James A. WellsDiane J. Rodi and Suneeta Mandava and Lee MakowskiValery A. Petrenko and George P. SmithFrederic A. Fellouse and Gabor PalMark S. DennisNienke E. Van Houten and Jamie K. ScottKurt DeshayesShuichi OhkuboZhaozhong Han and Ece Karatan and Brian K. KayRobert O. Carlson and Robin Hyde-DeRuyscher and Paul T. HamiltonMihriban Tuna and Derek N. WoolfsonReto Crameri and Claudio Rhyner and Michael Weichel and Sabine Fluckiger and Zoltan KonthurSara K. Avrantinis and Gregory A. WeissJulian Bertschinger and Christian Heinis and Dario NeriJonathan S. Marvin and Henry B. LowmanJody D. Berry and Mikhail PopkovClaire L. Dobson and Ralph R. Minter and Celia P. Hart-ShorrockFrederic A. Fellouse and Sachdev S. Sidhu

Foreword	p. v
Preface	p. vii
Contributors	p. xv
1 Filamentous Bacteriophage Structure and Biology	p. 1
I Introduction	p. 1
II Taxonomy and Genetics	p. 3
III Viral Gene Products	p. 5
IV Structure of the Virion	p. 11
V Filamentous Bacteriophage Life Cycle	p. 18
VI Phage Library Diversity	p. 34
VII Biological Bottlenecks: Sources of Library Censorship	p. 35
VIII Quantitative Diversity Estimation	p. 41
IX Improved Library Construction	p. 45
References	p. 47
2 Vectors and Modes of Display	p. 63
I Introduction	p. 63
II Most Display Vectors are Based on Filamentous Phage	p. 65
III General Cloning Vectors Based on Filamentous Phage	p. 71
IV Classification of Filamentous Phage Display Systems	p. 75
V Phage f1-The First Phage-Display Vector	p. 77
VI Low DNA Copy Number Display Vectors Based on fd-tet	p. 78
VII Diversity of Type 3 Vectors	p. 80
VIII Type 8 Vectors: First Lessons	p. 81
IX Mosaic Display in Type nn Systems	p. 83
X Mosaic Display in Phagemid Systems	p. 89
XI Vectors for C-Terminal Display	p. 91
XII Phage Proteins as Constraining Scaffolds	p. 93
XIII Conclusion	p. 95
References	p. 98
3 Methods for the Construction of Phage-Displayed Libraries	p. 111
I Introduction	p. 111
II Oligonucleotide-Directed Mutagenesis	p. 112
III Random Mutagenesis	p. 123
IV Combinatorial Infection and Recombination	p. 126
V DNA Shuffling	p. 129
References	p. 135
4 Selection and Screening Strategies	p. 143
I Introduction	p. 143
II General Considerations	p. 144
III The Selection Process	p. 146
IV Selections Methods	p. 150
References	p. 161
5 Phage Libraries for Developing Antibody-Targeted Diagnostics and Vaccines	p. 165
I Introduction	p. 165
II Phage-Display Libraries as Tools for Epitope Discovery	p. 170
III Diagnostics	p. 179
IV Phage Libraries for Epitope Mapping	p. 187
V Phage Display Libraries for Vaccine Development	p. 200
VI Developing Immunogens from Peptide Leads	p. 218
VII Summary	p. 235
VIII Conclusion	p. 238
IX Abbreviations	p. 239
References	p. 240
6 Exploring Protein-Protein Interactions Using Peptide Libraries Displayed on Phage	p. 255
I Introduction	p. 255
II Extracellular Protein-Protein Interactions	p. 256
III Intracellular Protein-Protein Interactions	p. 268
IV Conclusions	p. 274
References	p. 275
7 Substrate Phage Display	p. 283
I Overview	p. 283
II Introduction	p. 284
III The Concept of Substrate Phage Display	p. 285
IV Application of Substrate Phage Display to Cancer Research	p. 294
V Conclusions	p. 305
References	p. 308
8 Mapping Intracellular Protein Networks	p. 321
I Introduction	p. 321
II Domain-Mediated Interactions	p. 323
III Nondomain Mediated Protein-Protein Interactions	p. 336
IV Software for Identifying Candidate Interacting Partners	p. 336
V Analyzing Predicted Interactions	p. 337
VI Relevance to Biotechnology and Drug Discovery	p. 338
References	p. 340
9 High Throughput and High Content Screening Using Peptides	p. 347
I Introduction	p. 347
II Peptides as Enzyme Inhibitors	p. 348
III Peptides as Conformational Probes	p. 355
IV Summary	p. 376
References	p. 377
10 Engineering Protein Folding and Stability	p. 385
I Protein Redesign and Design	p. 385
II Early Combinatorial Studies Aimed at Repacking the Cores of Proteins	p. 387
III Phage Display in Engineering Protein Stability	p. 390
IV A Worked Example: Repacking the Hydrophobic Core of Ubiquitin	p. 397
V Studies that Build on the Original Methods	p. 406
VI Summary	p. 408
References	p. 409
11 Identification of Natural Protein-Protein Interactions with cDNA Libraries	p. 415
I Overview	p. 415
II Introduction	p. 416
III Cloning Vectors	p. 417
IV Display of cDNA Libraries on Phage Surface	p. 420
V Problems Associated with the Display of cDNA Libraries on Phage Surface	p. 425
VI Adaptability of Phage Display to High-Throughput Screening Technology	p. 427
VII Conclusions	p. 428
References	p. 429
12 Mapping Protein Functional Epitopes	p. 441
I Introduction	p. 441
II Single Point Alanine Mutagenesis	p. 443
III Combinatorial Site-Specific Mutagenesis	p. 447
IV Other Approaches to Phage-Displayed Functional Epitope Mapping	p. 455
V Conclusion	p. 456
References	p. 456
13 Selections for Enzymatic Catalysts	p. 461
I Introduction	p. 461
II Selection Methods	p. 464
III Discussion	p. 482
References	p. 486
14 Antibody Humanization and Affinity Maturation Using Phage Display	p. 493
I Introduction	p. 493
II Humanization Using Phage Display	p. 497
III In Vitro Affinity Maturation of Antibodies	p. 501
IV Emerging Approaches	p. 519
V Conclusions	p. 520
References	p. 521
15 Antibody Libraries from Immunized Repertoires	p. 529
I Introduction	p. 529
II Immune Antibody Library Construction	p. 538
III Immune Antibody Library Selection	p. 570
IV The Future	p. 622
References	p. 624
16 Naive Antibody Libraries from Natural Repertoires	p. 659
I Introduction	p. 659
II Construction of Naive Libraries	p. 660
III Applications of Naive Libraries	p. 674
IV Summary	p. 700
References	p. 700
17 Synthetic Antibody Libraries	p. 709
I Introduction	p. 709
II The Scripps Research Institute	p. 711
III The Medical Research Council	p. 714
IV Morphosys	p. 720
V Genentech	p. 726
VI Conclusions	p. 732
References	p. 733
Index	p. 741