Abstract
To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstrated local structural changes, such as hydrogen bond network rearrangements including water molecules, the large conformational changes at the helix level are not necessarily observed. Furthermore, the two reported crystal structures of an intermediate accumulated using a common method were distinct. To reconcile these apparent discrepancies, low-resolution projection maps were calculated from the crystal structures and compared to the low-resolution intermediate structures obtained using native membranes. The crystal structures can be categorized into three groups, which qualitatively correspond to the low-resolution structures of the M1-type, M2-type, and N-type determined in the native membrane. Based on these results, we conclude that at least three types of intermediate structures play a role during the photocycle.