Simulating Water and the Molecules of Life; November 1998; Scientific American Magazine; by Gerstein, Levitt; 6 Page(s)
Water is cheap, if not free, in most places in the world. But during the summer of 1986, one of us (Levitt) spent half a million dollars on an amount of water that would scarcely wet the point of a pin. The money was not to buy the vanishingly small amount of water. Rather it was to pay for the roughly two weeks of processing time on a gigantic stateof- the-art supercomputer required to create a model of how the water affected the structure and movement of a particular protein.
The protein was bovine pancreatic trypsin inhibitor (BPTI), which is found in the pancreases of cattle. BPTI is a favorite subject of computer modelers simply because it is relatively small and therefore easier to study than most other proteins. It had been modeled before, by Martin Karplus of Harvard University and his colleagues in 1977, but only "in vacuo" (as if in a vacuum)--without any other molecules interacting with it. No one had visualized BPTI as it really exists in a living cell, with thousands of water molecules surrounding it.