Polarity conserved positions in transmembrane domains of G-protein coupled receptors and bacteriorhodopsin.

The polarity of residues at certain positions in the transmembrane domains of G-protein coupled receptors (GPCR) is found to be conserved, and to indicate the pattern of specific helix-helix packing of the helices. A concept of polarity conserved positions (PCP) is proposed to describe this conserved property, and is applied to obtain insight into the structural features of the transmembrane proteins. The common pattern of PCPs for GPCRs indicates that they share a similar packing arrangement of their transmembrane helix bundles. For proteins in the bacteriorhodopsin family the PCP pattern suggests a common packing arrangement that differs from that of GPCRs, in agreement with experimental data. This difference in the packing arrangement underscores the shortcomings of a BR template for the construction of molecular models of GPCRs.