Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

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Multiple Sequence Alignment 249 program (47), which constructs multiple alignments based on segment-to-segment comparisons rather than the residue-to-residue comparisons used previously. The segments are incorporated into a multiple alignment using an iterative procedure. The PRRP program (46) optimizes a progressive, global alignment by iteratively dividing the sequences into two groups which are subsequently realigned using a global group-to-group alignment algorithm. PRALINE (14) employs profile-preprocessing and secondary structure prediction to guide the alignments in an optionally iterative fashion. The program SAGA (71) does not employ DP, but uses a genetic algorithm (GA) to select from an evolving alignment population the alignment, which optimizes, as an Objective Function (OF), the weighted sum of pairs as used in the MSA program (66). More recently, a measure of consistency between the considered multiple alignment and a corresponding library of CLUSTAL pairwise alignments was taken. This OF was developed for the COFFEE algorithm (43). As mentioned in Subheading 4.1., Hidden Markov models (HMM) have also been attempted as statistical models of the primary structure consensus for a sequence family (41,42). The program HMMT (48) uses a simulatedannealing method to maximise the probability that an HMM represents the sequences to be aligned. References 1. Kretsinger, R. H., Nockolds, C. E., Coffee, C. J., and Bradshaw, R. A. (1972) The structure of a calcium-binding protein from carp muscle, Cold Spring Harb. Symp. Quant. Biol. 36, 217–20. 2. Smith, P. D. and Moss, S. E. (1994) Structural evolution of the annexin supergene family. Trends Genet. 10, 241–246. 3. Nalefski, E. A. and Falke, J. J. (1996) The C2 domain calcium-binding motif: Structural and functional diversity, Protein Sci. 5, 2375–2390. 4. Handford, P. A., Mayhew, M., Baron, M., Winship, P. R., and Campbell, I. D., Brownlee, G. G. (1991) Key residues involved in calcium-binding motifs in EGF-like domains. Nature 351, 164–167. 5. Hofmann, K., Bucher, P., Falquet, L., and Bairoch, A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res. 27, 215–219. 6. Kawasaki, H. and Kretsinger, R. H. (1995) Calcium-binding Proteins 1:EF-hands. Protein Profiles 2, 305–490. 7. Heizmann, C. W. and Hunziker, W. (1991) Intracellular calcium-binding proteins: more sites than insights. Trends Biochem. Sci. 16, 98–103. 8. Nakayama, S., Moncrief, N. D., and Kretsinger, R. H. (1992) Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories. J. Mol. Evol. 34, 416–448. 9. Kretsinger, R. H. and Nakayama, S. (1993) Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins. J. Mol. Evol. 36, 477–488.
250 Weljie and Heringa 10. Kawasaki, H., Nakayama, S., and Kretsinger, R. H. (1998) Classification and evolution of EF-hand proteins. Biometals 11, 277–295. 11. Morgan, R. O. and Fernandez, M. P. (1997) Annexin gene structure and molecular evolutionary genetics. Cell Mol. Life Sci. 53, 508–515. 12. Morgan, R. O. and Fernandez, M. P. (1997) Distinct annexin subfamilies in plants and protists diverged prior to animal annexins and from a common ancestor. J. Mol. Evol. 44, 178–188. 13. Heringa, J., Frishman, D., and Argos, P. (1997) Computational methods relating proteins sequence and structure, in Proteins: A Comprehensive Treatise, vol. I (Allen, G. ed.), JAI Press, Greenwich, Connecticut, pp. 165–268. 14. Heringa, J. (1999) Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment. Comput. Chem. 23, 341–364. 15. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680. 16. Bairoch, A. and Apweiler, R. (1999) The SWISS-PROT protein sequence data bank and its supplement TREMBL. Nucleic Acids Res. 27, 49–54. 17. Stoesser, G., Tuli, M. A., Lopez, R., and Sterk, P. (1999) The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 27, 18–24. 18. Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J., Ouellette, B. F., Rapp, B. A., and Wheeler, D. L. (1999) Genbank. Nucleic Acids Res. 27, 12–17. 19. Barker, W. C., Garavelli, J. S., McGarvey, P. B., Marzec, C. R., Orcutt, B. C., Srinivasarao, G. Y., et al. (1999) The PIR-international protein sequence database. Nucleic Acids Res. 27, 39–43. 20. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882 21. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410. 22. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402. 23. Etzold, T., Ulyanov, A., and Argos, P. (1996) SRS: information retrieval system for molecular biology data banks. Methods Enzymol. 266, 114–128. 24. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Finn, R. D., and Sonnhammer, E. L. L. (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27, 260–262. 25. Heringa, J. and Argos, P. (1993) A method to recognize distant repeats in protein sequences. Proteins 17, 391–411. 26. Heringa, J., Sommerfeldt, H., Higgins, D., and Argos, P. (1992) OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput. Appl. Biosci., 8, 599–600.
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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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Page 219 and 220: 200 Berliner Fig. 3. ESR spectra of
Page 221 and 222: 202 Berliner Fig. 5. Low-temperatur
Page 223 and 224: 204 Berliner 14. Musci, G., Reed, G
Page 225 and 226: 206 Clarke and Vogel cal calcium-bi
Page 227 and 228: 208 Clarke and Vogel Fig. 1. 113 Cd
Page 233 and 234: 214 Clarke and Vogel The linewidth
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Page 237 and 238: 218 Drakenberg sands, of Hertz broa
Page 239 and 240: 220 Drakenberg 1. Bloch equations m
Page 241 and 242: 222 Drakenberg Fig. 2. Measurement
Page 243 and 244: 224 Drakenberg Fig. 3. (A) 43 Ca NM
Page 245 and 246: 226 Drakenberg Fig. 5. 43 Ca NMR sp
Page 247 and 248: 228 Drakenberg NMR at sub-mM concen
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Page 251 and 252: 232 Weljie and Heringa Table 1 Amin
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Page 255 and 256: 236 Weljie and Heringa diction meth
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Page 259 and 260: 240 Weljie and Heringa lineages. Th
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Page 263 and 264: 244 Weljie and Heringa sequences as
Page 265 and 266: 246 Weljie and Heringa much larger
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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
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
Page 313 and 314: 294 Werner et al. Fig. 4. (A) Line-
Page 315 and 316: 296 Werner et al. Table 2 Models of
Page 317 and 318: 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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