From bacteria to elephants, from flowers to humans, all living things follow instructions written in the universal language of DNA. All living things contain similar building blocks—proteins encoded by DNA. And all diseases can be traced back to malfunctioning genes or proteins.

To speed up the search for better treatments, some scientists are now moving on from genomics, the study of all the genes in an organism's cells, to the next step—proteomics, the study of all the proteins specified by these genes and how the proteins interact.

Proteins are the body's beams and rafters, movers and engineers, as well as message givers and infection fighters. But proteins don't act alone—they bind to other proteins, affecting them. So when a mutant gene produces a defective protein, it can mess up whole chains of interactions with other proteins, causing disease.

The cure, then, might be to interrupt—or compensate for—some of the faulty interactions. But first these need to be precisely identified. This is where model organisms such as yeast and flies are proving particularly useful.

A decade ago, Stanley Fields, an HHMI investigator at the University of Washington, Seattle, devised an ingenious way to identify pairs of proteins that physically interact with one another. Now he and his collaborators are using this "two-hybrid" system to explore the protein interactions in yeast. The scientists recently identified 957 interactions involving 1,004 yeast proteins. Similar interactions are very likely to exist between the corresponding proteins in humans.

Meanwhile Stuart Schreiber and his colleagues at Harvard University have adapted Patrick Brown's microarrays technique—originally devised for DNA—for use with proteins, enabling them to study more than 10,000 proteins simultaneously. In this way, they detected large numbers of previously unknown protein interactions. They also screened hundreds of small molecules to see which ones would interact with the proteins in the microarrays.

Both of these approaches are providing new leads for a wide array of potential new drugs, as well as laying the groundwork for a far more precise medical science.

— Maya Pines

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A detail of the map showing a small fraction of the tangled network of yeast protein interactions. The entire map is viewable as an Adobe Acrobat PDF file.

Image: Nature Biotechnology, Vol. 18, December 2000

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