H O D S I N M O L E C U L A R
Page 5 and 6: © 2002 Humana Press Inc. 999 River
Page 8 and 9: 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
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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: 22 Linse tive to small alterations
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 and 60: 40 Haiech and Kilhoffer 29. Stewart
Page 61 and 62: 42 Haiech and Kilhoffer 62. Becking
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
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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
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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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20 Dean, Kelsey, and Reik
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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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238 Weljie and Heringa these databa
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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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