How does a topological inversion change the evolutionary constraints on membrane proteins?

Abstract

The members of the aquaporin family and those of the ClC chloride ion channel family consist of two-fold tandem repeats. The orientation of the N-terminal domain against membrane is opposite to that of the C-terminal domain. Several lines of evidence suggest that the extracellular and the cytoplasmic environments impose different evolutionary constraints on proteins (e.g. positive-inside rule). Therefore, the different constraints would affect the corresponding regions of the two domains, which are exposed to the different environments. To examine this hypothesis, the N- and the C-terminal domains were aligned and the difference in residue composition or conservation pattern between the two domains was calculated at each alignment site by several methods. Then, the residues corresponding to the sites exhibiting significant difference were mapped onto the tertiary structure. In spite of the difference in the methods, the mapped residues clustered on the pore surface of the channel; in contrast, the number of the residues mapped on the extracellular or cytoplasmic sides of the proteins was small. A minor modification of the methods improved the sensitivity to detect sites related to the positive-inside rule. The results support our hypothesis about the relationship between the topological inversion and the different constraints.