Protein Engineering, Vol. 13, No. 11, 771-778,
November 2000
© 2000 Oxford University Press
A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle
1 Department of Biotechnology, Tokyo University of Agriculture and Technology, Nakacho, Koganei, Tokyo 184-8588, 2 Ryoka System Inc., Computational Science and Technology Division, Irifune, Urayasu,Chiba Prefecture 279-0012 and 3 Helix Research Institute, Inc.,1532–3 Yana, Kisarazu-shi, Chiba 292, Japan
We developed a method of predicting the tertiary structures of seven transmembrane helical proteins in triangle lattice models, assuming that the configuration of helices is stabilized by polar interactions. Triangle lattice models having 12 or 11 nearest neighbor pairs were used as general templates of a seven-helix system, then the orientation angles of all helices were varied at intervals of 15°. The polar interaction energy for all possible positions of each helix was estimated using the calculated polar indices of transmembrane helices. An automated system was constructed and applied to bacteriorhodopsin, a typical membrane protein with seven transmembrane helices. The predicted optimal and actual structures were similar. The top 100 predicted helical configurations indicated that the helix-triangle, CFG, occurred at the highest frequency. In fact, this helix-triangle of bacteriorhodopsin forms an active proton-pumping site, suggesting that the present method can identify functionally important helices in membrane proteins. The possibility of studying the structure change of bacteriorhodopsin during the functional process by this method is discussed, and may serve to explain the experimental structures of photointermediate states.
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