Tokyo University of Agriculture and Technology, Faculty of Technology
School of Science and Engeneering, Waseda University
A method for the tertiary structure prediction of membrane proteins is proposed, with two steps: characterization of each transmembrane helix and solving a jigsaw puzzle problem of a bundle of helices. The first step was realized by the probe helix method in which interaction energy between a transmembrane helix and a probe helix was calculated. Transmembrane helices of bacteriorhodopsin indicated different profiles of polar arcs. Solving jigsaw puzzle problem of transmembrane helices, structures similar to the native one could be obtained on the assumption that neighboring helices in the primary structure are located side by side also in the tertiary structure.