Rhodopsins are a class of protein commonly found in the rod cells of the eye. These proteins are the driving force behind a process called visual phototransduction, which is the translation of a visual picture into an electrical signal that can be processed by the brain. These proteins are also found in bacteria, serving a similar purpose: they create electrical energy for the cell by moving proteins across the cell membrane, creating an electrical gradient.
The structure of rhodopsin is essential in allowing the protein to carry out its function. A picture showing the structure of bacteriorhodopsin can be found here.
The protein consists of 8 curled, spring-like structures called alpha helices. In order for the pump to move proteins through the membrane, these helices must move. This paper investigates the movement of this protein to allow protons to pass through the membrane. It involves a change in the complex between helices 3 and 6. The amino acid E134 (Glutamic acid/Glutamate at position 134 in the protein) gains a proton when helix 6 tilts about 4.0º. This rotation causes salt-bridge bonds between arginine and glutamate to break in two places on opposite ends of the protein complex. The pH and stability of the protein then provide motive force to push a proton out of the cell through the channel in the center of the protein