MODELING OF HALORHODOPSIN AND RHODOPSIN BASED ON BACTERIORHODOPSIN

Bacteriorhodopsin (BR), halorhodopsin (HE), and rhodopsin (Rh) all bel ong to the class of seven-helix membrane proteins. For BR, a structura l model at atomic resolution is available; for HR, diffraction data ar e available only down to a resolution of 6 Angstrom in the membrane pl ane, and for Rh, down to 9 Angstrom. BR and MR are closely related pro teins with a sequence homology of 34%, while Rh does not share any seq uence homology with BR. An atomic. model for HR is derived that is bas ed on sequence alignment and the atomic model for BR and is improved b y molecular dynamics simulations. The model structure obtained account s well for the experimentally observed difference between HR and BR in the projection map, where HR exhibits a higher density in the region between helices D and E. The reason for this difference lies partially in the different side chains and partially in slightly different heli x tilts. The scattering amplitudes and phases of the model structure a re calculated and agree with the experimental data down to a resolutio n of about 8 Angstrom. If the helix positions are adopted from the pro jection map for HR and used as input in the model, this number improve s to 7 Angstrom. Analogously, an atomic model for Rh is derived based on the atomic model for BR and subjected to molecular dynamics simulat ions. Optimal agreement with the experimental projection map for Rh is obtained when the entire model structure is rotated slightly about tw o axes in the membrane plane. The agreement with the experimental proj ection map is not as satisfactory as for HR, but the results indicate that even for a nonhomologous, but structurally related, protein such as Rh, an acceptable model structure can be derived from the structure of BR. (C) 1996 Wiley-Liss, Inc.