Skip to main content
PMC home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 1996;1(2):87–96. doi: 10.1007/BF01721323

Structural aspects of antibody-antigen interaction revealed through small random peptide libraries

Jerry W Slootstra 1,✉, Wouter C Puijk 1, Gerard J Ligtvoet 1, Jan P M Langeveld 1, Rob H Meloen 1
PMCID: PMC7088776  PMID: 9237197

Summary

Two small random peptide libraries, one composed of 4550 dodecapeptides and one of 8000 tripeptides, were synthesized in newly developed credit-card format miniPEPSCAN cards (miniPEPSCAN libraries). Each peptide was synthesized in a discrete well (455 peptides/card). The two miniPEPSCAN libraries were screened with three different monoclonal antibodies (Mabs). Two other random peptide libraries, expressed on the wall of bacteria (recombinant libraries) and composed of 107 hexa- and octapeptides, were screened with the same three Mabs. The aim of this study was to compare the amino acid sequence of peptides selected from small and large pools of random peptides and, in this way, investigate the potential of small random peptide libraries. The screening of the two miniPEPSCAN libraries resulted in the identification of a surprisingly large number of antibody-binding peptides, while the screening of the large recombinant libraries, using the same Mabs, resulted in the identification of only a small number of peptides. The large number of peptides derived from the small random peptide libraries allowed the determination of consensus sequences. These consensus sequences could be related to small linear and nonlinear parts of the respective epitopes. The small number of peptides derived from the large random peptide libraries could only be related to linear epitopes that were previously mapped using small libraries of overlapping peptides covering the antigenic protein. Thus, with respect to the cost and speed of identifying peptides that resemble linear and nonlinear parts of epitopes, small diversity libraries based on synthetic peptides appear to be superior to large diversity libraries based on expression systems.

Keywords: Antibody-antigen interaction, Random diversity libraries

Abbreviations

ABTS

2,2′-azino-di-3-ethylbenzthiazoline sulfonate

EGF

epidermal growth factor

Mab

monoclonal antibody

ODccd

optical density obtained using CCD camera

RAMPO

rabbit-antimouse peroxidase

SDS

sodium dodecylsulfate

TGEV

transmissible gastroenteritis virus

References

  • 1.Scott J.K., Craig L. Random peptide libraries. Curr. Opin. Biotechnol. 1994;5:40–48. doi: 10.1016/s0958-1669(05)80068-0. [DOI] [PubMed] [Google Scholar]
  • 2.Scott J.K., Smith G.P. Searching for peptide ligands with an epitope library. Science. 1990;249:386–390. doi: 10.1126/science.1696028. [DOI] [PubMed] [Google Scholar]
  • 3.Lam K.S., Salmon S.E., Hersch E.M., Hruby V.J., Kazmierski W.M., Knapp R.J. A new type of synthetic peptide library for identifying ligand binding activity. Nature. 1991;354:82–84. doi: 10.1038/354082a0. [DOI] [PubMed] [Google Scholar]
  • 4.Houghten R.A., Pinilla C., Blondelle S.E., Appel J.R., Dooley C.T., Cuervo J.H. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature. 1991;354:84–86. doi: 10.1038/354084a0. [DOI] [PubMed] [Google Scholar]
  • 5.Pinilla C., Appel J.R., Houghten R.A. Investigation of antigen-antibody interactions using a soluble, non-support bound synthetic decapeptide library composed of four trillion (4× 1012) sequences. Biochem. J. 1994;301:847–853. doi: 10.1042/bj3010847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Geysen H.M., Meloen R.H., Barteling S.J. Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc. Natl. Acad. Sci. USA. 1984;81:3998–4002. doi: 10.1073/pnas.81.13.3998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Langeveld J.P., Casal J.I., Osterhaus A.D., Cortes E., De Swart R., Vela C., Dalsgaard K., Puijk W.C., Schaaper W.M.M., Meloen R.H. First peptide vaccine providing protection against viral infection in the target animal: Studies of canine parvovirus in dogs. J. Virol. 1994;68:4506–4513. doi: 10.1128/jvi.68.7.4506-4513.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Meloen R.H., Puijk W.C., Langeveld J.P.M., Langedijk J.P.M., Van Amerongen A., Schaaper W.M.M. PEPSCAN to determine T and B cell epitopes. In: Zegers N., Boersma W., Ciaassen E., editors. Immunological Recognition of Peptides in Medicine and Biology. Boca Raton, FL: CRC Press; 1995. pp. 15–31. [Google Scholar]
  • 9.Berzofsky J.A. Intrinsic and extrinsic factors in protein antigenic structure. Science. 1985;229:932–940. doi: 10.1126/science.2410982. [DOI] [PubMed] [Google Scholar]
  • 10.Laver W.G., Air G.M., Webster R.G., Smith-Gill S.J. Epitopes on protein antigens: Misconceptions and realities. Cell. 1990;61:553–556. doi: 10.1016/0092-8674(90)90464-p. [DOI] [PubMed] [Google Scholar]
  • 11.Pinilla C., Appel J.R., Houghten R.A. Functional importance of amino acid residues making up peptide antigenic determinants. Mol. Immunol. 1993;30:577–585. doi: 10.1016/0161-5890(93)90032-7. [DOI] [PubMed] [Google Scholar]
  • 12.Posthumus W.P.A., Lenstra J.A., Schaaper W.M.M., Nieuwstadt A.P., Enjuanes L., Meloen R.H. Analysis and simulation of a neutralizing epitope of transmissible gastroenteritis virus. J. Virol. 1990;64:3304–3309. doi: 10.1128/jvi.64.7.3304-3309.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Posthumus W.P., Meloen R.H., Enjuanes L., Correa I., Van Nieuwstadt A.P., Koch G., De Groot R.J., Kusters J.G., Luytjes W., Spaan W.J., Van der Zeijst B.A.M., Lenstra J.A. Linear neutralizing epitopes on the peplomer protein of coronaviruses. Adv. Exp. Med. Biol. 1990;276:181–188. doi: 10.1007/978-1-4684-5823-7_25. [DOI] [PubMed] [Google Scholar]
  • 14.Gebauer F., Posthumus W.P.A., Correa I., Sune C., Smerdou C., Sanchez C.M., Lenstra J.A., Meloen R.H., Enjuanes L. Residues involved in the antigenic sites of transmissible gastroenteritis coronavirus S glycoprotein. Virology. 1991;183:225–238. doi: 10.1016/0042-6822(91)90135-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Van Amerongen A., Sauerwein R.W., Beckers P.J.A., Meloen R.H., Meuwissen J.H.E.T. Identification of a peptide sequence of the 25 kD surface protein of Plasmodium falciparum recognized by transmission-blocking monoclonal antibodies: Implications for synthetic vaccine development. Parasite Immunol. 1989;11:425–428. doi: 10.1111/j.1365-3024.1989.tb00679.x. [DOI] [PubMed] [Google Scholar]
  • 16.Lenstra J.A., Erkens J.H.F., Langeveld J.P.M., Posthumus W.P.A., Meloen R.H., Gebauer F., Correa I., Enjuanes L., Stanley K.K. Isolation of sequences from a random-sequence expression library that mimic viral epitopes. J. Immunol. Methods. 1992;152:149–157. doi: 10.1016/0022-1759(92)90136-H. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Van Amerongen A., Beckers P.J.A., Plasman H.H., Schaaper W.M.M., Sauerwein R.W., Meuwissen J.H.E.T., Meloen R.H. Peptides reactive with a transmission blocking monoclonal antibody against Plasmodium falciparum Pfs25: 2000-fold affinity increase by PEPSCAN-based amino acid substitutions. Pept. Res. 1992;5:269–274. [PubMed] [Google Scholar]
  • 18.Montelione G.T., Wüthrich K., Burgess A.W., Nice E.C., Wagner G., Gibson K.D., Scheraga H.A. Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints. Biochemistry. 1992;31:236–249. doi: 10.1021/bi00116a033. [DOI] [PubMed] [Google Scholar]
  • 19.Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Jr., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 1977;112:535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  • 20.Houghten R.A. Facile determination of exact amino acid involvement in peptide antigen/monoclonal antibody interactions. In: Peeters H., editor. Protides of the Biological Fluids, Proceedings of the 34th Colloquium. Oxford: Pergamon Press; 1986. pp. 19–22. [Google Scholar]
  • 21.Churchill M.E.A., Stura E.A., Pinilla C., Appel J.R., Houghten R.A., Kono D.H., Balderas R.S., Fieser G.G., Schulze-Gahmen U., Wilson I.A. Crystal structure of a peptide complex of antiinfluenza peptide antibody Fab 26/9. J. Mol. Biol. 1994;241:534–556. doi: 10.1006/jmbi.1994.1530. [DOI] [PubMed] [Google Scholar]
  • 22.Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science. 1995;267:383–386. doi: 10.1126/science.7529940. [DOI] [PubMed] [Google Scholar]
  • 23.Wells J.A. Structural and functional epitopes in the growth hormone receptor complex. Biotechnology. 1995;13:647–651. doi: 10.1038/nbt0795-647. [DOI] [PubMed] [Google Scholar]

Articles from Molecular Diversity are provided here courtesy of Nature Publishing Group

RESOURCES