Protein Engineering Protocols - Mycobacteriology research center

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Compartmentalized Self-Replication 2475. Joyce, C. M. and Steitz, T. A. (1994) Function and structure relationships in DNApolymerases. Annu. Rev. Biochem. 63, 777–822.6. Barnes, W. M. (1992) The fidelity of Taq polymerase catalyzing PCR is improvedby an N-terminal deletion. Gene 112, 29–35.7. Lawyer, F. C., Stoffel, S., Saiki, R. K., et al. (1993) High-level expression, purification,and enzymatic characterization of full-length Thermus aquaticus DNApolymerase and a truncated form deficient in 5′ to 3′ exonuclease activity. PCRMeth. Appl. 2, 275–287.8. Li, Y., Mitaxov, V., and Waksman, G. (1999) Structure-based design of Taq DNApolymerases with improved properties of dideoxynucleotide incorporation. Proc.Natl. Acad. Sci. USA 96, 9491–9496.9. Patel, P. H. and Loeb, L. A. (2000) Multiple amino acid substitutions allow DNApolymerases to synthesize RNA. J. Biol. Chem. 275, 40,266–40,272.10. Astatke, M., Ng, K., Grindley, N. D., and Joyce, C. M. (1998) A single side chainprevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporatingribonucleotides. Proc. Natl. Acad. Sci. USA 95, 3402–3407.11. Ignatov, K. B., Bashirova, A. A., Miroshnikov, A. I., and Kramarov, V. M. (1999)Mutation S543N in the thumb subdomain of the Taq DNA polymerase large fragmentsuppresses pausing associated with the template structure. FEBS Lett. 448, 145–148.12. Kunkel, T. A. and Bebenek, K. (2000) DNA replication fidelity. Annu. Rev. Biochem.69, 497–529.13. Bedford, E., Tabor, S., and Richardson, C. C. (1997) The thioredoxin binding domainof bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNApolymerase I. Proc. Natl. Acad. Sci. USA 94, 479–484.14. Suzuki, M., Baskin, D., Hood, L., and Loeb, L. A. (1996) Random mutagenesis ofThermus aquaticus DNA polymerase I: concordance of immutable sites in vivowith the crystal structure. Proc. Natl. Acad. Sci. USA 93, 9670–9675.15. Kim, B., Hathaway, T. R., and Loeb, L. A. (1996) Human immunodeficiency virusreverse transcriptase. Functional mutants obtained by random mutagenesis coupledwith genetic selection in Escherichia coli. J. Biol. Chem. 271, 4872–4878.16. Sweasy, J. B. and Loeb, L. A. (1993) Detection and characterization of mammalianDNA polymerase beta mutants by functional complementation in Escherichia coli.Proc. Natl. Acad. Sci. USA 90, 4626–4630.17. Glick, E., Vigna, K. L., and Loeb, L. A. (2001) Mutations in human DNA polymeraseeta motif II alter bypass of DNA lesions. EMBO J. 20, 7303–7312.18. Jestin, J. L., Kristensen, P., and Winter, G. (1999) A method for the selection of catalyticactivity using phage display and proximity coupling. Angew. Chem. Int. Ed.38, 1124–1127.19. Xia, G., Chen, L., Sera, T., Fa, M., Schultz, P. G., and Romesberg, F. E. (2002)Directed evolution of novel polymerase activities: mutation of a DNA polymeraseinto an efficient RNA polymerase. Proc. Natl. Acad. Sci. USA 99, 6597–6602.20. Ghadessy, F. J., Ong, J. L., and Holliger, P. (2001) Directed evolution of polymerasefunction by compartmentalized self-replication. Proc. Natl. Acad. Sci. USA98, 4552–4557.
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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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Degenerate Oligonucleotide Gene Shu
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Page 232: Engineered M13 Bacteriophage Coat P
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: 246 Ghadessy and Holliger2. After 6
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 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
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298 Hecky et al.Fig. 8. Unfolding o
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300 Hecky et al.for the first trans
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302 Hecky et al.7. Thompson, M. J.
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304 Hecky et al.40. Wang, X., Minas
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306 IndexCCalcium indicators, see C
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308 Indexchemiocompetent cellprepar
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310 Indexmaterials, 169, 170mutatio
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312 IndexTerminal truncation, see a
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