Affinity selective isolation of ligands from peptide libraries through display on a lac represser "headpiece dimer"

Journal of Molecular Biology

Volumn 255, Issue 3, 1996, Pages 373-386

  Gates, Christian M ^a   Stemmer, Willem P C ^a   Kaptein, Robert ^b   Schatz, Peter J ^a  

^a AFFYMAX RESEARCH INSTITUTE   (United States)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Affinity purification; Directed molecular evolution; Headpiece; Lac repressor; Peptide library

Indexed keywords

BACTERIAL PROTEIN; DIMER; DNA BINDING PROTEIN; LIGAND; REPRESSOR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; LACTOSE OPERON; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN PURIFICATION;

EID: 0029915311     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0031     Document Type: Article

References (59)

1. Barkley, M. D. & Bourgeois, S. (1980). Repressor recognition of operator and effectors. In The Operon (Miller, J. H. & Reznikoff, W. S., eds), 2nd edn, pp. 177-220. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Barrett, R. W. & Goldstein, A. (1985). A monoclonal antibody specific for a dynorphin precursor. Neuropeptides, 6, 113-120.
3. Barrett, R. W., Cwirla, S. E., Ackerman, M. S., Olson, A. E., Peters, E. A. & Dower, W. J. (1992). Selective enrichment and characterization of high affinity ligands from collections of random peptides on filamentous phage. Analyt. Biochem. 204, 357-364.
4. Bass, R., Greene, R. & Wells, J. A. (1990). Hormone phage: an enrichment method for variant proteins with altered binding properties. Proteins: Struct. Funct. Genet. 8, 309-314.
5. Bedouelle, H. & Duplay, P. (1988). Production in Escherichia coli and one-step purification of bifunctional hybrid proteins which bind maltose. Eur. J. Biochem. 171, 541-549.
6. Betz, J. L. & Sadler, J. R. (1976). Tight-binding repressors of the lactose operon. J. Mol. Biol. 105, 293-319.
7. Beyreuther, K. (1980). Chemical structure and functional organization of lac repressor from Escherichia coli. In The Operon (Miller, J. H. & Reznikoff, W. S., eds), 2nd edn, pp. 123-154. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. Blondel, A. & Bedouelle, H. (1991). Engineering the quarternary structure of an exported protein with a leucine zipper. Protein Engin. 4, 457-461.
9. Boelens, R., Scheek, R. M., van Boom, J. H. & Kaptein, R. (1987). Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance. J. Mol. Biol. 193, 213-216.
10. Chakerian, A. E. & Matthews, K. S. (1992). Effect of lac repressor oligomerization on regulatory outcome. Mol. Microbiol. 6, 963-968.
11. Chuprina, V. P., Rullmann, J. A. C., Lamerichs, R. M. J. N., van Boom, J. H., Boelens, R. & Kaptein, R. (1993). Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. J. Mol. Biol. 234, 446-462.
12. Clackson, T. & Wells, J. A. (1994). In vitro selection from protein and peptide libraries. Tibtech, 12, 173-183.
13. Cull, M. G., Miller, J. F. & Schatz, P. J. (1992). Screening for receptor ligands using large libraries of peptides linked to the C terminus of the lac repressor. Proc. Natl Acad. Sci. USA, 89, 1865-1869.
14. Cwirla, S. E., Peters, E. A., Barrett, R. W. & Dower, W. J. (1990). Peptides on phage: a vast library of peptides for identifying ligands. Proc. Natl Acad. Sci. USA, 87, 6378-6382.
15. Derman, A. I. & Beckwith, J. (1991). Escherichia coli alkaline phosphatase fails to acquire disulfide bonds when retained in the cytoplasm. J. Bacteriol. 173, 7719-7722.
16. Dower, W. J., Miller, J. F. & Ragsdale, C. W. (1988). High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16, 6127-6145.
17. Duplay, P., Bedouelle, H., Fowler, A., Zabin, I., Saurin, W. & Hofnung, M. (1984). Sequences of the malE gene and of its product, the maltose-binding protein of Escherichia coli K-12. J. Biol. Chem. 259, 10606-10613.
18. Ebright, R. H. (1986). Evidence for a contact between glutamine-18 of lac repressor and base-pair 7 of lac operator. Proc. Natl Acad. Sci. USA, 83, 303-307.
19. Garrard, L. J., Yang, M., O'Connell, M. P., Kelley R. F. & Henner, D. J. (1991). Fab assembly and enrichment in a monovalent phage display system. Bio/Technology, 9, 1373-1377.
20. Gilbert, H. F. (1990). Molecular and cellular aspects of thiol/disulfide exchange. Advan. Enzymol. 63, 69-172.
21. Gram, H., Marconi, L., Barbas, C. F., Collett, T. A., Lerner, R. & Kang, A. S. (1992). In vitro selection and affinity maturation of antibodies from a naive combinatorial immunoglobulin library. Proc. Natl Acad. Sci. USA, 89, 3576-3580.
22. Guan, C., Li, P., Riggs, P. D. & Inouye, H. (1988). Vectors that facilitate the expression and purification of foreign peptides in Escherichia coli by fusion to maltose-binding protein. Gene, 67, 21-30.
23. Hawkins, R. E., Russell, S. J. & Winter, G. (1992). Selection of phage antibodies by binding affinity: mimicking affinity maturation. J. Mol. Biol. 226, 889-896.
24. Hu, M. C.-T. & Davidson, N. (1991). Targeting the Escherichia coli lac repressor to the mammalian cell nucleus. Gene, 99, 141-150.
25. Kaptein, R., Lamerichs, R. M. J. N., Boelens, R. & Rullmann, J. A. C. (1990). Two-dimensional NMR study of a protein-DNA complex: lac repressor headpiece-operator interaction. Biochem. Pharmacol. 40, 89-96.
26. Kellerman, O. K. & Ferenci, T. (1982). Maltose binding protein from E. coli. Methods Enzymol. 90, 459-463.
27. Khoury A. M., Nick, H. S. & Lu, P. (1991). In vivo interaction of Escherichia coli lac repressor N-terminal fragments with the lac operator. J. Mol. Biol. 219, 623-634.
28. Kisters-Woike, B., Lehming, N., Sartorius, J., von Wilcken-Bergmann, B. & Müller-Hill, B. (1991). A model of the lac repressor-operator complex based on physical and genetic data. Eur. J. Biochem. 198, 411-419.
29. Kleina, L. G. & Miller, J. H. (1990). Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J. Mol. Biol. 212, 295-318.
30. Kolkhof, P. (1992). Specificities of three tight-binding lac repressors. Nucl. Acids Res. 20, 5035-5039.
31. Koob, M. & Szybalski, W. (1990). Cleaving yeast and Escherichia coli genomes at a single site. Science, 250, 271-273.
32. Labow, M. A., Baim, S. B., Shenk, T. & Levine, A. J. (1990). Conversion of the lac repressor into an allosterically regulated transcriptional activator for mammalian cells. Mol. Cell. Biol. 10, 3343-3356.
33. 1H NMR study of a complex between the lac repressor headpiece and a 22 base pair symmetric lac operator. Biochemistry, 28, 2985-2991.
34. Lehming, N., Sartorius, J., Niemöller, M., Genenger, G., von Wilcken-Bergmann, B. & Müller-Hill, B. (1987). The interaction of the recognition helix of lac repressor with lac operator. EMBO J. 6, 3145-3153.
35. Lehming, N., Sartorius, J., Oehler, S., von Wilcken-Bergmann, B. & Müller-Hill, B. (1988). Recognition helices of lac and lambda repressor are oriented in opposite directions and recognize similar DNA sequences. Proc. Natl Acad. Sci. USA, 85, 7947-7951.
36. Lehming, N., Sartorius, J., Kisters-Woike, B., von Wilcken-Bergmann, B. & Müller-Hill, B. (1990). Mutant lac repressors with new specificities hint at rules for protein-DNA recognition. EMBO J. 9, 615-621.
37. Leung, D. W., Chen, E. & Goeddel, D. V. (1989). A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique, 1, 11-15.
38. Levens, D. & Howley P. M. (1985). Novel method for identifying sequence-specific DNA-binding proteins. Mol. Cell. Biol. 5, 2307-2315.
39. Lowman, H. B., Bass, S. H., Simpson, N. & Wells, J. A. (1991). Selecting high-affinity binding proteins by monovalent phage display. Biochemistry, 30, 10832-10838.
40. Lundeberg, J., Wahlberg, J. & Uhlén, M. (1991). Rapid colorimetric quantification of PCR-amplified DNA. BioTechniques, 10, 68-75.
41. Maina, C. V., Riggs, P. D., Grandea, A. G. I., Slatko, B. E., Moran, L. S., Tagliamonte, J. A., McReynolds, L. A. & Guan, C. (1988). A vector to express and purify foreign proteins in Escherichia coli by fusion to, and separation from, maltose binding protein. Gene, 74, 365-373.
42. Markiewicz, P., Kleina, L. G., Cruz, C., Ehret, S. & Miller, J. H. (1994). Genetic studies of the lac repressor XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J. Mol. Biol. 240, 421-433.
43. Martens, C. L., Cwirla, S. E., Lee, R. Y.-W., Whitehorn, E., Chen, E. Y.-F., Bakker, A., Martin, E. L., Wagstrom, C., Gopalan, P., Smith, C. W., Tate, E., Koller, K. J., Schatz, P. J., Dower, W. J. & Barrett, R. W. (1995). Peptides which bind to E-selectin and block neutrophil adhesion. J. Biol. Chem. 270, 21129-21136.
44. Martin, E. L., Rens-Domiano, S., Schatz, P. J., Hamm, H. E. (1995). Potent peptide antagonists of a G protein receptor binding region obtained with a combinatorial library. J. Biol. Chem. 270, in the press.
45. Maurizot, J. C. & Grebert, P. (1988). Thermodynamic parameters of the binding of the tight-binding I12X86 lac repressor to operator and non-operator DNA. FEBS Letters, 239, 105-108.
46. Miller, J. H. (1980). The lad gene: its role in lac operon control and its use as a genetic system. In The Operon (Miller, J. H. & Reznikoff, W. S., eds), 2nd edn, pp. 31-88. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
47. Needels, M. C., Jones, D. G., Tate, E. H., Heinkel, G. L., Kochersperger, L. M., Dower, W J., Barrett, R. W. & Gallop, M. A. (1993). Generation and screening of an oligonucleotide-encoded synthetic peptide library. Proc. Natl Acad. Sci. USA, 90, 10700-10704.
48. Panayotatos, N., Fontaine, A. & Backman, S. (1989). Biosynthesis of a repressor/nuclease hybrid protein. J. Biol. Chem. 264, 15066-15069.
49. Pollitt, S. & Zalkin, H. (1983). Role of primary structure and disulfide bond formation in beta-lactamase secretion. J. Bacteriol. 153, 27-32.
50. Richarme, G. (1982). Associative properties of the Escherichia coli galactose binding protein and maltose binding protein. Biochem. Biophys. Res. Commun. 105, 476-481.
51. Richarme, G. (1983). Associative properties of the Escherichia coli galactose-binding protein and maltose-binding protein. Biochim. Biophys. Acta, 748, 99-108.
52. Roberts, B. L., Markland, W., Ley A. C., Kent, R. B., White, D. W., Guterman, S. K. & Ladner, R. C. (1992). Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on Ml3 fusion phage. Proc. Natl Acad. Sci. USA, 89, 2429-2433.
53. Sadler, J. R., Sasmor, H. & Betz, J. L. (1983). A perfectly symmetric lac operator binds the lac repressor very tightly Proc. Natl Acad. Sci. USA, 80, 6785-6789.
54. Sartorius, J., Lehming, N., Kisters, B., von Wilcken-Bergmann, B. & Müller-Hill, B. (1989). EMBO J. 8, 1265-1270.
55. Schatz, P. J., Cull, M. G., Martin, E. L. & Gates, C. M. (1995). Screening of peptide libraries linked to lac repressor. Methods Enzymol. In the press.
56. Scott, J. K. & Smith, G. P. (1990). Searching for peptide ligands with an epitope library. Science, 249, 386-390.
57. Simons, A., Tils, D., von Wilcken-Bergmann, B. & Müller-Hill, B. (1984). Possible ideal lac operator: Escherichia coli lac operator-like sequences from eukaryotic genomes lack the central G.C pair. Proc. Natl Acad. Sci. USA, 81, 1624-1628.
58. Steitz, T. A. (1990). Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Quart. Rev. Biophys. 23, 205-280.
59. Szostak, J. W. (1992). In vitro genetics. Trends Biochem. Sci. 17, 89-93.