Protein Engineering Protocols - Mycobacteriology research center

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Contributors xiKAZUNARI TAIRA • Department of Chemistry and Biotechnology, Schoolof Engineering, The University of Tokyo, Hongo, Tokyo, Japan; GeneFunction Research Laboratory, National Institute of Advanced IndustrialScience and Technology (AIST), Tsukuba Science City, JapanPETER THUMFORT • Department of Chemistry, Princeton University,Princeton, NJKEVIN TRUONG • Institute of Biomaterials and Biomedical Engineering,Department of Electrical and Computer Engineering, Universityof Toronto, Toronto, Ontario, CanadaWEI WANG • Makineni Theoretical Laboratories, Department of Chemistry,University of Pennsylvania, Philadelphia, PAYINAN WEI • Department of Chemistry, Princeton University, Princeton, NJGREGORY A. WEISS • Department of Chemistry and the Institute for Genomicsand Bioinformatics, University of California, Irvine, CACHRISTINE WURTH • Department of Chemistry, Princeton University,Princeton, NJJING-MIN ZHOU • Department of Chemistry and Biotechnology, Schoolof Engineering, The University of Tokyo, Hongo, Tokyo, Japan; GeneFunction Research Laboratory, National Institute of Advanced IndustrialScience and Technology (AIST), Tsukuba Science City, Japan
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 8 and 9: ContentsPreface ...................
Page 10 and 11: ContributorsKATJA M. ARNDT • Inst
Page 14: IDESIGN AND COMPUTATIONAL STRATEGIE
Page 17 and 18: 4 Kono et al.structure is specified
Page 19 and 20: 6 Kono et al.patterning hydrophobic
Page 21 and 22: 8 Kono et al.discuss several method
Page 23 and 24: 10 Kono et al.The sum extends over
Page 25 and 26: 12 Kono et al.and p(ρ) is the frac
Page 27 and 28: 14 Kono et al.Fig. 1. Sequence-conf
Page 29 and 30: 16 Kono et al.such a bias toward sp
Page 31 and 32: 18 Kono et al.the heat capacity, C
Page 33 and 34: 20 Kono et al.32. Calhoun, J. R., K
Page 35 and 36: 22 Kono et al.68. Wolf, E. and Kim,
Page 37 and 38: 24 Bacher and Ellingtonthe genetic
Page 39 and 40: 26 Bacher and EllingtonFig. 1. Effe
Page 41 and 42: 28 Bacher and Ellingtonon the forwa
Page 43 and 44: 30 Bacher and EllingtonTable 1Incor
Page 45 and 46: 32 Bacher and Ellington1. Purified
Page 47 and 48: 34 Bacher and Ellington13. Xu, Z. J
Page 49 and 50: 36 Mason et al.Fig. 1. Dimeric para
Page 51 and 52: 38 Mason et al.Understanding of the
Page 53 and 54: 40 Mason et al.1. Specific hydropho
Page 55 and 56: 42 Mason et al.desired structure, a
Page 57 and 58: 44 Mason et al.Table 2Systematic Ch
Page 59 and 60: 46 Mason et al.insertions of nonsta
Page 61 and 62: 48 Mason et al.Table 4Coupling Ener
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50 Mason et al.(see also Subheading
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52 Mason et al.determination of the
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54 Mason et al.the combined effects
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56 Mason et al.reasonable chance of
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58 Mason et al.Fig. 3. Listed are a
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60 Mason et al.The algorithm was us
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62 Mason et al.Position 12(d), indi
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64 Mason et al.25. Synthetic peptid
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66 Mason et al.20. Monera, O. D., S
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68 Mason et al.49. Monera, O. D., K
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70 Mason et al.85. West, M. W. and
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72 Truong et al.Fig. 1. Emission (s
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74 Truong et al.chain kinase CRS pe
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76 Truong et al.9. Gently mix the s
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78 Truong et al.Fig. 5. Digital flu
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80 Truong et al.10. Turn the filter
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82 Truong et al.3. Truong, K. and I
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84 Nomura and SugiuraBecause of the
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86 Nomura and SugiuraFig. 1. Schema
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88Fig. 2. Schematic representation
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90 Nomura and SugiuraFig. 3. Schema
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92 Nomura and Sugiura3.5.2. Constru
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6MonobodiesAntibody Mimics Based on
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Monobodies 97Fig. 1. (A) A schemati
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Monobodies 9910. Agarose-phosphate
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Monobodies 101and 100 µL of fresh
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Monobodies 103suspension. Centrifug
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Monobodies 105a reporter gene nor i
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Monobodies 1073.4.1. Cloning of a M
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Monobodies 1092. Nygren, P. -Å. an
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112 Friedhoff and Pingoudbackbone).
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114 Friedhoff and PingoudThe alignm
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116 Friedhoff and PingoudFig. 2. Su
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118 Friedhoff and Pingoud3.1. Selec
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120Fig. 3. Cleavage analysis of Mut
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122 Friedhoff and Pingoud2. Lanio,
Page 138:
IIEVOLUTIONARY STRATEGIES FOR PROTE
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128 Denault and Pelletierin the pas
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130 Denault and Pelletierall 64 10
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132 Denault and PelletierSubheading
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134Fig. 1. Excel worksheet describi
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136Fig. 3. Excel worksheet describi
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138 Denault and Pelletierwe analyze
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140 Denault and PelletierFig. 5. Pr
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142 Denault and Pelletierprobabilit
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144 Denault and Pelletierthat is, a
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146 Denault and PelletierThe answer
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148 Denault and Pelletier3.2.1. The
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150 Denault and Pelletieressentiall
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152 Denault and PelletierSee, for e
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154 Denault and Pelletier15. Ross,
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156 Bradley et al.Fig. 1. The desig
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158 Bradley et al.Fig. 3. The desig
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160 Bradley et al.Fig. 4. Assembly
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162 Bradley et al.two of these prot
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164 Bradley et al.of length, sequen
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166 Bradley et al.22. Hutchinson, E
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168 Stebel et al.Various methods ar
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170 Stebel et al.9. Gel extraction
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172 Stebel et al.Fig. 1. Overview a
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174 Stebel et al.UDG (13). The resu
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176 Stebel et al.for preparative ge
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178 Stebel et al.because of the add
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180 Stebel et al.close proximity to
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182 Stebel et al.with a truncated w
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184
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186 Stebel et al.1. Label DNA radio
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188 Stebel et al.12. We used bromph
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190 Stebel et al.21. Clark, J. M. (
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192 Bergquist and GibbsIf sequence
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194 Bergquist and GibbsFig. 1. Sche
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196 Bergquist and GibbsFig. 2. An e
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198
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200 Bergquist and GibbsFig. 4. An e
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202 Bergquist and Gibbsexperiments
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204 Bergquist and Gibbs17. Teather,
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206 Sidhu et al.is fused to the dis
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208 Sidhu et al.2.2. Selection and
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210 Sidhu et al.sites (Pro6, Lys8,
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212 Sidhu et al.Fig. 2. In vitro sy
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214 Sidhu et al.dsDNA (nicked dsDNA
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216 Sidhu et al.3.3. Selection and
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218 Sidhu et al.3. All steps can be
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13Ribosome-Inactivation Display Sys
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Ribosome-Inactivation Display Syste
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14Compartmentalized Self-Replicatio
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Compartmentalized Self-Replication
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15Synthesis of Degenerated Librarie
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Synthesis of Libraries and Screenin
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259Fig. 2. The caspase-activated de
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16A General Method of Terminal Trun
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Directed Evolution of Thermostabili
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Index 305IndexAAlpha-helix, see Bin
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Index 307parameters in creation and
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Index 309HHelix, see Binary pattern
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Index 311protein purification,anion
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