Design of Coiled Coil Structures 65References1. Wolf, E., Kim, P. S., and Berger, B. (1997) MultiCoil: a program for predictingtwo- and three-stranded coiled coils. <strong>Protein</strong> Sci. 6, 1179–1189.2. Lupas, A. (1996) Coiled coils: new structures and new functions. Trends Biochem.Sci. 21, 375–382.3. Landschulz, W. H., Johnson, P. F., and McKnight, S. L. (1988) The leucine zipper:a hypothetical structure common to a new class of DNA binding proteins. Science240, 1759–1764.4. Burkhard, P., Stetefeld, J., and Strelkov, S. V. (2001) Coiled coils: a highly versatileprotein folding motif. Trends Cell Biol. 11, 82–88.5. Kohn, W. D., Mant, C. T., and Hodges, R. S. (1997) Alpha-helical protein assemblymotifs. J. Biol. Chem. 272, 2583–2586.6. O’Shea, E. K., Klemm, J. D., Kim, P. S., and Alber, T. (1991) X-ray structure of theGCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254, 539–544.7. DeLano, W. L. (2002) The PyMOL molecular graphics system. DeLano Scientific,San Carlos, CA; http://www.pymol.org.8. Arndt, K. M., Pelletier, J. N., Müller, K. M., Plückthun, A., and Alber, T. (2002)Comparison of in vivo selection and rational design of heterodimeric coiled coils.Structure 10, 1235–1248.9. O’Shea, E. K., Lumb, K. J., and Kim, P. S. (1993) Peptide ‘Velcro’: design of aheterodimeric coiled coil. Curr. Biol. 3, 658–667.10. Mason, J. M. and Arndt, K. M. (2004) Coiled coil domains: stability, specificity,and biological implications. Chem. Biochem. 5, 170–176.11. Müller, K. M., Arndt, K. M., and Alber, T. (2000) <strong>Protein</strong> fusions to coiled-coildomains. Methods Enzymol. 328, 261–282.12. Arndt, K. M., Müller, K. M., and Plückthun, A. (2001) Helix-stabilized Fv (hsFv)antibody fragments: substituting the constant domains of a Fab fragment for a heterodimericcoiled-coil domain. J. Mol. Biol. 312, 221–228.13. Pack, P., Müller, K. M., Zahn, R., and Plückthun, A. (1995) Tetravalent miniantibodieswith high avidity assembling in Escherichia coli. J. Mol. Biol. 246, 28–34.14. Naik, R. R., Kirkpatrick, S. M., and Stone, M. O. (2001) The thermostability of analpha-helical coiled-coil protein and its potential use in sensor applications.Biosens. Bioelectron. 16, 1051–1057.15. Crick, F. H. S. (1953) The packing of α-helices: simple Coiled Coils. Acta Crystallogr.6, 689–697.16. Harbury, P. B., Zhang, T., Kim, P. S., and Alber, T. (1993) A switch between two-,three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262,1401–1407.17. Harbury, P. B., Kim, P. S., and Alber, T. (1994) Crystal structure of an isoleucinezippertrimer. Nature 371, 80–83.18. Betz, S. F., Bryson, J. W., and DeGrado, W. F. (1995) Native-like and structurallycharacterized designed alpha-helical bundles. Curr. Opin. Struct. Biol. 5, 457–463.19. Woolfson, D. N. and Alber, T. (1995) Predicting oligomerization states of coiledcoils. <strong>Protein</strong> Sci. 4, 1596–1607.
66 Mason et al.20. Monera, O. D., Sonnichsen, F. D., Hicks, L., Kay, C. M., and Hodges, R. S. (1996)The relative positions of alanine residues in the hydrophobic core control the formationof two-stranded or four-stranded alpha-helical coiled-coils. <strong>Protein</strong> Eng. 9,353–363.21. Malashkevich, V. N., Kammerer, R. A., Efimov, V. P., Schulthess, T., and Engel, J.(1996) The crystal structure of a five-stranded coiled coil in COMP: a prototypeion channel? Science 274, 761–765.22. Tang, Y. and Tirrell, D. A. (2001) Biosynthesis of a highly stable coiled-coil proteincontaining hexafluoroleucine in an engineered bacterial host. J. Am. Chem.Soc. 123, 11,089–11,090.23. Tang, Y., Ghirlanda, G., Petka, W. A., Nakajima, T., DeGrado, W. F., and Tirrell, D. A.(2001) Fluorinated coiled-coil proteins prepared in vivo display enhanced thermal andchemical stability. Angew. Chem. Int. Ed. 40, 1494–1496.24. Kretsinger, J. K. and Schneider, J. P. (2003) Design and application of basic aminoacids displaying enhanced hydrophobicity. J. Am. Chem. Soc. 125, 7907–7913.25. Akey, D. L., Malashkevich, V. N., and Kim, P. S. (2001) Buried polar residues incoiled-coil interfaces. Biochemistry 40, 6352–6360.26. Glover, J. N. and Harrison, S. C. (1995) Crystal structure of the heterodimeric bZIPtranscription factor c-Fos-c-Jun bound to DNA. Nature 373, 257–261.27. Gonzalez, L., Jr., Woolfson, D. N., and Alber, T. (1996) Buried polar residuesand structural specificity in the GCN4 leucine zipper. Nat. Struct. Biol. 3,1011–1018.28. Junius, F. K., Mackay, J. P., Bubb, W. A., Jensen, S. A., Weiss, A. S., and King, G. F.(1995) Nuclear magnetic resonance characterization of the Jun leucine zipperdomain: unusual properties of coiled-coil interfacial polar residues. Biochemistry 34,6164–6174.29. Potekhin, S. A., Medvedkin, V. N., Kashparov, I. A., and Venyaminov, S. (1994)Synthesis and properties of the peptide corresponding to the mutant form of theleucine zipper of the transcriptional activator GCN4 from yeast. <strong>Protein</strong> Eng. 7,1097–1101.30. Lumb, K. J. and Kim, P. S. (1995) A buried polar interaction imparts structuraluniqueness in a designed heterodimeric coiled coil. Biochemistry 34,8642–8648.31. Arndt, K. M., Pelletier, J. N., Müller, 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, 627–639.32. Tripet, B., Wagschal, K., Lavigne, P., Mant, C. T., and Hodges, R. S. (2000)Effects of side-chain characteristics on stability and oligomerization state of ade novo-designed model coiled-coil: 20 amino acid substitutions in position “d”.J. Mol. Biol. 300, 377–402.33. Wagschal, K., Tripet, B., Lavigne, P., Mant, C., and Hodges, R. S. (1999) The roleof position a in determining the stability and oligomerization state of alpha-helicalcoiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.<strong>Protein</strong> Sci. 8, 2312–2329.
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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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Combinatorial Protein Design Strate
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Combinatorial Protein Design Strate
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Combinatorial Protein Design Strate
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115Fig. 1. Mapping group-specific r
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Engineering Site-Specific Endonucle
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Engineering Site-Specific Endonucle
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Engineering Site-Specific Endonucle
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8Protein Library Design and Screeni
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Protein Library Design and Screenin
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Protein Library Design and Screenin
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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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Protein Library Design and Screenin
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Protein Library Design and Screenin
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9Protein Design by Binary Patternin
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Protein Design by Binary Patterning
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Protein Design by Binary Patterning
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Protein Design by Binary Patterning
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Protein Design by Binary Patterning
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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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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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222 Fujita et al.The methods that h
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224 Fujita et al.3. Streptavidin an
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226 Fujita et al.Fig. 2. (Continued
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228 Fujita et al.Fig. 3. (Continued
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230 Fujita et al.Fig. 3. (A) Schema
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232 Fujita et al.1. Add 2 µg mRNA
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234 Fujita et al.Innovative Bioscie
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236 Fujita et al.30. Kim, Y., Mlsa,
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238 Ghadessy and Holligeraffinity m
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240 Ghadessy and HolligerFig. 1. (A
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242 Ghadessy and HolligerFinally, t
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244 Ghadessy and Holliger2. Prepare
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246 Ghadessy and Holliger2. After 6
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248 Ghadessy and Holliger21. Oberho
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250 Campbell-Valois and Michnickscr
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252 Campbell-Valois and Michnickfol
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254 Campbell-Valois and Michnick7.
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256 Campbell-Valois and MichnickFig
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258 Campbell-Valois and Michnickres
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260Fig. 3. BL21 pREP4 cells were co
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262 Campbell-Valois and MichnickFig
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264 Campbell-Valois and Michnickvar
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266 Campbell-Valois and Michnick3.
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268 Campbell-Valois and Michnick7.
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270 Campbell-Valois and Michnick21.
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272 Campbell-Valois and Michnick16.
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274 Campbell-Valois and Michnick48.
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276 Hecky et al.improved half-life
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278 Hecky et al.Fig. 1. (A) Scheme
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280 Hecky et al.11. Reverse primer
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282 Hecky et al.high variability in
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284 Hecky et al.coding sequence for
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286 Hecky et al.4. Analyze the resu
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Table 1Amino Acid Substitutions Sel
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290 Hecky et al.Fig. 4. Structure o
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292 Hecky et al.Fig. 5. Expression
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294 Hecky et al.Table 2Kinetic Para
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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