Magazine article Science News

Twirling Ribbons, Billowing Bubbles: Computer Visualization Brings Complex Aspects of Life into View

Magazine article Science News

Twirling Ribbons, Billowing Bubbles: Computer Visualization Brings Complex Aspects of Life into View

Article excerpt

It's no big deal to sketch a water molecule, with its two hydrogen atoms linked to an oxygen, or to picture how those atoms interact with another substance. But when molecules contain hundreds or thousands of atoms, even a brilliant chemist has trouble keeping them all straight, never mind tracking how each atom moves or changes when confronted with other molecules.

Nor does the challenge end with molecules. Researchers, teachers, and physicians want to compile the massive amounts of data acquired through various imaging and analytical technologies in order to make and manipulate clear pictures of cells, organs, even entire organisms.

That's where computers, particularly computer graphics, come in. By incorporating computational and visualization techniques into their experimental repertoire, researchers can make sense of ever more complex data and substances. X-ray crystallographers, for example, have demonstrated that amino acids, the building blocks of proteins, form chains that twist into incredibly convoluted configurations, or motifs. Sometimes these structures are shaped by other, helper molecules. "But from my point of view, that's just the beginning," says Arthur J. Olson of the Scripps Research Institute in La Jolla, Calif.

Like other computational chemists and molecular biologists, Olson has built on those data and, with certain mathematical procedures, has reenacted molecular minglings. "That's really the crucial aspect of biology," adds Michael Colvin of Sandia National Laboratories in Livermore, Calif.

As part of these efforts, researchers have become artists, sketching with a keyboard instead of pastels. Each new line of computer code, each faster chip has brought a little more of the world beyond our vision into view. Sometimes, the scientists ask the computer simply to compile all the data into a comprehensible picture, one based totally, or as much as possible, on existing physical and chemical laws. Other times, researchers tap the computer program's intuition to filter out unimportant data and fill in missing details. "[Visualization] lets you see things that you might not have been able to see before," says Helen M. Berman, an X-ray crystallographer at Rutgers University in New Brunswick, N.J.

Berman remembers the early days of computer graphics, when images came only in black, white, and shades of gray. "I thought, What do we need color for? It's just a luxury," she recalls. Now, she realizes how much better colors are at capturing the personalities of molecules. The bright blues, yellows, and purples help experts as well as novices make sense of what sometimes seems little more than a tangled mess of squiggles or -- in the case of ultrasound data -- a fuzzy image.

Already, an explosion in visualization techniques has revolutionized the depiction and analysis of molecules. But computer graphics experts and their scientist-collaborators have not stopped there. They are also portraying, in ever clearer detail, cell membranes and the development of chick embryos. They are even attempting to make picture-perfect ultrasound images of the human fetus (see sidebar).

Recently, Berman and her colleagues captured on screen the structure of collagen, the one major protein motif left for X-ray crystallographers to decipher. Collagen is a protein in bone and connective tissue that forms from three parallel chains of amino acids that twist counterclockwise into spirals. Those spirals extend down a common axis, they report in the Oct. 7 SCIENCE. The spirals hold together because of a repetitive sequence: Every third amino acid is glycine, which allows the strands to lie close together. Should another amino acid replace the glycine, the collagen might become flexible or unstable and cause disease, Berman says.

Interestingly, a single switch between a glycine and an alanine made crystallization, the first step in this kind of analysis, possible, Berman notes. …

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