78s Biochemical Society Transactions ( 1 993) 21
Hydrophilic and Hydrophobic Surface Map Analysis of
Bactenorhodopsin.
IAN D. KERR and MARK S.P. SANSOM
Laboratory of Molecular Bioph sics, The Rex Richards
Buildin University of Oxford. {outh Parks Road. Oxford.
ox1 3%u.
Bacteriorhodo sin is an integral membrane light-driven
proton pump from ~ a L b u c t e r i u m~ o b i u mIt. 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 <E>
is obtained. the minimum in which defines the centre of
the
vs. 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
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. <EYIN>, 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.
hydrophilic faces are orientated towards the interior of the
seven helix bundle. The residues pro osed to be directly
involved in proton translocation. namely k 2 , DXS. D96. D2 12
and K216 are found on the most markedly amphipathic helices
(C and G). The hydrophilic face of helix A is orientated
towards the helix A - helix G interface. Helix B is revealed to
be only marginally amphipathic by both hydrophilic and
hydrophobic surface map calculations. Helix F is somewhat
anomalous in that the centre of its hydrophilic face is orientated
directly away from the helix bundle. towards the lipid phase.
Molecular hydrophobicity analysis reveals a similar.
pattern. However. the least hydrophobic face of helix F is
directed towards the helix F - helix E inteiface.
The results suggest that hydrophilic and hydrophobic
surface map calculations are valuable tools for predicting the
orientation of helices in transmembrane bundles of ion transport
The hydrophilic faces of markedly
predicted to be orientated towards the
ct with other helices.
IDK is supported by an SERClShell CASE s~udciitship
1. Henderson, R., Baldwin, J.M., Ceska, T.A.. Zeinlin. F.. Bcckin;uin. E. &
Downing, K.H. 1990. J. Mol. Biol. 213: 899-029.
2. Kerr, I.D. & Sansom, M.S.P. Biochrm. Soc. T m f l s . 20: 323s.
3. Brasseur, R. 1991. J. Biol. Chem. 266: 16120-161?7.
t
8
25
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Figure 2. Orientation of the helices of bacteriorhodopsin. For
each helix. represented by an a-carbon trace, an arrow is
depicted, extending from the centre of the helix, in the direction
of the centre of the hydrophilic surface. The length of the arrow
is proportional to the maximum interaction energy of the
peptide with a water molecule. as determined from the plot of
<E> vs. $. Two arrows are shown for helix C to represent the
two halves of the proline-kinked helix.