Three theoretical models of proton pumps are discussed at the molecular level. The models contain hydrogenhyphen;bonded chains, which are the best understood channels, structurally and kinetically, for proton conduction within membranes. The first model, called the integral injector model, has an active site which involves apKchange. The second model, called the switch model, utilizes a conformational change in a retinal as the active site. The third model, called the active chain model, involves a conformational change in the protein, and the active site is delocalized to include the entire hydrogenhyphen;bonded chain. The models presented were chosen in part because of their possible relevance to the bacteriorhodopsin proton pump and comparisons are made to this system, but the basic principles involved have greater generality. In greater part they were chosen to explore the general family of theoretical proton pumps. Each model illustrates general principles that form a basis for generating additional models in the family.
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