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We report on the location of the chain part of the retinylidene chromophore in the projected density of bacteriorhodopsin as determined by neutron diffraction from the two-dimensional purple membrane lattice. For this purpose, partially deuterated retinal was synthesized containing 10 deuterons at positions C-8, C-10, C-12, C-14, C-19(3), and C-20(3) of the polyene chain. Two sets of dark-adapted samples were prepared in entirely different ways: (i) Deuterated retinal was incorporated biosynthetically during growth of the bacteria by using the mutant JW5, which is deficient in the synthesis of retinal. (ii) The chromophore was converted to retinal oxime, the resulting colorless apomembrane was regenerated with deuterated retinal, and the residual retinal oxime was removed by washing with bovine serum albumin. Characterization of these samples by x-ray diffraction, absorption, and flash spectroscopy showed that they were identical to native purple membrane samples as judged by these criteria. Fourier difference maps were calculated from the differences in inplane diffraction from the deuterated membranes and from protonated samples that were prepared in exactly the same way. At 8.7 A resolution, both maps show a single major peak at the same position with the center of mass of the labeled part of the chain (C-11) between helices 6 and 3 but closer to helix 6. It appears likely that the COOH-terminal helix G, to which retinal is attached at lysine-216, is either helix 2 or 6.

A neutron diffraction study on the location of the polyene chain of retinal in bacteriorhodopsin.