Protein Engineering Protocols - Mycobacteriology research center

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Synthesis of Libraries and Screening With the DHFR PCA 27333. Michnick, S. W., Remy, I., Campbell-Valois, F. X., Vallee-Belisle, A., and Pelletier,J. N. (2000) Detection of protein-protein interactions by protein fragment complementationstrategies. Methods Enzymol. 328, 208–230.34. Michnick, S. W. (2001) Exploring protein interactions by interaction-induced foldingof proteins from complementary peptide fragments. Curr. Opin. Struct. Biol.11, 472–477.35. Appleman, J. R., Prendergast, N., Delcamp, T. J., Freisheim, J. H., and Blakley, R.L. (1988) Kinetics of the formation and isomerization of methotrexate complexes ofrecombinant human dihydrofolate reductase. J. Biol. Chem. 263, 10,304–10,313.36. Arndt, K. M., Pelletier, J. N., Muller, K. M., Alber, T., Michnick, S. W., andPlückthun, A. (2000) A heterodimeric coiled-coil peptide pair selected in vivo froma designed library-versus-library ensemble. J. Mol. Biol. 295, 627–639.37. Mossner, E., Koch, H., and Plückthun, A. (2001) Fast selection of antibodies withoutantigen purification: adaptation of the protein fragment complementation assayto select antigen-antibody pairs. J. Mol. Biol. 308, 115–122.38. Michnick, S. W. and Shakhnovich, E. (1998) A strategy for detecting the conservationof folding-nucleus residues in protein superfamilies. Fold. Des. 3, 239–251.39. Campbell-Valois, F. X., Tarassov, K., and Michnick, S. W. (2005) Massive sequenceperturbation of a small protein. Proc. Natl. Acad. Sci. USA 102, 14,988–14,993.40. Gu, H., Yi, Q., Bray, S. T., Riddle, D. S., Shiau, A. K., and Baker, D. (1995)A phage display system for studying the sequence determinants of protein folding.<strong>Protein</strong> Sci. 4, 1108–1117.41. Emerson, S. D., Waugh, D. S., Scheffler, J. E., Tsao, K. L., Prinzo, K. M., and Fry,D. C. (1994) Chemical shift assignments and folding topology of the Ras-bindingdomain of human Raf-1 as determined by heteronuclear three-dimensional NMRspectroscopy. Biochemistry 33, 7745–7752.42. Emerson, S. D., Madison, V. S., Palermo, R. E., et al. (1995) Solution structure ofthe Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface.Biochemistry 34, 6911–6918.43. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Bacterial media, antibioticsand bacterial strains, in Molecular Cloning (Nolan, C., ed.), vol. 3. Cold SpringHarbor Laboratory Press, Cold Spring Harbor, NY, p. A.3.44. Remy, I., Wilson, I. A., and Michnick, S. W. (1999) Erythropoietin receptor activationby a ligand-induced conformation change. Science 283, 990–993.45. Nassar, N., Horn, G., Herrmann, C., Scherer, A., McCormick, F., and Wittinghofer, A.(1995) The 2.2 A crystal structure of the Ras-binding domain of the serine/threoninekinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375, 554–560.46. Block, C., Janknecht, R., Herrmann, C., Nassar, N., and Wittinghofer, A. (1996)Quantitative structure-activity analysis correlating Ras/Raf interaction in vitro toRaf activation in vivo. Nat. Struct. Biol. 3, 244–251.47. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Alkalyne lysis and PEGpreparation for large scale DNA preparation, in Molecular Cloning, vol. 1 (Nolan, C.,ed.) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 1.38–1.41.
274 Campbell-Valois and Michnick48. Seidman, C. E., Struhl, K., Sheen, J., and Jessen, T. (1997) Introduction of plasmidDNA into cells, basic protocol 2, in Current <strong>Protocols</strong> in Molecular Biology, vol. 1,Suppl 37 (Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman,J. G., Smith, J. A., and Struhl, K., eds.) John Wiley & Sons, Inc., New York, NY,pp. 1.8.4–1.8.5.49. Inoue, H., Nojima, H., and Okayama, H. (1990) High efficiency transformation ofEscherichia coli with plasmids. Gene 96, 23–28.50. Sarkar, G. and Sommer, S. S. (1990) The “megaprimer” method of site-directedmutagenesis. Biotechniques 8, 404–407.51. Brons-Poulsen, J., Petersen, N. E., Horder, M., and Kristiansen, K. (1998) Animproved PCR-based method for site directed mutagenesis using megaprimers.Mol. Cell Probes 12, 345–348.
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METHODS IN MOLECULAR BIOLOGY 352Pr
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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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PrefaceProtein engineering is a fas
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ContentsPreface ...................
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ContributorsKATJA M. ARNDT • Inst
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Contributors xiKAZUNARI TAIRA • D
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1Combinatorial Protein Design Strat
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Combinatorial Protein Design Strate
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2Global Incorporation of Unnatural
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Incorporation of Unnatural Amino Ac
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3Considerations in the Design and O
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Design of Coiled Coil Structures 37
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4Calcium Indicators Based on Calmod
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Protein-Based Ca 2+ Indicators 73Fi
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Protein-Based Ca 2+ Indicators 7512
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Protein-Based Ca 2+ Indicators 8145
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5Design and Synthesis of Artificial
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Design of Zinc Finger Proteins 853.
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Design of Zinc Finger Proteins 89pr
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Design of Zinc Finger Proteins 91Fi
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96 Koide and Koidewhile retaining t
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98 Koide and Koide5. M9-tryptone: M
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100 Koide and Koidetarget-binding s
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102 Koide and Koide4. Discard the s
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104 Koide and Koideup to 1 mM for h
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106 Koide and Koideplate. Incubate
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108 Koide and Koide1. Perform steps
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7Engineering Site-Specific Endonucl
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Engineering Site-Specific Endonucle
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115Fig. 1. Mapping group-specific r
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8Protein Library Design and Screeni
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Protein Library Design and Screenin
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135Fig. 2. Excel worksheet describi
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137Fig. 4. Excel worksheet describi
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9Protein Design by Binary Patternin
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Protein Design by Binary Patterning
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10Versatile DNA Fragmentation and D
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NExT DNA Shuffling 169This chapter
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NExT DNA Shuffling 1713. Methods3.1
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NExT DNA Shuffling 17372°C, 4 min.
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NExT DNA Shuffling 175Fig. 2. Varia
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NExT DNA Shuffling 1773.5.1. Direct
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NExT DNA Shuffling 179Fig. 3. Reass
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181
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NExT DNA Shuffling 183likelihood of
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NExT DNA Shuffling 1853.9.2. Calibr
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NExT DNA Shuffling 187staining. Bec
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NExT DNA Shuffling 1894. Zhao, H.,
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11Degenerate Oligonucleotide Gene S
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Degenerate Oligonucleotide Gene Shu
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12M13 Bacteriophage Coat Proteins E
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Engineered M13 Bacteriophage Coat P
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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 285: 272 Campbell-Valois and Michnick16.
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
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