Hydrophilic and hydrophobic surface map analysis of bacteriorhodopsin.

Bacteriorhodo sin is an integral membrane light-driven proton pump from ~aLbucter ium ~ o b i u m . It consists of seven transmembrane helices, surrounding a central proton translocation channel, in a 1:l complex with a retinal chromophore. The structure of the transmembrane helices has been resolved by high-resolution electron cryo-microscopy [ 11. We have investigated the amphipathic nature of the helices by determining the h drophilic and hydrophobic surface maps of each helix. The iydrophilic surface IS calculated using an em irical peptide-water interaction energy function 121. while hy8ophobic surfaces are determined using molecular hydrophobicity potentials [ 3 ] . The resultant surface maps are displayed as contour plots that can be used to define the centre of the hydrophilic and hydrophobic faces of each helix. Figure 1 illustrates the hydrophilic surface for helix G. Between z= 0.5 nm and z= +2.0 nm there is a hydrophilic interaction with the polar residues E204. T205. D212 and K216, with additional favourable interactions at S214 and R225. If the hydrophilic surface map is averaged over all values of i. a graph of is obtained. the minimum in which defines the centre of the vs. t ydrophilic surface of the helix, corresponding in this case to the C a positions, on q, of D212 and K216. Although the latter residue forms a Schiff base with the retinal chromophore and thus would not contain a free amino terminus (as used here) the hydrophilic surface would still be determined by D212. The centres of the h dro hilic and hydrophobic surfaces of the helices are compareYwitt! their orientation within the 3d structure of bacteriorhodopsin. The result of such an analysis for the hydrophilic surfaces is shown in fi ure 2. For four of the helices, namely helices C, D, E and 8 the centre of the Figure 1. Upper Half. Hydrophilic surface map of helix G of bacteriorhodopsin. Contours are drawn at -18 (thick line). -12 (thin line) and -6 (broken line) kcaldmol. The positions of selected C a atoms are indicated. Lower Half. , the average on i of the hydrophilic surface map, as a function of $. Dotted lines indicate the positions of the Ca atoms of D2 12 and K216.