Structural clues in the sequences of the aquaporins

The large number of sequences available for the aquaporin family represents a valuable source of information to incorporate into three-dimensional str ucture determination. Phylogenetic analysis was used to define type sequenc es to avoid extreme over-representation of some subfamilies, and as a measu re of the quality of multiple sequence alignment. Inspection of the sequenc e alignment suggested eight conserved segments that define the core archite cture of six transmembrane helices and two functional loops, B and E, proje cting into the plane of the membrane. The sum of the core segments and the minimum lengths of the interlinking loops constitute the 208 residues neces sary to satisfy the aquaporin architecture. Analysis of hydrophobic and con servation periodicity and of correlated mutations across the alignment indi cated the likely assignment and orientation of the helices in the bilayer. This assignment is examined with respect to the structure of the erythrocyt e aquaporin 1 determined by electron crystallography. The aquaporin 1 tetra mer is described as three rings of helices, each ring with a different expo sure to the lipid environment. The sequence analysis clearly suggests that two helices are exposed along their whole lengths, two helices are exposed only at their N termini, and two helices are not exposed to lipid. It is fu rther proposed that, besides loops B and E, the highly conserved motifs on helices 1 and 4, ExxxTxxF/L, could line the water channel. (C) 2000 Academi c Press.