Sequence divergence analysis for the prediction of seven-helix membrane protein structures: I. Comparison with...

A method using protein sequence divergence to predict the three-dimensional structure of the transmembrane domain of seven-helix membrane proteins is described. The key component in the multistep procedure is the calculation of a hydrophilic and lipophilic variability index for each amino acid in an alignment of a family of homologous proteins. The variability profile, a plot of the calculated variability index versus alignment position, can be used to predict a tertiary model of the backbone conformation of the transmembrane domain. This method was applied to bacteriorhodopsin (BR) and the model obtained was compared with the known structure of this protein. Using an alignment of the amino acid sequences of BR and closely related (> or = 20% identity) proteins, the boundaries of the transmembrane regions, their secondary structures and orientations inside the membrane bilayer were predicted based on the variability profile. Additional information about the shape of the helix bundle was also obtained from the average variability of each transmembrane helix with the assumption that the helices are packed sequentially and form a closed helix bundle. Correct features of the known structure of BR were found in the model structure, suggesting that a similar strategy can be used to predict transmembrane helices and the packing shape of other membrane proteins with seven transmembrane helices, such as the opsins and other G-protein coupled receptors.