A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle

We developed a method of predicting the tertiary structures of seven transm embrane helical proteins in triangle lattice models, assuming that the conf iguration of helices is stabilized by polar interactions. Triangle lattice models having 12 or 11 nearest neighbor pairs were used as general template s of a seven-helix system, then the orientation angles of all helices were varied at intervals of 15 degrees. The polar interaction energy for all pos sible positions of each helix was estimated using the calculated polar indi ces of transmembrane helices. An automated system was constructed and appli ed to bacteriorhodopsin, a typical membrane protein with seven transmembran e helices, The predicted optimal and actual structures were similar. The to p 100 predicted helical configurations indicated that the helix-triangle, C FG, occurred at the highest frequency. In fact, this helix-triangle of bact eriorhodopsin forms an active proton-pumping site, suggesting that the pres ent method can identify functionally important helices in membrane proteins , The possibility of studying the structure change of bacteriorhodopsin dur ing the functional process by this method is discussed, and may serve to ex plain the experimental structures of photointermediate states.