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Molecular architecture and action of a proton pump

Max Planck scientists uncover the molecular structure and mode of operation of a proton pump typically found in fungi and yeasts


Proton pumps in the membrane surrounding plant and yeast cells maintain the intracellular pH. The resulting membrane potential drives the uptake of other ions and nutrients. Hence, the proper function of the proton pump is essential for survival of these organisms. Kühlbrandt and colleagues at the Max Planck Institute of Biophysics in Frankfurt, Germany have generated a model of this key membrane protein and have deduced the mechanism by which it is regulated, as just published in Science.

The yeast proton pump is a member of the family of the so-called P-type ATPases. They are large membrane proteins which use the energy harnessed in adenosine triphosphate (ATP) to transport cations against a concentration gradient in an out of the cell. Other prominent family members include the sodium-potassium ATPase which regulates the heartbeat, the proton-potassium ATPase which acidifies the stomach, and the calcium ATPase which controls muscle contraction.

Detailed knowledge of the three-dimensional structure of any protein is the most important prerequisite for understanding how it works. The first, and so far only detailed structure of a P-type ion pump was that of the calcium ATPase from rabbit muscle, determined two years ago at Tokyo University by means x-ray crystallography. A less detailed structural model of the yeast proton ATPase was determined in 1998 by the group at the Max Planck Institute of Biophysics using the method of electron cryo-microscopy on two-dimensional crystals. Taking advantage of the molecular family resemblance, the Frankfurt group used the calcium pump structure to calculate a homology model of the proton pump. The model was fitted to the lower-resolution map determined by electron crystallography (fig.1). This revealed that the P-type ion pumps are surprisingly dynamic. The part which binds ATP rotates by more than 70° during the ion pumping cycle, enabling the release of energy which is then transmitted via conserved structural elements to the proton binding site in the membrane. There it causes a conformational change, as a result of which the proton is released on the outer cell surface (fig. 2).

The model provides important clues about the mechanism by which the activity of the proton pump is regulated. The Frankfurt group discovered that the last 38 of the proton pump's 920 amino acids form a separate entity which appears to inhibit the molecular motions and the release of energy that drives the pumping process. A synthetic peptide of these 38 amino acids stimulates the pump's activity by more than 10-fold, apparently by replacing the inhibitory entity from its binding site.

Since mammalian cells do not contain the proton pump, it represents a key target for the design of drugs against yeasts and fungi. Substances that interfere with the regulatory mechanism of the yeast proton pump therefore provide a promising basis for the future development of new fungicides.


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