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Making sense of the disorder inside viruses.

Using data that most crystallographers throw away, biophysicists have for the first time taken a close look at the interior organization of a tumor virus.

That look reveals an inner structure resembling the seed casing of a horse chestnut: rounded, with prongs sticking out in all directions. These prongs form a bridge between the virus' genetic material and its enveloping protein coat, says Donald L.D. Caspar of Brandeis University in Waltham, Mass. In the Feb. 13 NATURE, he and his colleagues describe their findings, which provide new clues about how disordered structures link up with ordered ones.

The Brandeis group studied the polyomavirus, a mouse virus related to viruses associated with warts and cervical cancer. Just a few months ago, Harvard scientists developed an atomic-scale picture showing how multiple copies of a protein can bundle into five-sided units to make the outside coats of viruses in this family (SN: 12/7/91, p.372).

Like the Harvard team, the Brandeis group used X-ray diffraction data to determine the structure of a virus. X-ray diffraction provides information about the location of electrons -- and, consequently, atoms -- in a crystal. But that information results from averaging the locations of electrons in millions of molecules or, in this case, virus particles. Thus, the technique yields atomic-scale resolution only when the structures are highly ordered; otherwise, the locations cannot be pinpointed and the data have low resolution. "Everybody in protein crystallography usually throws away the low-resolution data," says Lee Makowski, a biophysicist at Boston University.

The viruses' interiors lack a high degree of order, but the Brandeis group decided that the information from low-resolution data could be useful. By focusing on these fuzzy results, they could see how the proteins and genetic material were arranged, even though they could not tell exactly where the atoms were. Still, getting a sense of the inside of the virus proved tricky.

Using computers to help with their analysis, the researchers took lots of measurements of the empty coat and then subtracted those data from measurements of whole viruses. "By looking at the differences, we were able to get a map of the inside," Caspar explains.

"This remarkable use of low-resolution data is providing a basis for understanding the structural interface between the ordered and disordered structures," comments Makowski. "It's going to help build our philosophical underpinnings about biological structure."

The results indicate that 72 copies of a virus protein and a look-alike protein that is one-third shorter act as prongs. One end of each prong fits into one of the 72 holes formed by the building of the coat protein into sets of five-sided units, says Caspar. The other end extends into the genetic material of the virus, but in a less well-defined manner.

The genetic material consists of 26 nucleosomes -- the basic units of chromosomes -- each with DNA folded tightly around eight histone molecules. Four nucleosomes crowd together and are surrounded by the other 22, making a compactly folded, circular minichromosome, says Caspar.

The exterior protein bundles do not need any guidance -- or even any genetic material inside -- to assemble into a coat, but the prongs may serve to direct the coat to assemble around the right piece of DNA, says Caspar.

While the Brandeis study sheds light on this particular virus, "the subtraction method for looking at disordered structures is a general one," says Caspar. Researchers could, as the Brandeis group did, subtract the ordered structural data from data about the whole material, or they could create a computer model of the structure, subtract the model from the experimental data and then focus on what is left over.
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Author:Pennisi, Elizabeth
Publication:Science News
Date:Feb 22, 1992
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