Designed armadillo repeat proteins: Library generation, characterization and selection of peptide binders with high specificity

Journal of Molecular Biology

Volumn 424, Issue 1-2, 2012, Pages 68-87

  Varadamsetty, Gautham ^a   Tremmel, Dirk ^a   Hansen, Simon ^a   Parmeggiani, Fabio ^a,b   Plückthun, Andreas ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Armadillo repeat; combinatorial library; neurotensin; peptide recognition; ribosome display

Indexed keywords

ALANINE; AMINO ACID; ARMADILLO REPEAT PROTEIN; BACTERIAL PROTEIN; CYSTEINE; NEUROTENSIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMBINATORIAL LIBRARY; CONTROLLED STUDY; CYTOPLASM; ESCHERICHIA COLI; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; PROTEIN UNFOLDING; RIBOSOME;

ARMADILLO; ESCHERICHIA COLI;

EID: 84868213104     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.08.029     Document Type: Article

References (53)

1. H.K. Binz, P. Amstutz, and A. Plückthun Engineering novel binding proteins from nonimmunoglobulin domains Nat. Biotechnol. 23 2005 1257 1268
2. Y.L. Boersma, and A. Plückthun DARPins and other repeat protein scaffolds: advances in engineering and applications Curr. Opin. Biotechnol. 22 2011 849 857
3. J. Löfblom, F.Y. Frejd, and S. Ståhl Non-immunoglobulin based protein scaffolds Curr. Opin. Biotechnol. 22 2011 843 848
4. Y.D. Clonis Affinity chromatography matures as bioinformatic and combinatorial tools develop J. Chromatogr., A 1101 2005 1 24
5. S. Spisak, and A. Guttman Biomedical applications of protein microarrays Curr. Med. Chem. 16 2009 2806 2815
6. R.M. MacCallum, A.C. Martin, and J.M. Thornton Antibody-antigen interactions: contact analysis and binding site topography J. Mol. Biol. 262 1996 732 745
7. I.A. Wilson, J.B. Ghiara, and R.L. Stanfield Structure of anti-peptide antibody complexes Res. Immunol. 145 1994 73 78
8. J.C. Almagro Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires J. Mol. Recognit. 17 2004 132 143
9. 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
10. 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
11. M. Hiipakka, K. Poikonen, and K. Saksela SH3 domains with high affinity and engineered ligand specificities targeted to HIV-1 Nef J. Mol. Biol. 293 1999 1097 1106
12. 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
13. D. Cowburn Peptide recognition by PTB and PDZ domains Curr. Opin. Struct. Biol. 7 1997 835 838
14. S. Schneider, M. Buchert, O. Georgiev, B. Catimel, M. Halford, and S.A. Stacker Mutagenesis and selection of PDZ domains that bind new protein targets Nat. Biotechnol. 17 1999 170 175
15. A. Ernst, D. Gfeller, Z. Kan, S. Seshagiri, P.M. Kim, G.D. Bader, and S.S. Sidhu Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing Mol. Biosyst. 6 2010 1782 1790
16. O. Esteban, and H. Zhao Directed evolution of soluble single-chain human class II MHC molecules J. Mol. Biol. 340 2004 81 95
17. T.Z. Grove, A.L. Cortajarena, and L. Regan Ligand binding by repeat proteins: natural and designed Curr. Opin. Struct. Biol. 18 2008 507 515
18. A.V. Kajava Review: proteins with repeated sequence - structural prediction and modeling J. Struct. Biol. 134 2001 132 144
19. M.A. Andrade, C. Petosa, S.I. O'Donoghue, C.W. Muller, and P. Bork Comparison of ARM and HEAT protein repeats J. Mol. Biol. 309 2001 1 18
20. M. Marfori, A. Mynott, J.J. Ellis, A.M. Mehdi, N.F. Saunders, and P.M. Curmi Molecular basis for specificity of nuclear import and prediction of nuclear localization Biochim. Biophys. Acta 1813 2011 1562 1577
21. W. Xu, and D. Kimelman Mechanistic insights from structural studies of β-catenin and its binding partners J. Cell Sci. 120 2007 3337 3344
22. R. Tewari, E. Bailes, K.A. Bunting, and J.C. Coates Armadillo-repeat protein functions: questions for little creatures Trends Cell Biol. 20 2010 470 481
23. M. Hatzfeld The armadillo family of structural proteins Int. Rev. Cytol. 186 1999 179 224
24. A.L. Cortajarena, and L. Regan Ligand binding by TPR domains Protein Sci. 15 2006 1193 1198
25. E. Conti, M. Uy, L. Leighton, G. Blobel, and J. Kuriyan Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin α Cell 94 1998 193 204
26. E. Conti, and J. Kuriyan Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin α Structure 8 2000 329 338
27. A.H. Huber, and W.I. Weis The structure of the β-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by β-catenin Cell 105 2001 391 402
28. C. Madhurantakam, G. Varadamsetty, M.G. Grütter, A. Plückthun, and P.R. Mittl Structure-based optimization of designed Armadillo-repeat proteins Protein Sci. 21 2012 1015 1028
29. F. Parmeggiani, R. Pellarin, A.P. Larsen, G. Varadamsetty, M.T. Stumpp, and O. Zerbe Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core J. Mol. Biol. 376 2008 1282 1304
30. B. Catimel, T. Teh, M.R. Fontes, I.G. Jennings, D.A. Jans, and G.J. Howlett Biophysical characterization of interactions involving importin-α during nuclear import J. Biol. Chem. 276 2001 34189 34198
31. B. Virnekäs, L. Ge, A. Plückthun, K.C. Schneider, G. Wellnhofer, and S.E. Moroney Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis Nucleic Acids Res. 22 1994 5600 5607
32. 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
33. A. Plückthun Ribosome display: a perspective Methods Mol. Biol. 805 2012 3 28
34. P. Alfarano, G. Varadamsetty, C. Ewald, F. Parmeggiani, R. Pellarin, and O. Zerbe Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy Protein Sci. 21 1996 1298 1314
35. K.W. Tripp, and D. Barrick Enhancing the stability and folding rate of a repeat protein through the addition of consensus repeats J. Mol. Biol. 365 2007 1187 1200
36. T. Kajander, A.L. Cortajarena, E.R. Main, S.G. Mochrie, and L. Regan A new folding paradigm for repeat proteins J. Am. Chem. Soc. 127 2005 10188 10190
37. S.K. Wetzel, G. Settanni, M. Kenig, H.K. Binz, and A. Plückthun Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins J. Mol. Biol. 376 2008 241 257
38. 1H NMR Int. J. Pept. Protein Res. 28 1986 315 323
39. J. Hanes, and A. Plückthun In vitro selection and evolution of functional proteins by using ribosome display Proc. Natl. Acad. Sci. USA 94 1997 4937 4942
40. C. Zahnd, P. Amstutz, and A. Plückthun Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target Nat. Methods 4 2007 269 279
41. B. Dreier, and A. Plückthun Rapid selection of high-affinity binders using ribosome display Methods Mol. Biol. 805 2012 261 286
42. H.K. Binz, P. Amstutz, A. Kohl, M.T. Stumpp, C. Briand, and P. Forrer High-affinity binders selected from designed ankyrin repeat protein libraries Nat. Biotechnol. 22 2004 575 582
43. A.E. Hodel, M.T. Harreman, K.F. Pulliam, M.E. Harben, J.S. Holmes, and M.R. Hodel Nuclear localization signal receptor affinity correlates with in vivo localization in Saccharomyces cerevisiae J. Biol. Chem. 281 2006 23545 23556
44. J. Huang, K. Makabe, M. Biancalana, A. Koide, and S. Koide Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution J. Mol. Biol. 392 2009 1221 1231
45. S.J. Li, and J.E. Cronan Jr The gene encoding the biotin carboxylase subunit of Escherichia coli acetyl-CoA carboxylase J. Biol. Chem. 267 1992 855 863
46. R.R. Fall, A.W. Alberts, and P.R. Vagelos Analysis of bacterial biotin-proteins Biochim. Biophys. Acta 379 1975 496 503
47. J. Sambrook, and D.W. Russell Molecular Cloning: A Laboratory Manual 3rd edit 2001 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
48. H. Inoue, H. Nojima, and H. Okayama High efficiency transformation of Escherichia coli with plasmids Gene 96 1990 23 28
49. D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940
50. J.A. Jaeger, D.H. Turner, and M. Zuker Improved predictions of secondary structures for RNA Proc. Natl. Acad. Sci. USA 86 1989 7706 7710
51. M. Zuker On finding all suboptimal foldings of an RNA molecule Science 244 1989 48 52
52. M.G. Cull, and P.J. Schatz Biotinylation of proteins in vivo and in vitro using small peptide tags Methods Enzymol. 326 2000 430 440
53. J. Wen, T. Arakawa, and J.S. Philo Size-exclusion chromatography with on-line light-scattering, absorbance, and refractive index detectors for studying proteins and their interactions Anal. Biochem. 240 1996 155 166