Protein Engineering Protocols - Mycobacteriology research center

More documents

Recommendations

Info

ContentsPreface ..............................................................................................................vContributors ..................................................................................................... ixPART I DESIGN AND COMPUTATIONAL STRATEGIES FOR PROTEIN ENGINEERING1 Combinatorial Protein Design StrategiesUsing Computational MethodsHidetoshi Kono, Wei Wang, and Jeffery G. Saven ............................... 32 Global Incorporation of Unnatural Amino Acids in Escherichia coliJamie M. Bacher and Andrew D. Ellington......................................... 233 Considerations in the Design and Optimizationof Coiled Coil StructuresJody M. Mason, Kristian M. Müller, and Katja M. Arndt.................... 354 Calcium Indicators Based on Calmodulin–Fluorescent Protein FusionsKevin Truong, Asako Sawano, Atsushi Miyawaki,and Mitsuhiko Ikura........................................................................ 715 Design and Synthesis of Artificial Zinc Finger ProteinsWataru Nomura and Yukio Sugiura ................................................... 836 Monobodies: Antibody Mimics Based on the Scaffoldof the Fibronectin Type III DomainAkiko Koide and Shohei Koide............................................................ 957 Engineering Site-Specific EndonucleasesPeter Friedhoff and Alfred Pingoud .................................................. 111PART II EVOLUTIONARY STRATEGIES FOR PROTEIN ENGINEERING8 Protein Library Design and Screening: Working Out the ProbabilitiesMichel Denault and Joelle N. Pelletier ............................................. 1279 Protein Design by Binary Patterning of Polarand Nonpolar Amino AcidsLuke H. Bradley, Yinan Wei, Peter Thumfort, Christine Wurth,and Michael H. Hecht .................................................................. 15510 Versatile DNA Fragmentation and Directed EvolutionWith Nucleotide Exchange and Excision TechnologySabine C. Stebel, Katja M. Arndt, and Kristian M. Müller................ 167vii
viiiContents11 Degenerate Oligonucleotide Gene ShufflingPeter L. Bergquist and Moreland D. Gibbs....................................... 19112 M13 Bacteriophage Coat Proteins Engineeredfor Improved Phage DisplaySachdev S. Sidhu, Birte K. Feld, and Gregory A. Weiss ................... 20513 Ribosome-Inactivation Display SystemSatoshi Fujita, Jing-Min Zhou, and Kazunari Taira........................... 22114 Compartmentalized Self-Replication: A Novel Methodfor the Directed Evolution of Polymerases and Other EnzymesFarid J. Ghadessy and Philipp Holliger ............................................. 23715 Synthesis of Degenerated Libraries of the Ras-Binding Domainof Raf and Rapid Selection of Fast-Folding and Stable ClonesWith the Dihydrofolate Reductase Protein FragmentComplementation AssayFrançois-Xavier Campbell-Valois and Stephen W. Michnick ........... 24916 A General Method of Terminal Truncation, Evolution,and Re-Elongation to Generate Enzymes of Enhanced StabilityJochen Hecky, Jody M. Mason, Katja M. Arndt,and Kristian M. Müller ................................................................. 275Index ............................................................................................................ 305
Page 1 and 2: METHODS IN MOLECULAR BIOLOGY 352Pr
Page 4 and 5: M E T H O D S I N M O L E C U L A R
Page 6 and 7: PrefaceProtein engineering is a fas
Page 10 and 11: ContributorsKATJA M. ARNDT • Inst
Page 12: Contributors xiKAZUNARI TAIRA • D
Page 16 and 17: 1Combinatorial Protein Design Strat
Page 18 and 19: Combinatorial Protein Design Strate
Page 36 and 37: 2Global Incorporation of Unnatural
Page 38 and 39: Incorporation of Unnatural Amino Ac
Page 48 and 49: 3Considerations in the Design and O
Page 50 and 51: Design of Coiled Coil Structures 37
Page 58 and 59:
Design of Coiled Coil Structures 45
Page 60 and 61:
Page 62 and 63:
Page 64 and 65:
Page 66 and 67:
Page 68 and 69:
Page 70 and 71:
Page 72 and 73:
Page 74 and 75:
Page 76 and 77:
Page 78 and 79:
Page 80 and 81:
Page 82 and 83:
Page 84 and 85:
4Calcium Indicators Based on Calmod
Page 86 and 87:
Protein-Based Ca 2+ Indicators 73Fi
Page 88 and 89:
Protein-Based Ca 2+ Indicators 7512
Page 90 and 91:
Page 92 and 93:
Page 94 and 95:
Protein-Based Ca 2+ Indicators 8145
Page 96 and 97:
5Design and Synthesis of Artificial
Page 98 and 99:
Design of Zinc Finger Proteins 853.
Page 100 and 101:
Page 102 and 103:
Design of Zinc Finger Proteins 89pr
Page 104 and 105:
Design of Zinc Finger Proteins 91Fi
Page 106:
Page 109 and 110:
96 Koide and Koidewhile retaining t
Page 111 and 112:
98 Koide and Koide5. M9-tryptone: M
Page 113 and 114:
100 Koide and Koidetarget-binding s
Page 115 and 116:
102 Koide and Koide4. Discard the s
Page 117 and 118:
104 Koide and Koideup to 1 mM for h
Page 119 and 120:
106 Koide and Koideplate. Incubate
Page 121 and 122:
108 Koide and Koide1. Perform steps
Page 124 and 125:
7Engineering Site-Specific Endonucl
Page 126 and 127:
Engineering Site-Specific Endonucle
Page 128 and 129:
115Fig. 1. Mapping group-specific r
Page 130 and 131:
Page 132 and 133:
Page 134 and 135:
Page 136:
Page 140 and 141:
8Protein Library Design and Screeni
Page 142 and 143:
Protein Library Design and Screenin
Page 144 and 145:
Page 146 and 147:
Page 148 and 149:
135Fig. 2. Excel worksheet describi
Page 150 and 151:
137Fig. 4. Excel worksheet describi
Page 152 and 153:
Page 154 and 155:
Page 156 and 157:
Page 158 and 159:
Page 160 and 161:
Page 162 and 163:
Page 164 and 165:
Page 166 and 167:
Page 168 and 169:
9Protein Design by Binary Patternin
Page 170 and 171:
Protein Design by Binary Patterning
Page 172 and 173:
Page 174 and 175:
Page 176 and 177:
Page 178 and 179:
Page 180 and 181:
10Versatile DNA Fragmentation and D
Page 182 and 183:
NExT DNA Shuffling 169This chapter
Page 184 and 185:
NExT DNA Shuffling 1713. Methods3.1
Page 186 and 187:
NExT DNA Shuffling 17372°C, 4 min.
Page 188 and 189:
NExT DNA Shuffling 175Fig. 2. Varia
Page 190 and 191:
NExT DNA Shuffling 1773.5.1. Direct
Page 192 and 193:
NExT DNA Shuffling 179Fig. 3. Reass
Page 194 and 195:
181
Page 196 and 197:
NExT DNA Shuffling 183likelihood of
Page 198 and 199:
NExT DNA Shuffling 1853.9.2. Calibr
Page 200 and 201:
NExT DNA Shuffling 187staining. Bec
Page 202 and 203:
NExT DNA Shuffling 1894. Zhao, H.,
Page 204 and 205:
11Degenerate Oligonucleotide Gene S
Page 206 and 207:
Degenerate Oligonucleotide Gene Shu
Page 208 and 209:
Page 210 and 211:
Page 212 and 213:
Page 214 and 215:
Page 216 and 217:
Page 218 and 219:
12M13 Bacteriophage Coat Proteins E
Page 220 and 221:
Engineered M13 Bacteriophage Coat P
Page 222 and 223:
Page 224 and 225:
Page 226 and 227:
Page 228 and 229:
Page 230 and 231:
Page 232:
Page 235 and 236:
222 Fujita et al.The methods that h
Page 237 and 238:
224 Fujita et al.3. Streptavidin an
Page 239 and 240:
226 Fujita et al.Fig. 2. (Continued
Page 241 and 242:
228 Fujita et al.Fig. 3. (Continued
Page 243 and 244:
230 Fujita et al.Fig. 3. (A) Schema
Page 245 and 246:
232 Fujita et al.1. Add 2 µg mRNA
Page 247 and 248:
234 Fujita et al.Innovative Bioscie
Page 249 and 250:
236 Fujita et al.30. Kim, Y., Mlsa,
Page 251 and 252:
238 Ghadessy and Holligeraffinity m
Page 253 and 254:
240 Ghadessy and HolligerFig. 1. (A
Page 255 and 256:
242 Ghadessy and HolligerFinally, t
Page 257 and 258:
244 Ghadessy and Holliger2. Prepare
Page 259 and 260:
246 Ghadessy and Holliger2. After 6
Page 261 and 262:
248 Ghadessy and Holliger21. Oberho
Page 263 and 264:
250 Campbell-Valois and Michnickscr
Page 265 and 266:
252 Campbell-Valois and Michnickfol
Page 267 and 268:
254 Campbell-Valois and Michnick7.
Page 269 and 270:
256 Campbell-Valois and MichnickFig
Page 271 and 272:
258 Campbell-Valois and Michnickres
Page 273 and 274:
260Fig. 3. BL21 pREP4 cells were co
Page 275 and 276:
262 Campbell-Valois and MichnickFig
Page 277 and 278:
264 Campbell-Valois and Michnickvar
Page 279 and 280:
Page 281 and 282:
Page 283 and 284:
Page 285 and 286:
Page 287 and 288:
Page 289 and 290:
276 Hecky et al.improved half-life
Page 291 and 292:
278 Hecky et al.Fig. 1. (A) Scheme
Page 293 and 294:
280 Hecky et al.11. Reverse primer
Page 295 and 296:
282 Hecky et al.high variability in
Page 297 and 298:
284 Hecky et al.coding sequence for
Page 299 and 300:
286 Hecky et al.4. Analyze the resu
Page 301 and 302:
Table 1Amino Acid Substitutions Sel
Page 303 and 304:
290 Hecky et al.Fig. 4. Structure o
Page 305 and 306:
292 Hecky et al.Fig. 5. Expression
Page 307 and 308:
294 Hecky et al.Table 2Kinetic Para
Page 309 and 310:
296 Hecky et al.The thermoactivity
Page 311 and 312:
298 Hecky et al.Fig. 8. Unfolding o
Page 313 and 314:
300 Hecky et al.for the first trans
Page 315 and 316:
302 Hecky et al.7. Thompson, M. J.
Page 317 and 318:
304 Hecky et al.40. Wang, X., Minas
Page 319 and 320:
306 IndexCCalcium indicators, see C
Page 321 and 322:
308 Indexchemiocompetent cellprepar
Page 323 and 324:
310 Indexmaterials, 169, 170mutatio
Page 325:
312 IndexTerminal truncation, see a
show all

Protein Engineering Protocols - Mycobacteriology research center

Create successful ePaper yourself

Delete template?

Save as template?