Helix-packing motifs in membrane proteins

Abstract

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd </=1.5 A), allowing 90% of the library to be assigned to clusters consisting of at least five members. Surprisingly, three quarters of the helical pairs belong to one of five tightly clustered motifs whose structural features can be understood in terms of simple principles of helix-helix packing. Thus, the universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

Fig. 1.

Pie chart showing the fraction of the total number of pairs that fall within a given cluster.

Fig. 2.

Overlay of helical pairs in each cluster. Twenty members are shown, including the centroid and the 19 structures that are most similar to the centroid (based on rmsd).

Fig. 3.

Structures and sequence-specific propensities for GAS_Left (A) and GAS_Right (B) motifs. In each panel, an example of a structure of a helical pair from one of the clusters is shown together with the position-specific mean propensities for Ala, Gly, and Ser below the structure. The arrows connect positions of high propensity with specific locations in the structures. The example of a GAS_Left motif is taken from 1jb0 residues B42–64 and B134–155, and the residues at “a” positions of the pseudoheptad repeat are labeled. The residues at “a” positions are colored (C green and O red), and a “d” position is colored purple. The example of a GAS_Right motif in B is from 1u7g. Note that small residues (purple) occur every four residues on one of the two helices. These small residues fit between two ridges formed by larger residues on the other helix. The side chains that form one of these ridges are shown in green; the side chains occur with four-residue periodicity at positions i, i + 4, i + 8…. The second ridge is formed by residues shown in orange, also with four-residue periodicity but displaced by one residue in sequence (at positions i + 1, i + 5, i + 9…).

Fig. 4.

Helix crossing-angle histograms for each of the four most-populated clusters: cluster 1 (antiparallel GAS_Left) is shaded red, cluster 2 (parallel GAS_Left) is shaded blue, cluster 3 (parallel GAS_Right) is shaded yellow, and cluster 4 is shaded green.