Engineered proteins as specific binding reagents

Current Opinion in Biotechnology

Volumn 16, Issue 4, 2005, Pages 459-469

  Binz, H Kaspar ^a   Plückthun, Andreas ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL APPLICATIONS; PROTEIN ARCHITECTURES; PROTEIN ENGINEERING; PROTEIN-BINDING SCAFFOLDS;

BIOMEDICAL ENGINEERING; BIOTECHNOLOGY; MOLECULAR STRUCTURE; MONOCLONAL ANTIBODIES;

PROTEINS;

AMYLASE INHIBITOR; AMYLOID BETA PROTEIN; ANKYRIN; APROTININ; BETA LACTAMASE; CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; DISULFIDE; FATTY ACID BINDING PROTEIN; LIPOCALIN; MONOCLONAL ANTIBODY; PROTEINASE INHIBITOR; THROMBIN INHIBITOR; TRASTUZUMAB;

AFFINITY CHROMATOGRAPHY; ALPHA HELIX; BACTERIOPHAGE; BETA CHAIN; CARBOXY TERMINAL SEQUENCE; CHIMERA; COMPLEMENTARITY DETERMINING REGION; DISULFIDE BOND; DRUG PROTEIN BINDING; ENTROPY; ENZYME LINKED IMMUNOSORBENT ASSAY; FLUORESCENCE ACTIVATED CELL SORTING; HYDROPHOBICITY; IC 50; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE IMAGING; PHAGE DISPLAY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS; WESTERN BLOTTING;

PEPTIDE LIBRARY; PROTEIN BINDING; PROTEIN ENGINEERING;

EID: 23644452792     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2005.06.005     Document Type: Review

References (80)

1. A. Plückthun, and P. Pack New protein engineering approaches to multivalent and bispecific antibody fragments Immunotechnology 3 1997 83 105
2. A. Knappik, L. Ge, A. Honegger, P. Pack, M. Fischer, G. Wellnhofer, A. Hoess, J. Wölle, A. Plückthun, and B. Virnekäs Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides J Mol Biol 296 2000 57 86
3. T.J. Vaughan, A.J. Williams, K. Pritchard, J.K. Osbourn, A.R. Pope, J.C. Earnshaw, J. McCafferty, R.A. Hodits, J. Wilton, and K.S. Johnson Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library Nat Biotechnol 14 1996 309 314
4. S. Ewert, A. Honegger, and A. Plückthun Stability improvement of antibodies for extracellular and intracellular applications: CDR grafting to stable frameworks and structure-based framework engineering Methods 34 2004 184 199
5. M. Visintin, G.A. Meli, I. Cannistraci, and A. Cattaneo Intracellular antibodies for proteomics J Immunol Methods 290 2004 135 153
6. A. Skerra Engineered protein scaffolds for molecular recognition J Mol Recognit 13 2000 167 187
7. P.-Å. Nygren, and A. Skerra Binding proteins from alternative scaffolds J Immunol Methods 290 2004 3 28
8. P. Mathonet, and J. Fastrez Engineering of non-natural receptors Curr Opin Struct Biol 14 2004 505 511
9. R. Li, R.H. Hoess, J.S. Bennett, and W.F. DeGrado Use of phage display to probe the evolution of binding specificity and affinity in integrins Protein Eng 16 2003 65 72
10. L. Xu, P. Aha, K. Gu, R.G. Kuimelis, M. Kurz, T. Lam, A.C. Lim, H. Liu, P.A. Lohse, and L. Sun Directed evolution of high-affinity antibody mimics using mRNA display Chem Biol 9 2002 933 942
11. E. Karatan, M. Merguerian, Z. Han, M.D. Scholle, S. Koide, and B.K. Kay Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain Chem Biol 11 2004 835 844 Using phage display and fibronectin libraries, Src SH3 domain binders were isolated that could be used in 'immuno'-precipitation experiments.
12. S.E. Hufton, N. van Neer, T. van den Beuken, J. Desmet, E. Sablon, and H.R. Hoogenboom Development and application of cytotoxic T lymphocyte-associated antigen 4 as a protein scaffold for the generation of novel binding ligands FEBS Lett 475 2000 225 231
13. L.K. Chlewicki, P.D. Holler, B.C. Monti, M.R. Clutter, and D.M. Kranz High-affinity, peptide-specific T cell receptors can be generated by mutations in CDR1, CDR2 or CDR3 J Mol Biol 346 2005 223 239
14. Y. Li, R. Moysey, P.E. Molloy, A.L. Vuidepot, T. Mahon, E. Baston, S. Dunn, N. Liddy, J. Jacob, and B.K. Jakobsen Directed evolution of human T-cell receptors with picomolar affinities by phage display Nat Biotechnol 23 2005 349 354 Selection of picomolar binders for peptide-MHC complexes from T-cell receptor libraries using phage display. This became possible as the T-cell receptor was stabilized by a non-native interchain disulfide bond in the constant domains.
15. M. Nicaise, M. Valerio-Lepiniec, P. Minard, and M. Desmadril Affinity transfer by CDR grafting on a nonimmunoglobulin scaffold Protein Sci 13 2004 1882 1891
16. B. Heyd, F. Pecorari, B. Collinet, E. Adjadj, M. Desmadril, and P. Minard In vitro evolution of the binding specificity of neocarzinostatin, an enediyne-binding chromoprotein Biochemistry 42 2003 5674 5683
17. A. Koide, C.W. Bailey, X. Huang, and S. Koide The fibronectin type III domain as a scaffold for novel binding proteins J Mol Biol 284 1998 1141 1151
18. A. Koide, S. Abbatiello, L. Rothgery, and S. Koide Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor Proc Natl Acad Sci USA 99 2002 1253 1258
19. S. Schlehuber, and A. Skerra Lipocalins in drug discovery: from natural ligand-binding proteins to 'anticalins' Drug Discov Today 10 2005 23 33 An informative review giving perspectives on licocalins as drug candidates.
20. M. Vogt, and A. Skerra Construction of an artificial receptor protein ('anticalin') based on the human apolipoprotein D ChemBioChem 5 2004 191 199
21. T. Lamla, and V.A. Erdmann Searching sequence space for high-affinity binding peptides using ribosome display J Mol Biol 329 2003 381 388
22. L. Cicortas Gunnarsson, E. Nordberg Karlsson, A.S. Albrekt, M. Andersson, O. Holst, and M. Ohlin A carbohydrate binding module as a diversity-carrying scaffold Protein Eng Des Sel 17 2004 213 221
23. K. Nord, E. Gunneriusson, J. Ringdahl, S. Ståhl, M. Uhlén, and P.-Å. Nygren Binding proteins selected from combinatorial libraries of an α-helical bacterial receptor domain Nat Biotechnol 15 1997 772 777
24. K. Sandström, Z. Xu, G. Forsberg, and P.-Å. Nygren Inhibition of the CD28-CD80 co-stimulation signal by a CD28-binding affibody ligand developed by combinatorial protein engineering Protein Eng 16 2003 691 697
25. M. Wikman, A.C. Steffen, E. Gunneriusson, V. Tolmachev, G.P. Adams, J. Carlsson, and S. Ståhl Selection and characterization of HER2/neu-binding affibody ligands Protein Eng Des Sel 17 2004 455 462 In selections against the breast tumor marker Her2, nanomolar affinity affibodies were selected. One more closely analyzed binder was found not to compete with trastuzumab.
26. ••]). The affibody appears as a molten globule that adopts the three-helical bundle fold upon binding to the target.
27. ••].
28. V. Dincbas-Renqvist, C. Lendel, J. Dogan, E. Wahlberg, and T. Härd Thermodynamics of folding, stabilization, and binding in an engineered protein-protein complex J Am Chem Soc 126 2004 11220 11230
29. C. Lendel, V. Dincbas-Renqvist, A. Flores, E. Wahlberg, J. Dogan, P.-Å. Nygren, and T. Härd Biophysical characterization of Z(SPA-1) - a phage-display selected binder to protein A Protein Sci 13 2004 2078 2088
30. K. Bernath, S. Magdassi, and D.S. Tawfik Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery J Mol Biol 345 2005 1015 1026
31. P. Forrer, M.T. Stumpp, H.K. Binz, and A. Plückthun A novel strategy to design binding molecules harnessing the modular nature of repeat proteins FEBS Lett 539 2003 2 6
32. H.K. Binz, P. Amstutz, A. Kohl, M.T. Stumpp, C. Briand, P. Forrer, M.G. Grütter, and A. Plückthun High-affinity binders selected from designed ankyrin repeat protein libraries Nat Biotechnol 22 2004 575 582 Using designed ankyrin repeat protein libraries of varying repeat numbers [33], the authors selected nanomolar binders against maltose-binding protein and two mitogen-activated protein kinases using ribosome display. The crystal structure of the complex between a selected binder and maltose-binding protein was determined confirming the scaffold design.
33. H.K. Binz, M.T. Stumpp, P. Forrer, P. Amstutz, and A. Plückthun Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins J Mol Biol 332 2003 489 503
34. A. Kohl, H.K. Binz, P. Forrer, M.T. Stumpp, A. Plückthun, and M.G. Grütter Designed to be stable: crystal structure of a consensus ankyrin repeat protein Proc Natl Acad Sci USA 100 2003 1700 1705
35. Amstutz P, Binz HK, Parizek P, Stumpp MT, Kohl A, Grütter MG, Forrer P, Plückthun A: Intracellular kinase inhibitors selected from combinatorial libraries of designed ankyrin repeat proteins. J Biol Chem 2005, in press. A combined selection/screening approach using designed ankyrin repeat protein libraries allowed the identification of inhibitors to a bacterial aminoglycoside phosphotransferase. Inhibition could be shown both in vitro and in vivo, where the best inhibitors led to a phenotype comparable to the gene knock out.
36. •] was analyzed in more detail, revealing an allosteric enzyme inhibition mechanism, and co-crystallized with the target. The crystal structure emphasized the allosteric inhibition mechanism again and showed that the inhibitor trapped the enzyme in a catalytically inactive state.
37. A.L. Cortajarena, T. Kajander, W. Pan, M.J. Cocco, and L. Regan Protein design to understand peptide ligand recognition by tetratricopeptide repeat proteins Protein Eng Des Sel 17 2004 399 409
38. M.T. Stumpp, P. Forrer, H.K. Binz, and A. Plückthun Designing repeat proteins: modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family J Mol Biol 332 2003 471 487
39. S. Panni, L. Dente, and G. Cesareni In vitro evolution of recognition specificity mediated by SH3 domains reveals target recognition rules J Biol Chem 277 2002 21666 21674
40. M. Hiipakka, P. Huotari, A. Manninen, G.H. Renkema, and K. Saksela Inhibition of cellular functions of HIV-1 Nef by artificial SH3 domains Virology 286 2001 152 159
41. M. Hiipakka, and K. Saksela Capacity of simian immunodeficiency virus strain mac Nef for high-affinity Src homology 3 (SH3) binding revealed by ligand-tailored SH3 domains J Gen Virol 83 2002 3147 3152
42. M.G. Malabarba, E. Milia, M. Faretta, R. Zamponi, P.G. Pelicci, and P.P. Di Fiore A repertoire library that allows the selection of synthetic SH2s with altered binding specificities Oncogene 20 2001 5186 5194
43. S. Schneider, M. Buchert, O. Georgiev, B. Catimel, M. Halford, S.A. Stacker, T. Baechi, K. Moelling, and C.M. Hovens Mutagenesis and selection of PDZ domains that bind new protein targets Nat Biotechnol 17 1999 170 175
44. D. Junqueira, L. Cilenti, L. Musumeci, J.M. Sedivy, and A.S. Zervos Random mutagenesis of PDZ(Omi) domain and selection of mutants that specifically bind the Myc proto-oncogene and induce apoptosis Oncogene 22 2003 2772 2781
45. J. Reina, E. Lacroix, S.D. Hobson, G. Fernandez-Ballester, V. Rybin, M.S. Schwab, L. Serrano, and C. Gonzalez Computer-aided design of a PDZ domain to recognize new target sequences Nat Struct Biol 9 2002 621 627 Using a rational design approach PDZ variants with new peptide-binding specificities were generated with micromolar affinities. The variants could be used for western blotting, affinity purification and in 'immuno'-precipitation experiments.
46. P.A. Dalby, R.H. Hoess, and W.F. DeGrado Evolution of binding affinity in a WW domain probed by phage display Protein Sci 9 2000 2366 2376
47. I.P. Korndörfer, S. Schlehuber, and A. Skerra Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin J Mol Biol 330 2003 385 396
48. I.P. 4Korndörfer, G. Beste, and A. Skerra Crystallographic analysis of an 'anticalin' with tailored specificity for fluorescein reveals high structural plasticity of the lipocalin loop region Proteins 53 2003 121 129
49. P. Colas Combinatorial protein reagents to manipulate protein function Curr Opin Chem Biol 4 2000 54 59
50. T.C. Norman, D.L. Smith, P.K. Sorger, B.L. Drees, S.M. O'Rourke, T.R. Hughes, C.J. Roberts, S.H. Friend, S. Fields, and A.W. Murray Genetic selection of peptide inhibitors of biological pathways Science 285 1999 591 595
51. G.B. Karlsson, A. Jensen, L.F. Stevenson, Y.L. Woods, D.P. Lane, and M.S. Sørensen Activation of p53 by scaffold-stabilised expression of Mdm2-binding peptides: visualisation of reporter gene induction at the single-cell level Br J Cancer 91 2004 1488 1494
52. B. Klevenz, K. Butz, and F. Hoppe-Seyler Peptide aptamers: exchange of the thioredoxin-A scaffold by alternative platform proteins and its influence on target protein binding Cell Mol Life Sci 59 2002 1993 1998
53. A.H. Kwan, D.A. Gell, A. Verger, M. Crossley, J.M. Matthews, and J.P. Mackay Engineering a protein scaffold from a PHD finger Structure 11 2003 803 813
54. E. Bianchi, A. Folgori, A. Wallace, M. Nicotra, S. Acali, A. Phalipon, G. Barbato, R. Bazzo, R. Cortese, and F. Felici A conformationally homogeneous combinatorial peptide library J Mol Biol 247 1995 154 160
55. M.E. Houston Jr., A. Wallace, E. Bianchi, A. Pessi, and R.S. Hodges Use of a conformationally restricted secondary structural element to display peptide libraries: a two-stranded α-helical coiled-coil stabilized by lactam bridges J Mol Biol 262 1996 270 282
56. V.A. Petrenko, G.P. Smith, M.M. Mazooji, and T. Quinn α-Helically constrained phage display library Protein Eng 15 2002 943 950
57. S.K. Sia, and P.S. Kim Protein grafting of an HIV-1-inhibiting epitope Proc Natl Acad Sci USA 100 2003 9756 9761
58. B. Peelle, T.L. Gururaja, D.G. Payan, and D.C. Anderson Characterization and use of green fluorescent proteins from Renilla mulleri and Ptilosarcus guernyi for the human cell display of functional peptides J Protein Chem 20 2001 507 519
59. Y. Hitoshi, T. Gururaja, D.M. Pearsall, W. Lang, P. Sharma, B. Huang, S.M. Catalano, J. McLaughlin, E. Pali, and B. Peelle Cellular localization and antiproliferative effect of peptides discovered from a functional screen of a retrovirally delivered random peptide library Chem Biol 10 2003 975 987
60. M.R. Abedi, G. Caponigro, and A. Kamb Green fluorescent protein as a scaffold for intracellular presentation of peptides Nucleic Acids Res 26 1998 623 630
61. M. Abedi, G. Caponigro, J. Shen, S. Hansen, T. Sandrock, and A. Kamb Transcriptional transactivation by selected short random peptides attached to lexA-GFP fusion proteins BMC Mol Biol 2 2001 10
62. D. Legendre, B. Vucic, V. Hougardy, A.L. Girboux, C. Henrioul, J. Van Haute, P. Soumillion, and J. Fastrez TEM-1 β-lactamase as a scaffold for protein recognition and assay Protein Sci 11 2002 1506 1518
63. A.S. Tanaka, M.M. Silva, R.J. Torquato, M.A. Noguti, C.A. Sampaio, H. Fritz, and E.A. Auerswald Functional phage display of leech-derived tryptase inhibitor (LDTI): construction of a library and selection of thrombin inhibitors FEBS Lett 458 1999 11 16
64. I.T. Campos, M.M. Silva, S.S. Azzolini, A.F. Souza, C.A. Sampaio, H. Fritz, and A.S. Tanaka Evaluation of phage display system and leech-derived tryptase inhibitor as a tool for understanding the serine proteinase specificities Arch Biochem Biophys 425 2004 87 94
65. L.R. Ceci, M. Volpicella, Y. Rahbé, R. Gallerani, J. Beekwilder, and M.A. Jongsma Selection by phage display of a variant mustard trypsin inhibitor toxic against aphids Plant J 33 2003 557 566
66. M. Volpicella, L.R. Ceci, R. Gallerani, M.A. Jongsma, and J. Beekwilder Functional expression on bacteriophage of the mustard trypsin inhibitor MTI-2 Biochem Biophys Res Commun 280 2001 813 817
67. A.A. Stoop, and C.S. Craik Engineering of a macromolecular scaffold to develop specific protease inhibitors Nat Biotechnol 21 2003 1063 1068 In analogy to previous studies, the protease inhibitor ecotin was used for the selection of specific, picomolar affinity inhibitors of plasma kallikrein.
68. M.C. Laboissière, M.M. Young, R.G. Pinho, S. Todd, R.J. Fletterick, I. Kuntz, and C.S. Craik Computer-assisted mutagenesis of ecotin to engineer its secondary binding site for urokinase inhibition J Biol Chem 277 2002 26623 26631
69. C. Vita, J. Vizzavona, E. Drakopoulou, S. Zinn-Justin, B. Gilquin, and A. Ménez Novel miniproteins engineered by the transfer of active sites to small natural scaffolds Biopolymers 47 1998 93 100
70. C. Li, C.S. Dowd, W. Zhang, and I.M. Chaiken Phage randomization in a charybdotoxin scaffold leads to CD4-mimetic recognition motifs that bind HIV-1 envelope through non-aromatic sequences J Pept Res 57 2001 507 518
71. W. Zhang, G. Canziani, C. Plugariu, R. Wyatt, J. Sodroski, R. Sweet, P. Kwong, W. Hendrickson, and I. Chaiken Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic Biochemistry 38 1999 9405 9416
72. L. Martin, F. Stricher, D. Missé, F. Sironi, M. Pugnière, P. Barthe, R. Prado-Gotor, I. Freulon, X. Magne, and C. Roumestand Rational design of a CD4 mimic that inhibits HIV-1 entry and exposes cryptic neutralization epitopes Nat Biotechnol 21 2003 71 76 Generation of a CD4 mimetic, chimeric scorpion toxin that binds to viral particles and diverse HIV-1 envelopes with CD4-like affinity.
73. C.S. Dowd, S. Leavitt, G. Babcock, A.P. Godillot, D. Van Ryk, G.A. Canziani, J. Sodroski, E. Freire, and I.M. Chaiken β-Turn Phe in HIV-1 Env binding site of CD4 and CD4 mimetic miniprotein enhances Env binding affinity but is not required for activation of co-receptor/17b site Biochemistry 41 2002 7038 7046
74. E. Drakopoulou, K. Uray, G. Mezõ, M.R. Price, C. Vita, and F. Hudecz Synthesis and antibody recognition of mucin 1 (MUC1)-α-conotoxin chimera J Pept Sci 6 2000 175 185
75. J. Lehtiö, T.T. Teeri, and P.-Å. Nygren α-Amylase inhibitors selected from a combinatorial library of a cellulose binding domain scaffold Proteins 41 2000 316 322
76. G.P. Smith, S.U. Patel, J.D. Windass, J.M. Thornton, G. Winter, and A.D. Griffiths Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage J Mol Biol 277 1998 317 332
77. A. Zhao, Y. Xue, J. Zhang, B. Gao, J. Feng, C. Mao, L. Zheng, N. Liu, F. Wang, and H. Wang A conformation-constrained peptide library based on insect defensin A Peptides 25 2004 629 635
78. R. Baggio, P. Burgstaller, S.P. Hale, A.R. Putney, M. Lane, D. Lipovsek, M.C. Wright, R.W. Roberts, R. Liu, and J.W. Szostak Identification of epitope-like consensus motifs using mRNA display J Mol Recognit 15 2002 126 134
79. G. Mezõ, E. Drakopoulou, V. Paál, E. Rajnavölgyi, C. Vita, and F. Hudecz Synthesis and immunological studies of α-conotoxin chimera containing an immunodominant epitope from the 268-284 region of HSV gD protein J Pept Res 55 2000 7 17
80. R. Koradi, M. Billeter, and K. Wüthrich MOLMOL: a program for display and analysis of macromolecular structures J Mol Graph 14 1996 51 55