1. MRC Laboratory of Molecular Biology , Cambridge CB2 2QH, UK
2. Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892 , USA

Correspondence to: Sriram Subramaniam^1,2 Correspondence and requests for materials should be addressed to S.S. (e-mail: Email: ss1@nih.gov). The coordinates for the structures reported here are deposited in the Protein Data Base (accession numbers 1FBB for wild-type bacteriorhodopsin and 1FBK for the mutant).

Abstract

Bacteriorhodopsin, a membrane protein with a relative molecular mass of 27,000, is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum. The chromophore retinal is covalently attached to the protein via a protonated Schiff base. Upon illumination, retinal is isomerized. The Schiff base then releases a proton to the extracellular medium, and is subsequently reprotonated from the cytoplasm. An atomic model for bacteriorhodopsin was first determined by Henderson et al¹, and has been confirmed and extended by work in a number of laboratories in the last few years². Here we present an atomic model for structural changes involved in the vectorial, light-driven transport of protons by bacteriorhodopsin. A 'switch' mechanism ensures the vectorial nature of pumping. First, retinal unbends, triggered by loss of the Schiff base proton, and second, a protein conformational change occurs. This conformational change, which we have determined by electron crystallography at atomic (3.2 Å in-plane and 3.6 Å vertical) resolution, is largely localized to helices F and G, and provides an 'opening' of the protein to protons on the cytoplasmic side of the membrane.