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Bioinformatics Vol. 18 no. 4 2002
Pages 608-616
© 2002 Oxford University Press

Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane–water interfaces

Shigeki Mitaku 1,*, Takatsugu Hirokawa 1,2 and Toshiyuki Tsuji 1

1 Tokyo University of Agriculture and Technology, Faculty of Technology, Department of Biotechnology, Nakacho, Koganei, Tokyo 184-8588, Japan
2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koutou-ku, Tokyo 135-0064, Japan

Received on December 12, 2000 ; revised on May 10, 2001 ; accepted on September 20, 2001

Motivation: An amphiphilicity index of amino acid residues was developed for improving the method of transmembrane helix prediction.

Results: The transfer energy of a hydrocarbon stem group beyond the {gamma}-carbon was calculated from the accessible surface area, and used to index the amphiphilicity of the residue. Non-zero amphiphilicity index values were obtained for lysine, arginine, histidine, glutamic acid, glutamine, tyrosine and tryptophan. Those residues were found to be abundant in the end regions of transmembrane helices, indicating their preference for the membrane–water interface. The moving average of the amphiphilicity index actually showed significant peaks in the end regions of most transmembrane helices. A dispersion diagram of average amphiphilicity index versus average hydrophobicity index was devised to facilitate discrimination of transmembrane helices.

Availability: The amphiphilicity index has been incorporated into a system, SOSUI, for the discrimination of membrane proteins and the prdiction of tranmembrane helical regions (http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html).

Contact: mitaku{at}cc.tuat.ac.jp

* To whom correspondence should be addressed.


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