Improvement of the Transmembrane Helix Prediction System by Three-Stage Model

Takatsugu Hirokawa (hirokawa@cc.tuat.ac.jp)
Seah Boon-Chieng (seah@cc.tuat.ac.jp)
Shigeki Mitaku (mitaku@cc.tuat.ac.jp)

Department of Biotechnology,
Tokyo University of Agriculture and Technology
Nakacho 2-24-16, Koganei, Tokyo 184, Japan

A new method to predict the transmembrane helices from amino acid sequences was developed, in which the effect of the stabilization of helices by interhelix binding was taken into account. It was assumed that there are three stages of transmembrane helix conformation: the binding to membrane surface, the formation of transmembrane core region, and the maturation of helix due to the tertiary structure formation in membrane. This method was applied to the amino acid sequences of membrane proteins whose number of transmembrane helix are given, and most transmembrane helices were truly predicted.