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Helmut Grubmüller
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December 17, 2001
Volume 79, Number 51
CENEAR 79 51 p. 14
ISSN 0009-2347
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To pass through a membrane pore quickly, H2O must 'change partners'


Researchers at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, have used molecular dynamics simulations to solve a biological mystery: how water molecules can pass through a protein pore in a cell membrane as rapidly as they do without ferrying extra protons across with them.

Theoretical biophysicist Helmut Grubmüller and chemist Bert L. de Groot combined the atomic resolution structure of the protein aquaporin with a virtual bilayer membrane surrounded by a large number of water molecules to create one of the largest and most complex computer simulations of the movement of molecules ever generated [Science, 294, 2353 (2001)]. The researchers were able to accurately calculate the movements of some 100,000 atoms for a period of 10 nanoseconds. That's long enough to "watch" 16 water molecules pass through the channel of the protein.

"This is one of a very few, if not the first, complete biological processes to be fully visualized by a simulation," Grubmüller says.

In nature, aquaporin rapidly filters water through membranes. Larger molecules are kept from passing through the protein pore by the pore's small size. But tiny protons would be expected to skim through easily by hopping along the network of hydrogen bonds that inevitably forms when water molecules are near one another.

The simulation reveals a delicately choreographed dance of the water molecules, directed by carefully positioned amino acid residues throughout the channel interior. "The water molecules are handed off from one residue to the next," Grubmüller explains. "Each time you break a hydrogen bond between two water molecules, you form another between water and the protein." The result is an energy-efficient process that allows the water molecules to move rapidly through the membrane and leaves the protons behind.

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