Identification of D-peptide ligands through mirror-image phage display

Science

Volumn 271, Issue 5257, 1996, Pages 1854-1857

  Schumacher, Ton N M ^a   Mayr, Lorenz M ^a,b   Minor Jr , Daniel L ^a   Milhollen, Michael A ^a   Burgess, Michael W ^a   Kim, Peter S ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b BAYER AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; OLIGONUCLEOTIDE; PEPTIDE; PROTEIN KINASE P60;

ARTICLE; BINDING SITE; CONTROLLED STUDY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN SYNTHESIS;

EID: 0029670478     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.271.5257.1854     Document Type: Article

References (61)

1. J. K Scott and G P Smith, Science 249, 386 (1990).
2. J. J. Devlin, L C. Panganiban, P. E. Devlin, ibid., p. 404, S E. Cwirla et al., Proc. Natl. Acad Sci U. S A. 87, 6378 (1990).
3. J. J. Devlin, L C. Panganiban, P. E. Devlin, ibid., p. 404, S E. Cwirla et al., Proc. Natl. Acad Sci U. S A. 87, 6378 (1990).
4. M. G. Cull, J. F. Miller, P. J. Schatz, Proc. Natl. Acad. Sci U S.A 89, 1865 (1992)
5. L C. Mattheakis, R. R. Bhatt, W. J Dower, ibid 91, 9022 (1994).
6. B. A Bunin, M. J Plunkett, J A. Ellman, ibid, p. 4708; E. M Gordon, R W. Barrett, W J. Dower, S. P Fodor, M. A Gallop, J Med. Chem. 37, 1385 (1994).
7. B. A Bunin, M. J Plunkett, J A. Ellman, ibid, p. 4708; E. M Gordon, R W. Barrett, W J. Dower, S. P Fodor, M. A Gallop, J Med. Chem. 37, 1385 (1994).
8. C T Dooley et al., Science 266, 2019 (1994).
9. T. J. Gill, H. J. Gould, P. Doty, Nature 197, 746 (1963), P. H Mauer, J Exp. Med. 121, 339 (1965); F. Borek, Y. Stupp, S. Fuchs, M. Sela, Biochem. J. 96, 577 (1965); C. A Janeway and M Sela, Immunology 13, 29 (1967); H. M Dintzis, D. E. Symer, R. Z. Dintzis, L E Zawadzke. J. M. Berg, Proteins 16, 306 (1993).
10. T. J. Gill, H. J. Gould, P. Doty, Nature 197, 746 (1963), P. H Mauer, J Exp. Med. 121, 339 (1965); F. Borek, Y. Stupp, S. Fuchs, M. Sela, Biochem. J. 96, 577 (1965); C. A Janeway and M Sela, Immunology 13, 29 (1967); H. M Dintzis, D. E. Symer, R. Z. Dintzis, L E Zawadzke. J. M. Berg, Proteins 16, 306 (1993).
11. T. J. Gill, H. J. Gould, P. Doty, Nature 197, 746 (1963), P. H Mauer, J Exp. Med. 121, 339 (1965); F. Borek, Y. Stupp, S. Fuchs, M. Sela, Biochem. J. 96, 577 (1965); C. A Janeway and M Sela, Immunology 13, 29 (1967); H. M Dintzis, D. E. Symer, R. Z. Dintzis, L E Zawadzke. J. M. Berg, Proteins 16, 306 (1993).
12. T. J. Gill, H. J. Gould, P. Doty, Nature 197, 746 (1963), P. H Mauer, J Exp. Med. 121, 339 (1965); F. Borek, Y. Stupp, S. Fuchs, M. Sela, Biochem. J. 96, 577 (1965); C. A Janeway and M Sela, Immunology 13, 29 (1967); H. M Dintzis, D. E. Symer, R. Z. Dintzis, L E Zawadzke. J. M. Berg, Proteins 16, 306 (1993).
13. T. J. Gill, H. J. Gould, P. Doty, Nature 197, 746 (1963), P. H Mauer, J Exp. Med. 121, 339 (1965); F. Borek, Y. Stupp, S. Fuchs, M. Sela, Biochem. J. 96, 577 (1965); C. A Janeway and M Sela, Immunology 13, 29 (1967); H. M Dintzis, D. E. Symer, R. Z. Dintzis, L E Zawadzke. J. M. Berg, Proteins 16, 306 (1993).
14. M L. Pasteur, "Recherches sur la dissymétrie moléculaire des produits organiques naturels," Leçons Professées a la Société Chimique de Paris (1860)
15. For a review of the historical background of chirality in chemistry, see V. Prelog, Science 193, 17 (1976).
16. R C. deL. Milton, S C F. Milton, S. B H. Kent, ibid 256, 1445 (1992).
17. L. E. Zawadzke and J. M. Berg, J. Am Chem Soc. 114, 4002 (1992); Proteins 16, 301 (1993).
18. L. E. Zawadzke and J. M. Berg, J. Am Chem Soc. 114, 4002 (1992); Proteins 16, 301 (1993).
19. J Sohlessinger, Curr. Opin. Genet. Dev. 4, 25 (1994).
20. P. Soriano, C. Montgomery, R. Geske, A. Bradley, Cell 64, 693 (1992), C. Lowe et al., Proc. Natl. Acad. Sci U S A. 90, 4485 (1993), J. F. Seymour, Sci. Med. 2, 48 (1995).
21. P. Soriano, C. Montgomery, R. Geske, A. Bradley, Cell 64, 693 (1992), C. Lowe et al., Proc. Natl. Acad. Sci U S A. 90, 4485 (1993), J. F. Seymour, Sci. Med. 2, 48 (1995).
22. P. Soriano, C. Montgomery, R. Geske, A. Bradley, Cell 64, 693 (1992), C. Lowe et al., Proc. Natl. Acad. Sci U S A. 90, 4485 (1993), J. F. Seymour, Sci. Med. 2, 48 (1995).
23. H. Yu et al., Cell 76, 933 (1994).
24. R. J. Rickles et al , EMBO J. 13, 5598 (1994), A B. Sparks, L. A. Quilliam, J. M. Thorn, J Der Charming, B. K. Kay, J Biol. Chem. 269, 23853 (1994); C Cheadle et al., ibid , p. 24034
25. R. J. Rickles et al , EMBO J. 13, 5598 (1994), A B. Sparks, L. A. Quilliam, J. M. Thorn, J Der Charming, B. K. Kay, J Biol. Chem. 269, 23853 (1994); C Cheadle et al., ibid , p. 24034
26. R. J. Rickles et al , EMBO J. 13, 5598 (1994), A B. Sparks, L. A. Quilliam, J. M. Thorn, J Der Charming, B. K. Kay, J Biol. Chem. 269, 23853 (1994); C Cheadle et al., ibid , p. 24034
27. S. Feng, J. K. Chen, H. Yu, J. A. Simon, S. L. Schreiber, Science 266, 1241 (1994)
28. W. A. Um, F. M. Richards, R. O. Fox, Nature 372, 375 (1994).
29. -1 in Ins-buffered saline (50 mM tns, pH 7.5, and 150 mM NaCl) containing 1 mM biotin The protein was purified by affinity chromatography with a D-amino acid peptide Ilgand (36) that was biotinylated and immobilized on a streptavidin-agarose column (Pierce). Chromatography fractions were analyzed by laser desorption mass spectrometry on a Voyager mass spectrometer (Perseptive Biosystems) Fractions containing material of the expected mass (expected, 7027 daltons; observed, 7027 to 7035 daltons) were pooled and dialyzed against water for 72 hours, lyophilized, and taken up in water at a concentration of 107 μg/ml.
30. 2+ column (after cleavage, the isolated SH3 domain flows through the column, whereas uncleaved fusion protein and the cleaved TrpLE leader sequence are retained). After dialysis [against phosphate-buffered saline (PBS) buffers of decreasing ionic strength and finally against water] and lyophilization. the purity and identity of the SH3 domain were confirmed by high-performance liquid chromatography (HPLC) analysis at neutral pH and by laser deSorption mass spectrometry (expected, 6686 daltons; observed, 6683 daltons)
31. T. N. M. Schumacher and P. S. Kim, unpublished results.
32. 10 transforming units to infect K91-kan cells to generate an amplified library. The quality of the library was confirmed by selection of phages that expressed inserts that interact with the lectin concanavalin A [K R. Oldenburg, D. Loganathan, I. J. Goldstein, P. G Schultz, M. A Gallop, Proc. Natl Acad Sci. U.S.A. 89, 5393 (1992), J K Scott, D. Loganathan, B. Eas ley, X Gong, I. J. Goldstein, ibid., p. 5398].
33. 10 transforming units to infect K91-kan cells to generate an amplified library. The quality of the library was confirmed by selection of phages that expressed inserts that interact with the lectin concanavalin A [K R. Oldenburg, D. Loganathan, I. J. Goldstein, P. G Schultz, M. A Gallop, Proc. Natl Acad Sci. U.S.A. 89, 5393 (1992), J K Scott, D. Loganathan, B. Eas ley, X Gong, I. J. Goldstein, ibid., p. 5398].
34. G. P. Smith and J K Scott, Methods Enzymol. 217, 228 (1993).
35. Sequence analysis of a small number of isolates after four rounds of selection with the L-SH3 domain revealed the following two peptide sequences: CLARSRLPAIPS (nine isolates) and SRMSPLV-PLRNS (one isolate). The sequences of these peptides have features consistent with those described for class I and class II ligands of the c-Src SH3 domain (14, 15)
36. -1 of BSA, with increasing incubation times in the later rounds of the selection procedure (Table 1). Bound phage particles were eluted by the addition of 100 μl of D-SH3 peptide ligand [sequence (D)-YGGRELPPLPRF-amide (36)] for 15 min at 4°C, at a final concentration of 700 to 1000 μM peptide The eluate was used to infect K91-kan cells. Acid elution of phages in the screen gives no detectable preferential binding to D-SH3-coated wells after four rounds of selection
37. Single-letter abbreviations for the amino acids are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile, K, Lys; L, Leu; M, Met, N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val, W, Trp; and Y, Tyr.
38. 18 column and a water-acetonitrile gradient in 0.1 % trifluoroacetic acid. The identity of the products was confirmed by laser desorption mass spectrometry.
39. 18 column and a water-acetonitrile gradient in 0.1 % trifluoroacetic acid. The identity of the products was confirmed by laser desorption mass spectrometry.
40. F. A. Gomez, J. K. Chen, A. Tanaka, S L. Schreiber, G. M Whitesides, J. Org. Chem. 59, 2885 (1994).
41. The affinity of Pep-D1 for the L-SH3 domain was determined by a competitive enzyme-linked immunosorbent assay (ELISA). Single wells of a 96-well plate were coated with 5 μg of the L- SH3 domain (1, 22). Wells were blocked with BSA, and phages expressing the L-SH3-binding insert CLARSRLPAIPS
42. 4, pH 7.2. Tryptophan fluorescence was induced by excitation at 295 nm (5 nm slit width), and emission was measured at 339 nm (10 nm slit width), with a Hitachi F-4500 fluorescence spectrometer. The dissociation constant was determined by Scatchard analysis
43. 133, which forms part of pocket B, cannot be observed in this type of experiment. Attenuation of chemical shifts was interpreted to indicate sites of peptide-protein interactions. It is formally possible that some of these changes result from an indirect effect of peptide binding. However, the general pattern of the perturbations observed here is consistent with the changes observed by Schreiber and colleagues [ S Feng, C. Kasahara, R. J. Rickles, S. L. Schreiber, Proc Natl. Acad. Sci. U.S.A. 92, 12408 (1995)].
44. 133, which forms part of pocket B, cannot be observed in this type of experiment. Attenuation of chemical shifts was interpreted to indicate sites of peptide-protein interactions. It is formally possible that some of these changes result from an indirect effect of peptide binding. However, the general pattern of the perturbations observed here is consistent with the changes observed by Schreiber and colleagues [ S Feng, C. Kasahara, R. J. Rickles, S. L. Schreiber, Proc Natl. Acad. Sci. U.S.A. 92, 12408 (1995)].
45. 133, which forms part of pocket B, cannot be observed in this type of experiment. Attenuation of chemical shifts was interpreted to indicate sites of peptide-protein interactions. It is formally possible that some of these changes result from an indirect effect of peptide binding. However, the general pattern of the perturbations observed here is consistent with the changes observed by Schreiber and colleagues [ S Feng, C. Kasahara, R. J. Rickles, S. L. Schreiber, Proc Natl. Acad. Sci. U.S.A. 92, 12408 (1995)].
46. H. Yu et al. Science 258, 1665 (1992).
47. R. F. Doolittle and P. Bork, Sci. Am. 269, 50 (1993), A. V. Efimov, FEBS Lett. 355, 213 (1994); G. B. Cohen, R. Ren, D. Baltimore, Cell 80, 237 (1995).
48. R. F. Doolittle and P. Bork, Sci. Am. 269, 50 (1993), A. V. Efimov, FEBS Lett. 355, 213 (1994); G. B. Cohen, R. Ren, D. Baltimore, Cell 80, 237 (1995).
49. R. F. Doolittle and P. Bork, Sci. Am. 269, 50 (1993), A. V. Efimov, FEBS Lett. 355, 213 (1994); G. B. Cohen, R. Ren, D. Baltimore, Cell 80, 237 (1995).
50. T. W Muir, Structure 3, 649 (1995).
51. The sequences of the resulting peptide ligands may may also be used to guide the design of biased synthetic D-peptide and peptide-based libraries Because of the structural relatedness of SH3 domains and of their L-amino acid ligands, biased libraries based on the sequence or structure of D-peptide ligands for the SH3 domain may contain ligands for a variety of SH3 domains, Thus, D-peptide ligands for other SH3 domains may be obtained through the direct screening of appropriately biased synthetic D-peptide libranes with other L-SH3 domains.
52. C. Tuerk and L Gold, Science 249, 505 (1990), A. D. Ellington and J. W. Szostak, Nature 346, 818 (1990).
53. C. Tuerk and L Gold, Science 249, 505 (1990), A. D. Ellington and J. W. Szostak, Nature 346, 818 (1990).
54. L. C. Bock, L.C. Griffin, J A. Latham, E. H. Vermaas, J. J. Toole, Nature 355, 564 (1992).
55. 2-terminal YGG added to facilitate concentration determination (38).
56. J. P. Staley and P. S. Kim, Protein Sci. 3, 1822 (1994).
57. H. Edelhoch, Biochemistry 6, 1948 (1967).
58. H Yu, M K Rosen, S. L. Schreiber, FEBS Lett. 324, 87 (1993).
59. G. Bodenhausen and D. J. Rubin, Chem. Phys Lett. 69, 185 (1980).
60. T. N. M. Schumacher, D. L. Minor Jr, P. S. Kim, unpublished results
61. We thank J. Pang for synthesis of some of the peptides, D. Kantesana for help in the construction of the phage library, and Z. Maliga for help with affinity measurements. We thank G P. Smith (University of Missouri at Columbia) for his kind gift of the FUSE-5 vector and accompanying protocols and B. Mayer (Children's Hospital, Boston) for the chicken c-Src complementary DNA We are grateful to B M. Hagmeyer and members of the Kim lab for their support and suggestions T. N M S. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation This research was supported by the Howard Hughes Medical Institute.