Predicting the point at which transmembrane helices protrude from the bilayer: a model of the antenna complexes from photosynthetic bacteria.

We describe a method for predicting the point at which a transmembrane helix leaves the bilayer and enters the more polar region of the aqueous exterior. This is achieved by comparing the relative directions of the hydrophobic and internal faces of the transmembrane helices which should be opposite for the regions within the bilayer but equivalent for the regions on the outside. This information provides a strong constraint in the process of modelling membrane proteins. We go on to use the approach to model the monomers of the bacterial light-harvesting antenna complexes. This information is then combined with some preliminary crystallographic data and biochemical results to produce a 3-D model of a tetramer