Abstract
A simple method is described to locate 'antigenic' peptides from the alpha-carbon co-ordinates of a protein, based on protrusion from the protein's globular surface. A good correlation is found between those parts of a protein which protrude and the experimentally determined antigenic peptides in myoglobin, lysozyme and myohemerythrin. A comparison is made between the use of protrusion index, mobility, solvent accessibility and hydrophilicity for predicting the most likely antigenic peptides.
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Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Amit A. G., Mariuzza R. A., Phillips S. E., Poljak R. J. Three-dimensional structure of an antigen-antibody complex at 6 A resolution. Nature. 1985 Jan 10;313(5998):156–158. doi: 10.1038/313156a0. [DOI] [PubMed] [Google Scholar]
- Atassi M. Z. Antigenic structures of proteins. Their determination has revealed important aspects of immune recognition and generated strategies for synthetic mimicking of protein binding sites. Eur J Biochem. 1984 Nov 15;145(1):1–20. doi: 10.1111/j.1432-1033.1984.tb08516.x. [DOI] [PubMed] [Google Scholar]
- Benjamin D. C., Berzofsky J. A., East I. J., Gurd F. R., Hannum C., Leach S. J., Margoliash E., Michael J. G., Miller A., Prager E. M. The antigenic structure of proteins: a reappraisal. Annu Rev Immunol. 1984;2:67–101. doi: 10.1146/annurev.iy.02.040184.000435. [DOI] [PubMed] [Google Scholar]
- 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]
- Berthou J., Lifchitz A., Artymiuk P., Jollès P. An X-ray study of the physiological-temperature form of hen egg-white lysozyme at 2 A resolution. Proc R Soc Lond B Biol Sci. 1983 Mar 22;217(1209):471–489. doi: 10.1098/rspb.1983.0021. [DOI] [PubMed] [Google Scholar]
- Davies D. R., Metzger H. Structural basis of antibody function. Annu Rev Immunol. 1983;1:87–117. doi: 10.1146/annurev.iy.01.040183.000511. [DOI] [PubMed] [Google Scholar]
- De L Milton R. C., van Regenmortel M. H. Immunochemical studies of tobacco mosaic virus--III. Demonstration of five antigenic regions in the protein sub-unit. Mol Immunol. 1979 Mar;16(3):179–184. doi: 10.1016/0161-5890(79)90143-3. [DOI] [PubMed] [Google Scholar]
- Hopp T. P., Woods K. R. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824–3828. doi: 10.1073/pnas.78.6.3824. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ibrahimi I. M., Eder J., Prager E. M., Wilson A. C., Arnon R. The effect of a single amino acid substitution on the antigenic specificity of the loop region of lysozyme. Mol Immunol. 1980 Jan;17(1):37–46. doi: 10.1016/0161-5890(80)90122-4. [DOI] [PubMed] [Google Scholar]
- Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
- Leach S. J. How antigenic are antigenic peptides? Biopolymers. 1983 Jan;22(1):425–440. doi: 10.1002/bip.360220156. [DOI] [PubMed] [Google Scholar]
- Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
- Rossmann M. G., Arnold E., Erickson J. W., Frankenberger E. A., Griffith J. P., Hecht H. J., Johnson J. E., Kamer G., Luo M., Mosser A. G. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature. 1985 Sep 12;317(6033):145–153. doi: 10.1038/317145a0. [DOI] [PubMed] [Google Scholar]
- Sheriff S., Hendrickson W. A., Stenkamp R. E., Sieker L. C., Jensen L. H. Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1104–1107. doi: 10.1073/pnas.82.4.1104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Tainer J. A., Getzoff E. D., Paterson Y., Olson A. J., Lerner R. A. The atomic mobility component of protein antigenicity. Annu Rev Immunol. 1985;3:501–535. doi: 10.1146/annurev.iy.03.040185.002441. [DOI] [PubMed] [Google Scholar]
- Thornton J. M., Sibanda B. L. Amino and carboxy-terminal regions in globular proteins. J Mol Biol. 1983 Jun 25;167(2):443–460. doi: 10.1016/s0022-2836(83)80344-1. [DOI] [PubMed] [Google Scholar]
- 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]
- Young D. R., Schmitz H. E., Atassi M. Z. Antibodies with specificities to preselected protein regions evoked by free synthetic peptides representing protein antigenic sites or other surface locations: demonstration with myoglobin. Mol Immunol. 1983 May;20(5):567–570. doi: 10.1016/0161-5890(83)90096-2. [DOI] [PubMed] [Google Scholar]