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Journal of Biochemistry Advance Access published online on October 8, 2009
Journal of Biochemistry, doi:10.1093/jb/mvp150
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© The authors 2009. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Characteristic amino acid distribution around segments unique to allergens

Naoyuki Asakawa1,*, Noriyuki Sakiyama1,2, Reiko Teshima3 and Shigeki Mitaku1

1Department of Applied Physics, School of Engineering, Nagoya University
2Venture Business Laboratory, Nagoya University
3Novel Foods and Immunochemistry Division, National Institute of Health Sciences

Corresponding Author: Noriyuki Sakiyama Chiku-sa-ku Frocho, Nagoya, Aichi, 464-8607 Phone: +81-(0)52-789-4465, Fax: +81-(0)52-789-3706 E-mail: sakiyama{at}bp.nuap.nagoya-u.ac.jp

Received July 1, 2009; Accepted September 8, 2009


  Abstract

Epitopes are located at the surface of allergens with which antibodies specifically bind. On the assumption that fragments unique to allergens have common, characteristic amino acid sequences, we compared the amino acid sequences of allergens with those of non-allergens. Segments around fragments unique to allergens showed wavelet-like distributions for several amino acids. Charged residues, alanine and glycine had positive peaks at the center of the unique segments with small valleys on both sides, while aromatic residues, proline and cysteine showed the inverse distribution. Furthermore, the wavelet-like distribution of amino acids could be represented by a universal distribution function together with an index characterizing the intensity of the wavelet. Using the universal distribution function and the novel index of amino acids, we developed a simple method for extracting segments and fragments that are unique to allergens. The significance of the universal distribution function and the novel index is also discussed, by comparing the plot of the AUF index and dynamic fluctuation in the three-dimensional structure of birch pollen allergen as both a single molecule and a complex with the corresponding antibody.

Key Words: allergen, unique sequence fragment, protein-protein interaction, bioinformatics

*Present affiliation: Computational Science Department, Science & Technology Systems Division, Ryoka Systems, Inc.


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