Skip to main content
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1985 Aug;82(16):5255–5259. doi: 10.1073/pnas.82.16.5255

Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition.

I A Wilson, D H Haft, E D Getzoff, J A Tainer, R A Lerner, S Brenner
PMCID: PMC390546  PMID: 2410917

Abstract

The ability of antibodies raised against disordered short peptides to interact frequently with their cognate sequences in intact folded proteins has raised a major theoretical issue in protein chemistry. We propose to address this issue by using antibodies raised against peptides with identical sequences, but different conformations, in pairs of unrelated proteins of known three-dimensional structure. The general search method presented here enabled us to detect candidate sequences for such immunological studies.

Full text

PDF
5255

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bernstein F. C., Koetzle T. F., Williams G. J., 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 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  2. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. doi: 10.1002/9780470122921.ch2. [DOI] [PubMed] [Google Scholar]
  3. Connolly M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 1983 Aug 19;221(4612):709–713. doi: 10.1126/science.6879170. [DOI] [PubMed] [Google Scholar]
  4. Evans P. R., Hudson P. J. Structure and control of phosphofructokinase from Bacillus stearothermophilus. Nature. 1979 Jun 7;279(5713):500–504. doi: 10.1038/279500a0. [DOI] [PubMed] [Google Scholar]
  5. Green N., Alexander H., Olson A., Alexander S., Shinnick T. M., Sutcliffe J. G., Lerner R. A. Immunogenic structure of the influenza virus hemagglutinin. Cell. 1982 Mar;28(3):477–487. doi: 10.1016/0092-8674(82)90202-1. [DOI] [PubMed] [Google Scholar]
  6. Holmes M. A., Matthews B. W. Structure of thermolysin refined at 1.6 A resolution. J Mol Biol. 1982 Oct 5;160(4):623–639. doi: 10.1016/0022-2836(82)90319-9. [DOI] [PubMed] [Google Scholar]
  7. Kabsch W., Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci U S A. 1984 Feb;81(4):1075–1078. doi: 10.1073/pnas.81.4.1075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Niman H. L., Houghten R. A., Walker L. E., Reisfeld R. A., Wilson I. A., Hogle J. M., Lerner R. A. Generation of protein-reactive antibodies by short peptides is an event of high frequency: implications for the structural basis of immune recognition. Proc Natl Acad Sci U S A. 1983 Aug;80(16):4949–4953. doi: 10.1073/pnas.80.16.4949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ploegman J. H., Drent G., Kalk K. H., Hol W. G. Structure of bovine liver rhodanese. I. Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains. J Mol Biol. 1978 Aug 25;123(4):557–594. [PubMed] [Google Scholar]
  10. Szebenyi D. M., Obendorf S. K., Moffat K. Structure of vitamin D-dependent calcium-binding protein from bovine intestine. Nature. 1981 Nov 26;294(5839):327–332. doi: 10.1038/294327a0. [DOI] [PubMed] [Google Scholar]
  11. Tainer J. A., Getzoff E. D., Alexander H., Houghten R. A., Olson A. J., Lerner R. A., Hendrickson W. A. The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature. 1984 Nov 8;312(5990):127–134. doi: 10.1038/312127a0. [DOI] [PubMed] [Google Scholar]
  12. Thieme R., Pai E. F., Schirmer R. H., Schulz G. E. Three-dimensional structure of glutathione reductase at 2 A resolution. J Mol Biol. 1981 Nov 15;152(4):763–782. doi: 10.1016/0022-2836(81)90126-1. [DOI] [PubMed] [Google Scholar]
  13. Varghese J. N., Laver W. G., Colman P. M. Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 A resolution. Nature. 1983 May 5;303(5912):35–40. doi: 10.1038/303035a0. [DOI] [PubMed] [Google Scholar]
  14. Westhof E., Altschuh D., Moras D., Bloomer A. C., Mondragon A., Klug A., Van Regenmortel M. H. Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature. 1984 Sep 13;311(5982):123–126. doi: 10.1038/311123a0. [DOI] [PubMed] [Google Scholar]
  15. Wilson I. A., Niman H. L., Houghten R. A., Cherenson A. R., Connolly M. L., Lerner R. A. The structure of an antigenic determinant in a protein. Cell. 1984 Jul;37(3):767–778. doi: 10.1016/0092-8674(84)90412-4. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES