Top7: From computer-aided design, a new protein

One of the biggest news stories at the close of 2003 touched on the biggest mystery facing biochemistry today. Bovine spongiform encephalopathy (BSE), or mad cow disease, is one of many incurable diseases caused by malformed proteins in the body. The discovery of a BSE-infected dairy cow in Washington state just before Christmas caused widespread concern in the United States, and with good reason: humans can contract a version of the disease by consuming infected meat, and nine out of 10 Americans eat beef. How protein molecules form into useful shapes and what causes proteins to go wrong - as with BSE - is unknown. It's a puzzle called the protein-folding problem, and it's key to developing treatments for diseases as diverse as Alzheimer's, Parkinson's, cataracts, cystic fibrosis, and diabetes' most common form. One month before this latest BSE incident, scientists took one small but intriguing step toward solving the protein-folding problem by synthesizing a protein called Top7. Yet the news barely registered with the mainstream media-perhaps because this new protein, while showing that scientists might be on the right track to a solution, defies easy description. One way to better decipher the hows and whys of folding is to try to imitate nature by designing a protein. The task is well suited for parallel-processor computing. In fact, D. Baker, head of the Howard Hughes Medical Institute laboratory that created Top7, calls his software methodology "embarrassingly parallel.".