Channel Protein Steers Gas

A family of membrane-spanning proteins that mediate gas transport has finally yielded its secrets. Scientists at the University of California, San Francisco, have used X-ray crystallography to reveal the molecular architecture of a bacterial protein that ushers ammonia across cell membranes [Science, 305, 1587 (2004)]

This structure--the first of any gas channel protein--provides "a quantum leap forward in our understanding of gas transport," note biochemists Peter Agre of Johns Hopkins University School of Medicine and Mark A. Knepper of the National Institutes of Health in an accompanying Science commentary.

Ammonia is a gas, but in aqueous solution it exists predominantly as ammonium ion (NH₄⁺). Bacteria use ammonia as a nitrogen source to make amino acids. In humans, ammonia is an important reactant in a variety of reactions. Although this crucial molecule can slowly diffuse through cell membranes on its own, nearly all organisms contain membrane-spanning channel proteins that allow ammonia to cross the lipid bilayer in a rapid and controlled manner.

Professor Robert M. Stroud, postdoc Shahram Khademi, and their coworkers in the biochemistry and biophysics department at UC San Francisco have now solved the structure of a model bacterial ammonia channel to 1.35 Å, an unprecedented level of resolution for a membrane-spanning protein. The structure reveals that the channel is made up of three identical membrane-spanning subunits, each of which contains a 20-Å-long hydrophobic tunnel just wide enough for NH₃ molecules to pass through single file. Wider vestibules flank each end of this narrow tunnel.

Stroud suggests that the constellation of aromatic residues in the extracellular vestibule binds ammonium ions from solution via -cation interactions. In this vestibule, it appears that ammonium ions are converted to ammonia molecules. In the narrow tunnel beyond the vestibule, two histidine residues poking out of the tunnel's waxy wall stabilize the NH₃ molecules via weak C–H···N hydrogen bonds. Because NH₄⁺ ions can't accept any hydrogen bonds, they cannot pass through the tunnel, Stroud notes.

The channel's ability to discriminate against NH₄⁺ is crucial because the protein must not alter the charge balance across the membrane by mistakenly letting K⁺ or other cations through. Indeed, Stroud's team has confirmed that the channel conducts NH₃--and not ammonium ion--via a fluorescence assay using channel-studded vesicles loaded with a pH-sensitive fluorescent dye.

The mechanistic insights provided by the structure of this bacterial ammonia channel are likely to shed light on the workings of its human cousins, Stroud says. Those relatives include the Rh blood group proteins found on red blood cells--which are reported to ferry both ammonia and carbon dioxide across the cell membrane--as well as a number of physiologically important ammonia channels that regulate body pH and protect against ammonia toxicity. Stroud suggests that the structure might be used to understand the molecular basis of diseases caused by ammonia toxicity and perhaps even to design drugs to treat them.