Protein engineering

Molecular Biomethods Handbook: Second Edition

Volumn , Issue , 2008, Pages 587-629

  Willemsen, Thomas ^a   Hagemann, Urs B ^a   Jouaux, Eva M ^a   Stebel, Sabine C ^a   Mason, Jody M ^a   Müller, Kristian M ^a   Arndt, Katja M ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84900091781     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-60327-375-6_35     Document Type: Chapter

References (185)

1. Marshall SA, Lazar GA, Chirino AJ, Desjarlais JR (2003) Rational design and engineering of therapeutic proteins. Drug Discov Today 8:212-221
2. Hellinga HW (1997) Rational protein design: combining theory and experiment. Proc Natl Acad Sci USA 94:10015-10017
3. Creveld LD (2001) Molecular dynamics simulations in rational protein design: stabilization of fusarium solani pisi cutinase against anionic surfactants. University of Groningen
4. Balland A, Courtney M, Jallat S, Tessier LH, Sondermeyer P, de la Salle H, Harvey R, Degryse E, Tolstoshev P (1985) Use of synthetic oligonucleotides in gene isolation and manipulation. Biochimie 67:725-736
5. Garvey EP, Matthews CR (1990) Site-directed mutagenesis and its application to protein folding. Biotechnology 14:37-63
6. Wagner CR, Benkovic SJ (1990) Site directed mutagenesis: A tool for enzyme mechanism dissection. Trends Biotechnol 8:263-270
7. Kammann M, Laufs J, Schell J, Gronenborn B (1989) Rapid insertional mutagenesis of DNA by polymerase chain reaction (PCR). Nucleic Acids Res 17:5404
8. Antikainen NM, Martin SF (2005) Altering protein specificity: techniques and applications. Bioorg Med Chem 13:2701-2716
9. Desjarlais JR, Clarke ND (1998) Computer search algorithms in protein modification and design. Curr Opin Struct Biol 8:471-475
10. Voigt CA, Gordon DB, Mayo SL (2000) Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J Mol Biol 299:789-803
11. Fishman GS (1995) Monte Carlo: concepts, algorithms, and applications. Springer Verlag, New York
12. Metropolis NaU, S (1949) The Monte Carlo method. J Am Stat As 44:335
13. Desmet J, de Maeyer M, Hazes B, Lasters I (1992) The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539-542
14. Gordon DB, Marshall SA, Mayo SL (1999) Energy functions for protein design. Curr Opin Struct Biol 9:509-513
15. Pokala N, Handel TM (2001) Review: protein design -where we were, where we are, where were going. J Struct Biol 134:269-281
16. Street AG, Mayo SL (1999) Computational protein design. Structure 7:R105-109
17. van Gunsteren WF, Mark AE (1992) On the interpretation of biochemical data by molecular dynamics computer simulation. Fur J Biochem 204:947-961
18. Smith GP, Petrenko VA (1997) Phage Display. Chem Rev 97:391-410
19. Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315-1317
20. Kehoe JW, Kay BK (2005) Filamentous phage display in the new millennium. Chem Rev 105:4056-4072
21. Willats WG (2002) Phage display: practicalities and prospects. Plant Mol Biol 50:837-854
22. Jung S, Honegger A, Plückthun A (1999) Selection for improved protein stability by phage display. J Mol Biol 294:163-180
23. Jaye DL, Geigerman CM, Fuller RE, Akyildiz A, Parkos CA (2004) Direct fluorochrome labeling of phage display library clones for studying binding specificities: Applications in flow cytometry and fluorescence microscopy. J Immunol Methods 295:119-127
24. Steiner D, Forrer P, Stumpp MT, Pluckthun A (2006) Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat Biotechnol 24:823-831
25. Arndt KM, Jung S, Krebber C, Plückthun A (2000) Selectively infective phage technology. Methods Enzymol 328:364-388
26. Jung S, Arndt KM, Müller KM, Plückthun A (1999) Selectively infective phage (SIP) technology: scope and limitations. J Immunol Methods 231:93-104
27. Jiang J, Abu-Shilbayeh L, Rao VB (1997) Display of a PorA peptide from Neisseria meningitidis on the bacteriophage T4 capsid surface. Infect Immun 65:4770-4777
28. Danner S, Belasco JG (2001) T7 phage display: A novel genetic selection system for cloning RNA-binding proteins from cDNA libraries. Proc Natl Acad Sci USA 98:12954-12959
29. Mattheakis LC, Bhatt RR, Dower WJ (1994) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci USA 91:9022-9026
30. Wilson DS, Keefe AD, Szostak JW (2001) The use of mRNA display to select high-Affinity protein-binding peptides. Proc Natl Acad Sci USA 98:3750-3755
31. Hanes J, Jermutus L, Weber-Bornhauser S, Bosshard HR, Plückthun A (1998) Ribosome display efficiently selects and evolves high-Affinity antibodies in vitro from immune libraries. Proc Natl Acad Sci USA 95:14130-14135
32. Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245-246
33. Ma J, Ptashne M (1988) Converting a eukaryotic transcriptional inhibitor into an activator. Cell 55:443-446
34. Walhout AJ, Vidal M (2001) High-throughput yeast two-hybrid assays for largescale protein interaction mapping. Methods 24:297-306
35. Shih HM, Goldman PS, DeMaggio AJ, Hollenberg SM, Goodman RH, Hoekstra MF (1996) A positive genetic selection for disrupting protein-protein interactions: identification of CREB mutations that prevent association with the coactivator CBP. Proc Natl Acad Sci USA 93:13896-13901
36. Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci USA 93:10315-10320
37. Vidal M, Braun P, Chen E, Boeke JD, Harlow E (1996) Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse twohybrid system. Proc Natl Acad Sci USA 93:10321-10326
38. Aronheim A (1997) Improved efficiency sos recruitment system: expression of the mammalian GAP reduces isolation of Ras GTPase false positives. Nucleic Acids Res 25:3373-3374
39. Aronheim A, Zandi E, Hennemann H, Elledge SJ, Karin M (1997) Isolation of an AP-1 repressor by a novel method for detecting protein/protein interactions. Mol Cell Biol 17:3094-3102
40. Khler F, Müller KM (2003) Adaptation of the Ras-recruitment system to the analysis of interactions between membrane-Associated proteins. Nucleic Acids Res 31:e28
41. Osborne MA, Dalton S, Kochan JP (1995) The yeast tribrid system-genetic detection of trans-phosphorylated ITAM-SH2-interactions. Biotechnology (NY) 13:1474-1478
42. Zhang J, Lautar S (1996) A yeast three-hybrid method to clone ternary protein complex components. Anal Biochem 242:68-72
43. Licitra EJ, Liu JO (1996) A three-hybrid system for detecting small lig-And-protein receptor interactions. Proc Natl Acad Sci USA 93:12817-12821
44. Tafelmeyer P, Johnsson N, Johnsson K (2004) Transforming a (beta/alpha)8-barrel enzyme into a split-protein sensor through directed evolution. Chem Biol 11:681-689
45. Johnsson N, Varshavsky A (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci USA 91:10340-10344
46. Pelletier JN, Campbell-Valois FX, Michnick SW (1998) Oligomerization domaindirected reassembly of active dihydrofolate reductase from rationally designed fragments. Proc Natl Acad Sci USA 95:12141-12146
47. Stammers DK, Champness JN, Beddell CR, Dann JG, Eliopoulos E, Geddes AJ, Ogg D, North AC (1987) The structure of mouse L1210 dihydrofolate reductasedrug complexes and the construction of a model of human enzyme. FEBS Lett 218:178-184
48. Blakley RL (1984). Folates and pterins: chemistry and biochemistry of Folates. In: Blakley RL, Cenkovic S (eds), Folates and pterins: chemistry and biochemistry of folates, Vol. 1. John Wiley & Sons, New York, pp 191-253
49. Appleman JR, Prendergast N, Delcamp TJ, Freisheim JH, Blakley RL (1988) Kinetics of the formation and isomerization of methotrexate complexes of recombinant human dihydrofolate reductase. J Biol Chem 263:10304-10313
50. Buchwalder A, Szadkowski H, Kirschner K (1992) A fully active variant of dihydrofolate reductase with a circularly permuted sequence. Biochemistry 31:1621-1630
51. Pelletier JN, Arndt KM, Plückthun A, Michnick SW (1999) An in vivo libraryversus-library selection of optimized protein-protein interactions. Nat Biotechnol 17:683-690
52. Rossi F, Charlton CA, Blau HM (1997) Monitoring protein-protein interactions in intact eukaryotic cells by beta-galactosidase complementation. Proc Natl Acad Sci USA 94:8405-8410
53. Rossi FM, Blakely BT, Blau HM (2000) Interaction blues: protein interactions monitored in live mammalian cells by beta-galactosidase complementation. Trends Cell Biol 10:119-122
54. Ullmann A, Perrin D, Jacob F, Monod J (1965) [Identification, by in vitro complementation and purification, of a peptide fraction of Escherichia coli beta-galactosidase]. J Mol Biol 12:918-923
55. Villarejo M, Zamenhof PJ, Zabin I (1972) Beta-galactosidase. In vivo -complementation. J Biol Chem 247:2212-2216
56. Mohler WA, Blau HM (1996) Gene expression and cell fusion analyzed by lacZ complementation in mammalian cells. Proc Natl Acad Sci USA 93:12423-12427
57. Beckwith JR (1964) A deletion analysis of the Lac operator region in Escherichia coli. J Mol Biol 78:427-430
58. Prentki P (1992) Nucleotide sequence of the classical lacZ deletion delta M15. Gene 122:231-232
59. Galarneau A, Primeau M, Trudeau LE, Michnick SW (2002) Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions. Nat Biotechnol 20:619-622
60. Wehrman T, Kleaveland B, Her JH, Balint RF, Blau HM (2002) Protein-protein interactions monitored in mammalian cells via complementation of beta -lactamase enzyme fragments. Proc Natl Acad Sci USA 99:3469-3474
61. Zlokarnik G, Negulescu PA, Knapp TE, Mere L, Burres N, Feng L, Whitney M, Roemer K, Tsien RY (1998) Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter. Science 279:84-88
62. Ambler RP, Coulson AF, Frere JM, Ghuysen JM, Joris B, Forsman M, Levesque RC, Tiraby G, Waley SG (1991) A standard numbering scheme for the class A beta-lactamases. Biochem J 276 (Pt 1) 269-270
63. Farzaneh S, Chaibi EB, Peduzzi J, Barthelemy M, Labia R, Blazquez J, Baquero F (1996) Implication of lle-69 and Thr-182 residues in kinetic characteristics of IRT-3 (TEM-32) beta-lactamase. Antimicrob Agents Chemother 40:2434-2436
64. Paulmurugan R, Umezawa Y, Gambhir SS (2002) Noninvasive imaging of protein-protein interactions in living subjects by using reporter protein complementation and reconstitution strategies. Proc Natl Acad Sci USA 99:15608-15613
65. Massoud TF, Gambhir SS (2003) Molecular imaging in living subjects: seeing fundamental biological processes in a new light. Genes Dev 17:545-580
66. Paulmurugan R, Gambhir SS (2003) Monitoring protein-protein interactions using split synthetic renilla luciferase protein-fragment-Assisted complementation. Anal Chem 75:1584-1589
67. Remy I, Michnick SW (2006) A highly sensitive protein-protein interaction assay based on Gaussia luciferase. Nat Methods 3:977-979
68. Ghosh I, AD, H, Regan L (2000) Antiparallel Leucine zipper-directed protein reassembly: Application to the green fluorescent protein. J Am Chem Soc 122:5658-5659
69. Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ (1996) Crystal structure of the Aequorea victoria green fluorescent protein. Science 273:1392-1395
70. Abedi MR, Caponigro G, Kamb A (1998) Green fluorescent protein as a scaffold for intracellular presentation of peptides. Nucleic Acids Res 26:623-630
71. Hu CD, Chinenov Y, Kerppola TK (2002) Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 9:789-798
72. Lee SY, Choi JH, Xu Z (2003) Microbial cell-surface display. Trends Biotechnol 21:45-52
73. Lunder M, Bratkovio T, Doljak B, Kreft S, Urleb U, Strukelj B, Plazar N (2005) Comparison of bacterial and phage display peptide libraries in search of targetbinding motif. Appl Biochem Biotechnol 127:125-131
74. Romanos MA, Scorer CA, Clare JJ (1992) Foreign gene expression in yeast: A review. Yeast 8:423-488
75. Gellissen G, Melber K, Janowicz ZA, Dahlems UM, Weydemann U, Piontek M, Strasser AW, Hollenberg CP (1992) Heterologous protein production in yeast. Antonie Van Leeuwenhoek, 62:79-93
76. Schreuder MP, Brekelmans S, van den Ende H, Klis FM (1993) Targeting of a heterologous protein to the cell wall of Saccharomyces cerevisiae. Yeast, 9:399-409
77. Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553-557
78. Kieke MC, Shusta EV, Boder ET, Teyton L, Wittrup KD, Kranz DM (1999) Selection of functional T cell receptor mutants from a yeast surface-display library. Proc Natl Acad Sci USA 96:5651-5656
79. Richman SA, Healan SJ, Weber KS, Donermeyer DL, Dossett ML, Greenberg PD, Allen PM, Kranz DM (2006) Development of a novel strategy for engineering high-Affinity proteins by yeast display. Protein Eng Des Sel 19:255-264
80. Oker-Blom C, Airenne KJ, Grabherr R (2003) Baculovirus display strategies: Emerging tools for eukaryotic libraries and gene delivery. Brief Funct Genomic Proteomic 2:244-253
81. Smith GE, Summers MD, Fraser MJ (1983) Production of human beta interferon in insect cells infected with a baculovirus expression vector. Mol Cell Biol 3:2156-2165
82. OReilly DR, Miller LK, Luckow VA (1992). Baculovirus expression vectors: A laboratory manual 1st ed, W.H. Freeman and Company, New York
83. Boublik Y, Di Bonito P, Jones IM (1995) Eukaryotic virus display: engineering the major surface glycoprotein of the Autographa californica nuclear polyhedrosis virus (AcNPV) for the presentation of foreign proteins on the virus surface. Biotechnology (NY) 13:1079-1084
84. Ernst W, Grabherr R, Wegner D, Borth N, Grassauer A, Katinger H (1998) Baculovirus surface display: construction and screening of a eukaryotic epitope library. Nucleic Acids Res 26:1718-1723
85. Buchholz CJ, Peng KW, Morling FJ, Zhang J, Cosset FL, Russell SJ (1998) In vivo selection of protease cleavage sites from retrovirus display libraries. Nat Biotechnol 16:951-954
86. Urban JH, Schneider RM, Compte M, Finger C, Cichutek K, Alvarez-Vallina L, Buchholz CJ (2005) Selection of functional human antibodies from retroviral display libraries. Nucleic Acids Res 33:e35
87. Wolkowicz R, Jager GC, Nolan GR (2005) A random peptide library fused to CCR5 for selection of mimetopes expressed on the mammalian cell surface via retroviral vectors. J Biol Chem 280:15195-15201
88. Ho M, Nagata S, Pastan I (2006) Isolation of anti-CD22 Fv with high affinity by Fv display on human cells. Proc Natl Acad Sci USA 103:9637-9642
89. Rothe A, Surjadi RN, Power BE (2006) Novel proteins in emulsions using in vitro compartmentalization. Trends Biotechnol 24:587-592
90. Szostak JW, Bartel DP, Luisi PL (2001) Synthesizing life. Nature 409:387-390
91. Leamon JH, Link DK, Egholm M, Rothberg JM (2006) Overview: methods and applications for droplet compartmentalization of biology. Nat Methods 3:541-543
92. Miller OJ, Bernath K, Agresti JJ, Amitai G, Kelly BT, Mastrobattista E, Taly V, Magdassi S, Tawfik DS, Griffiths AD (2006) Directed evolution by in vitro compartmentalization. Nat Methods 3:561-570
93. Ghadessy FJ, Ong JL, Holliger P (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA 98:4552-4557
94. Ong JL, Loakes D, Jaroslawski S, Too K, Holliger P (2006) Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J Mol Biol 361:537-550
95. Doi N, Kumadaki S, Oishi Y, Matsumura N, Yanagawa H (2004) In vitro selection of restriction endonucleases by in vitro compartmentalization. Nucleic Acids Res 32:e95
96. Sepp A, Tawfik DS, Griffiths AD (2002) Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS Lett 532:455-458
97. Bernath K, Hai M, Mastrobattista E, Griffiths AD, Magdassi S, Tawfik DS (2004) In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Anal Biochem 325:151-157
98. Agresti JJ, Kelly BT, Jaschke A, Griffiths AD (2005) Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc Natl Acad Sci USA 102:16170-16175
99. Worn A, Pluckthun A (2001) Stability engineering of antibody single-chain Fv fragments. J Mol Biol 305:989-1010
100. Lin L (1998) Betaseron. Dev Biol Stand 96:97-104
101. Arakawa T, Prestrelski SJ, Narhi LO, Boone TC, Kenney WC (1993) Cysteine 17 of recombinant human granulocyte-colony stimulating factor is partially solventexposed. J Protein Chem 12:525-531
102. Culajay JF, Blaber SI, Khurana A, Blaber M (2000) Thermodynamic characterization of mutants of human fibroblast growth factor 1 with an increased physiological half-life. Biochemistry 39:7153-7158
103. Tan PH, Chu V, Stray JE, Hamlin DK, Pettit D, Wilbur DS, Vessella RL, Stayton PS (1998) Engineering the isoelectric point of a renal cell carcinoma targeting antibody greatly enhances scFv solubility. Immunotechnology 4:107-114
104. Weintraub BD, Szkudlinski MW (1999) Development and in vitro characterization of human recombinant thyrotropin. Thyroid 9:447-450
105. Grossmann M, Leitolf H, Weintraub BD, Szkudlinski MW (1998) A rational design strategy for protein hormone superagonists. Nat Biotechnol 16:871-875
106. Siemeister G, Schimer M, Reusch P, Barleon B, Marme D, Martiny-Baron G (1998) An antagonistic vascular endothelial growth factor (VEGF) variant inhibits VEGF-stimulated receptor autophosphorylation and proliferation of human endothelial cells. Proc Natl Acad Sci USA 95:4625-4629
107. Savino R, Ciapponi L, Lahm A, Demartis A, Cabibbo A, Toniatti C, Delmastro P, Altamura S, Ciliberto G (1994) Rational design of a receptor super-Antagonist of human interleukin-6. Embo J 13:5863-5870
108. Fub G, Cunningham BC, Fukunaga R, Nagata S, Goeddel DV, Wells JA (1992) Rational design of potent antagonists to the human growth hormone receptor. Science 256:1677-1680
109. Cunningham BC, Lowman HB, Wells JA, Clark RG, Olson K, Fuh GG (1988) Human Growth Hormone Variants, USA
110. Lu C, Shimaoka M, Ferzly M, Oxvig C, Takagi J, Springer TA (2001) An isolated, surface-expressed I domain of the integrin alphaLbeta2 is sufficient for strong adhesive function when locked in the open conformation with a disulfide bond. Proc Natl Acad Sci USA 98:2387-2392
111. Shimaoka M, Lu C, Palframan RT, von Andrian UH, McCormack A, Takagi J, Springer TA (2001) Reversibly locking a protein fold in an active conformation with a disulfide bond: integrin alphaL I domains with high affinity and antagonist activity in vivo. Proc Natl Acad Sci USA 98:6009-6014
112. Shimaoka M, Shifman JM, Jing H, Takagi J, Mayo SL, Springer TA (2000) Computational design of an integrin I domain stabilized in the open high affinity conformation. Nat Struct Biol 7:674-678
113. DeSantis G, Liu J, Clark DP, Heine A, Wilson IA, Wong CH (2003) Structurebased mutagenesis approaches toward expanding the substrate specificity of D-2-deoxyribose-5-phosphate aldolase. Bioorg Med Chem 11:43-52
114. Heine A, DeSantis G, Luz JG, Mitchell M, Wong CH, Wilson IA (2001) Observation of covalent intermediates in an enzyme mechanism at atomic resolution. Science 294:369-374
115. Babu CS, Dudev T, Casareno R, Cowan JA, Lim C (2003) A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: Application to E coli ribonuclease H1. J Am Chem Soc 125:9318-9328
116. Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL (2002) Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell 10:895-905
117. Shifman JM, Mayo SL (2002) Modulating calmodulin binding specificity through computational protein design. J Mol Biol 323:417-423
118. Havranek JJ, Harbury PB (2003) Automated design of specificity in molecular recognition. Nat Struct Biol 10:45-52
119. Dwyer MA, Looger LL, Hellinga HW (2004) Computational design of a biologically active enzyme. Science 304:1967-1971
120. Pedone EM, Bartolucci S, Rossi M, Saviano M (1998) Computational analysis of the thermal stability in thioredoxins: A molecular dynamics approach. J Biomol Struct Dyn 16:437-446
121. Lazaridis T, Lee I, Karplus M (1997) Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci 6:2589-2605
122. Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278:82-87
123. Marvin JS, Hellinga HW (2001) Conversion of a maltose receptor into a zinc biosensor by computational design. Proc Natl Acad Sci USA 98:4955-4960
124. de Lorimier RM, Smith JJ, Dwyer MA, Looger LL, Sali KM, Paavola CD, Rizk SS, Sadigov S, Conrad DW, Loew L, Hellinga HW (2002) Construction of a fluorescent biosensor family. Protein Sci 11:2655-2675
125. Yang W, Jones LM, Isley L, Ye Y, Lee HW, Wilkins A, Liu ZR, Hellinga HW, Malchow R, Ghazi M, Yang JJ (2003) Rational design of a calcium-binding protein. J Am Chem Soc 125:6165-6171
126. Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190
127. Samoylova TI, Morrison NE, Globa LP, Cox NR (2006) Peptide phage display: opportunities for development of personalized anti-cancer strategies. Anticancer Agents Med Chem 6:9-17
128. Bongartz T, Sutton AJ, Sweeting MJ, Buchan I, Matteson EL, Montori V (2006) Anti-TNF antibody therapy in rheumatoid arthritis and the risk of serious infections and malignancies: systematic review and meta-Analysis of rare harmful effects in randomized controlled trials. Jama 295:2275-2285
129. Sieber V, Pluckthun A, Schmid (1998) Selecting proteins with improved stability by a phage-based method. Nat Biotechnol 16:955-960
130. Barry MA, Dower WJ, Johnston SA (1996) Toward cell-targeting gene therapy vectors: selection of cell-binding peptides from random peptide-presenting phage libraries. Nat Med 2:299-305
131. Sergeeva A, Kolonin MG, Molldrem JJ, Pasqualini R, Arap W (2006) Display technologies: Application for the discovery of drug and gene delivery agents. Adv Drug Deliv Rev 58:1622-1654
132. Oh Y, Mohiuddin I, Sun Y, Putnam JB, Jr, Hong WK, Arap W, Pasqualini R (2005) Phenotypic diversity of the lung vasculature in experimental models of metastases. Chest 128:596S-600S
133. Essler M, Ruoslahti E (2002) Molecular specialization of breast vasculature: A breast-homing phage-displayed peptide binds to aminopeptidase P in breast vasculature. Proc Natl Acad Sci USA 99:2252-2257
134. Rothe A, Hosse RJ, Power BE (2006) Ribosome display for improved biotherapeutic molecules. Expert Opin Biol Ther 6:177-187
135. Ihara H, Mie M, Funabashi H, Takahashi F, Sawasaki T, Endo Y, Kobatake E (2006) In vitro selection of zinc finger DNA-binding proteins through ribosome display. Biochem Biophys Res Commun 345:1149-1154
136. Amstutz P, Koch H, Binz HK, Deuber SA, Pluckthun A (2006) Rapid selection of specific MAP kinase-binders from designed ankyrin repeat protein libraries. Protein Eng Des Sel 19:219-229
137. Khosravi-Far R, White MA, Westwick JK, Solski PA, Chrzanowska-Wodnicka M, Van Aelst L, Wigler MH, Der CJ (1996) Oncogenic Ras activation of Raf/ mitogen-Activated protein kinase-independent pathways is sufficient to cause tumorigenic transformation. Mol Cell Biol 16:3923-3933
138. Bartel DP, Szostak JW (1993) Isolation of new ribozymes from a large pool of random sequences [see comment]. Science 261:1411-1418
139. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627
140. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M (2004) A map of the interactome network of the metazoan C. elegans. Science 303:540-543
141. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lin J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-1178
142. Arndt KM, Pelletier JN, Müller KM, Alber T, Michnick SW, Plückthun A (2000) A heterodimeric coiled-coil peptide pair selected in vivo from a designed libraryversus-library ensemble. J Mol Biol 295:627-639
143. Arndt KM, Pelletier JN, Müller KM, Plückthun A, Alber T (2002) Comparison of in vivo selection and rational design of heterodimeric coiled coils. Structure 10:1235-1248
144. Arndt KM, Müller KM, Plückthun A (2001) Helix-stabilized Fv (hsFv) antibody fragments: substituting the constant domains of a Fab fragment for a heterodimeric coiled-coil domain. J Mol Biol 312:221-228
145. Mason JM, Schmitz MA, Müller KM, Arndt KM (2006) Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design. Proc Natl Acad Sci USA 103:8989-8994
146. Mason JM, Müller KM, Arndt KM (2007) Positive Aspects of Negative Design: Simultaneous Selection of Specificity and Interaction Stability. Biochemistry 46:4804-4814
147. Mason JM, Hagemann UB, Arndt KM (2007) Improved Stability of the Jun-Fos Activator Protein-1 Coiled Coil Motif: A Stopped-flow Circluar Dichroism Kinetic Analysis. J Biol Chem 282:23015-23024
148. Jouaux, EM, Schmidkunz K, Müller KM, Arndt KM (2008) Targeting the c-Myc coiled coil with interfering peptides to inhibit DNA binding. J Pept Sci (in press)
149. Mossner E, Koch H, Plückthun A (2001) Fast selection of antibodies without antigen purification: Adaptation of the protein fragment complementation assay to select antigen-Antibody pairs. J Mol Biol 308:115-122
150. Remy I, Wilson IA, Michnick SW (1999) Erythropoietin receptor activation by a ligand-induced conformation change. Science 283:990-993
151. Laser H, Bongards C, Schuller J, Heck S, Johnsson N, Lehming N (2000) A new screen for protein interactions reveals that the Saccharomyces cerevisiae high mobility group proteins Nhp6A/B are involved in the regulation of the GAL1 promoter. Proc Natl Acad Sci USA 97:13732-13737
152. Stagljar I, Korostensky C, Johnsson N, te Heesen S (1998) A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc Natl Acad Sci USA 95:5187-5192
153. Ooi AT, Stains CI, Ghosh I, Segal DJ (2006) Sequence-enabled reassembly of beta-lactamase (SEER-LAC): A sensitive method for the detection of doublestranded DNA. Biochemistry 45:3620-3625
154. Stains CI, Porter JR, Ooi AT, Segal DJ, Ghosh I (2005) DNA sequence-enabled reassembly of the green fluorescent protein. J Am Chem Soc 127:10782-10783
155. Massoud TF, Paulmurugan R, Gambhir SS (2004) Molecular imaging of homodimeric protein-protein interactions in living subjects. Faseb J 18:1105-1107
156. Hu CD, Kerppola TK (2003) Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat Biotechnol 21:539-545
157. Bracha-Drori K, Shichrur K, Katz A, Oliva M, Angelovici R, Yalovsky S, Ohad N (2004) Detection of protein-protein interactions in plants using bimolecular fluorescence complementation. Plant J 40:419-427
158. Walter M, Chaban C, Schutze K, Batistio O, Weckermann K, Nake C, Blazevic D, Grefen C, Schumacher K, Oecking C, Harter K, Kudla J (2004) Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. Plant J 40:428-438
159. Christmann A, Wentzel A, Meyer C, Meyers G, Kolmar H (2001) Epitope mapping and affinity purification of monospecific antibodies by Escherichia coli cell surface display of gene-derived random peptide libraries. J Immunol Methods 257:163-173
160. Wentzel A, Christmann A, Kratzner R, Kolman H (1999) Sequence requirements of the GPNG beta-turn of the Ecballium elaterium trypsin inhibitor II explored by combinatorial library screening. J Biol Chem 274:21037-21043
161. Kjaergaard K, Schembri MA, Klemm P (2001) Novel Zn(2+)-chelating peptides selected from a fimbria-displayed random peptide library. Appl Environ Microbiol 67:5467-5473
162. James P, Vorherr T, Carafoli E (1995) Calmodulin-binding domains: just two faced or multi-faceted? Trends Biochem Sci 20:38-42
163. Weaver-Feldhaus JM, Miller KD, Feldhaus MJ, Siegel RW (2005) Directed evolution for the development of conformation-specific affinity reagents using yeast display. Protein Eng Des Sel 18:527-536
164. Williams T (1996) The iridoviruses. Adv Virus Res 46:345-412
165. Tamaru Y, Ohtsuka M, Kato K, Manabe S, Kuroda K, Sanada M, Ueda M (2006) Application of the arming system for the expression of the 380R antigen from red sea bream iridovirus (RSIV) on the surface of yeast cells: A first step for the development of an oral vaccine. Biotechnol Prog 22:949-953
166. Cho BK, Kieke MC, Boder ET, Wittrup KD, Kranz DM (1998) A yeast surface display system for the discovery of ligands that trigger cell activation. J Immunol Methods 220:179-188
167. Kondo A, Ueda M (2004) Yeast cell-surface display-Applications of molecular display. Appl Microbiol Biotechnol 64:28-40
168. Raty JK, Airenne KJ, Marttila AT, Marjomaki V, Hytonen VF, Lehtolainen P, Laitinen OH, Mahonen AJ, Kulomaa MS, Yla-Herttuala S (2004) Enhanced gene delivery by avidin-displaying baculovirus. Mol Ther 9:282-291
169. Riddle DS, Sanz L, Chong H, Thompson J, Vile RG (2005) Tumor cell surface display of immunoglobulin heavy chain Fc by gene transfer as a means to mimic antibody therapy. Hum Gene Ther 16:830-844
170. Winter G, Griffiths AD, Hawkins RE, Hoogenboom HR (1994) Making antibodies by phage display technology. Annu Rev Immunol 12:433-455
171. Low NM, Holliger PH, Winter G (1996) Mimicking somatic hypermutation: Affinity maturation of antibodies displayed on bacteriophage using a bacterial mutator strain. J Mol Biol 260:359-368
172. de Bruin R, Spelt K, Mol J, Koes R, Quattrocchio F (1999) Selection of high-Affinity phage antibodies from phage display libraries. Nat Biotechnol 17:397-399
173. Chowdhury PS, Pastan I (1999) Improving antibody affinity by mimicking somatic hypermutation in vitro. Nat Biotechnol 17:568-572
174. Francisco JA, Campbell R, Iverson BL, Georgiou G (1993) Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface. Proc Natl Acad Sci USA 90:10444-10448
175. Francisco JA, Georgiou G (1994) The expression of recombinant proteins on
176. Georgiou G, Stathopoulos C, Daugherty PS, Nayak AR, Iverson BL, Curtiss R, 3rd (1997) Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. Nat Biotechnol 15:29-34
177. Boder ET, Midelfort KS, Wittrup KD (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci USA 97:10701-10705
178. Feldhaus MJ, Siegel RW, Opresko LK, Coleman JR, Feldhaus JM, Yeung YA, Cochran JR, Heinzelman P, Colby D, Swers J, Graff C, Wiley HS, Wittrup KD (2003) Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library. Nat Biotechnol 21:163-170
179. Hanes J, Plückthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci USA 94:4937-4942
180. Gold L (2001) mRNA display: diversity matters during in vitro selection. Proc Natl Acad Sci USA 98:4825-4826
181. Pavlov AR, Pavlova NV, Kozyavkin SA, Slesarev AL (2004) Recent developments in the optimization of thermostable DNA polymerases for efficient applications. Trends Biotechnol 22:253-260
182. Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P (2004) Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol 22:755-759
183. Griffiths AD, Tawfik DS (2003) Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. Embo J 22:24-35
184. Cohen HM, Tawfik DS, Griffiths AD (2004) Altering the sequence specificity of Haelll methyltransferase by directed evolution using in vitro compartmentalization. Protein Eng Des Sel 17:3-11
185. Levy M, Griswold KE, Ellington AL (2005) Direct selection of transacting ligase ribozymes by in vitro compartmentalization. Rna 11:1555-1562