Internal packing of helical membrane proteins

Abstract

Helix packing is important in the folding, stability, and association of membrane proteins. Packing analysis of the helical portions of 7 integral membrane proteins and 37 soluble proteins show that the helices in membrane proteins have higher packing values (0.431) than in soluble proteins (0.405). The highest packing values in integral membrane proteins originate from small hydrophobic (G and A) and small hydroxyl-containing (S and T) amino acids, whereas in soluble proteins large hydrophobic and aromatic residues have the highest packing values. The highest packing values for membrane proteins are found in the transmembrane helix-helix interfaces. Glycine and alanine have the highest occurrence among the buried amino acids in membrane proteins, whereas leucine and alanine are the most common buried residue in soluble proteins. These observations are consistent with a shorter axial separation between helices in membrane proteins. The tight helix packing revealed in this analysis contributes to membrane protein stability and likely compensates for the lack of the hydrophobic effect as a driving force for helix-helix association in membranes.

Figure 1

Schematic of the OS calculation for the methyl group of threonine. The diagram depicts the normals extending from the molecular surface associated with the methyl group. The surface normals terminate if they encounter the van der Waals surface of residues within 2.8 Å.

Figure 2

Comparison of helix packing between membrane and soluble proteins. The soluble proteins were classified according to Michie et al. (26). (A) Contributions to helix packing by different amino acid classes. The packing values in Table 3 were combined for small (A,G), hydroxyl (S,T), amide (N,Q), charged (D,E,R,H,K), hydrophobic (I,L,M,V), and aromatic (F,W,Y) amino acids. The contribution of each amino acid class is plotted by taking the difference between the average packing value for the amino acid class and the average packing value for the protein class as described in the text. These data reflect only the helical portions of the proteins studied. (B) Contribution of amino acid classes to the overall packing in different classes of helical proteins. The packing value differences plotted in A are multiplied by the percent occurrence of the amino acid class for each protein class.

Figure 3

Distribution of the axial separation in membrane and α-bundle proteins determined by using the program define_s (42). The average axial separation for membrane proteins is 9.0 Å, whereas the separation in α-bundle proteins is 9.6 Å.