Cavity depth on the bacteriorhodopsin peptide surface near the proton carrier Asp96: Data of X-ray structure models

Three-dimensional X-ray models of the wild-type bacteriorhodopsin structure are investigated by means of the program PyMOL. Construction of the surfaces accessible to the solvent at the cytoplasmic side visualized a cavity near the proton carrier Asp96. The cavity shortens the way of the proton from the membrane surface to this carrier. The distance between the cavity surface and the centre of the carbonic atom of the Asp96 carboxylic group is ～6 Å. Besides, for model structures 1c3w, 1qhj, and 1BRR, a channel of radius 1.1 Å is revealed between the cytoplasmic surface and Asp96carboxyl. The channel diameter is narrower than the characteristic diameter of the water molecule and apparently does not create conductivity in the nonexcited pigment. It is possible however that along this channel a hydrated “gap” opens at the second phase of a bacteriorhodopsin photocycle related with reprotonation of Asp96.