the music of proteomics
by Angela Spivey

If proteins be the notes of life, play on.

our genes, fixed at birth, could be called your body's musical score. The DNA code instructs the body to make various proteins. But deep inside your cells, those proteins are carrying out your body's functions — making its music. "Proteins are the molecular machines that actually do the job," says Alex Tropsha, associate professor of pharmacy. Proteins fold into various structures, act upon each other, change in response to other parts of the cell. Proteins are so numerous and so busy that figuring out an organism's proteome — the properties and activities of each of its proteins — promises to be thousands of times more complicated than figuring out its genome.

Proteomics, as this new field is called, emerged only in the last five years, after scientists sequenced the genomes of humans, fruit flies, yeast, and other creatures. Proteomics wouldn't be possible without those genome definitions. An essential technique of proteomics — mass spectrometry — basically helps identify proteins by smashing them up and looking at their pieces. It separates proteins into charged particles, then "weighs" those particles. The weight, or mass, of each particle yields a "fingerprint" that a computer can match to a database of amino acids, which are the building blocks of proteins. The amino acid information can be matched to all known gene sequences to identify the protein. "You couldn't do proteomics without the genome sequences," says Bill Marzluff, professor of biochemistry. "That's why proteomics has become important recently."

The more familiar field of genomics and its burgeoning offshoot, proteomics, are helping scientists learn about how cells carry on the business of our bodies. But the more these two fields tell us, the more questions we have. Probably less than 50 percent of the time do genomics and proteomics agree, says Lee Graves, associate professor of pharmacology. For instance, some studies show that while levels of mRNA (an intermediate stage between DNA and protein) increase, the amount of protein produced actually decreases. So just because a gene codes for a protein doesn't necessarily mean that the protein gets made. Scientists hope that as the field of proteomics grows, it will provide more answers. "Proteomics allows us to skip over the complexity of gene regulation and look directly at changes in the proteins," Graves says. "This is one of the reasons why proteomics is now so popular."

arolina is getting into the proteomics field while it's new, thanks to an anonymous $25 million donation in honor of the late Chancellor Michael Hooker. The gift funded a new proteomics facility and equipment. "It has allowed all of us here to do experiments and accomplish things we couldn't have done before," Marzluff says. "Proteomics means a new tool to try to solve problems that people have been working on for twenty years in some cases."

For example, Richard Boucher, director of Carolina's Cystic Fibrosis Center, is applying proteomics to understand the protein that is known to be defective in Cystic Fibrosis (see Mapping Disease). And Jackson Stutts, associate professor of medicine, is leading a team that received a $1.79 million grant from the Cystic Fibrosis Foundation to apply proteomics to understanding the disease. Carolina departments involved in proteomics research include nearly all the departments in the medical and health sciences as well as chemistry and biology.

Proteomics promises to yield great insight into the workings of our bodies, but that insight won't come easy. Because proteins don't work alone, analyzing them will require digesting an amazing overload of information. Small modifications that happen to proteins can mean big changes in function. The addition of chemical groups such as phosphates or methyl groups, for instance, can be required for a protein to function, or they can make another protein stop working. Proteins can also modify each other. The possible combinations and outcomes boggle the mind.

Analyzing, storing, and retrieving these vast amounts of information will take some high-tech tools. At Carolina, Christoph Borchers, faculty director of Carolina's Proteomics Core Facility, is the keeper of those tools. Scientists perfecting proteomics technology are working toward achieving "high throughput" — analyzing as many proteins as fast as possible. Each week Borchers is getting new modifications for the facility; by the time you're reading this article, the equipment will be able to analyze 9,600 samples at once. Carolina is one of five U.S. "validation sites" that are testing some of the newest equipment before it's made available commercially.

.: The needle and outer workings of an electrospray mass spectrometer. Proteins or peptides are dissolved and placed into the fine needle, then the machine applies high voltage to the tip. Highly charged droplets enter the mass spectrometer through a small hole that is under high vacuum. Photo by Jason Smith; click to enlarge. :.

ut proteomics technology in general still has some growing to do. Compare the rate of proteomics analysis — 9,600 samples at once — to the fastest genomics analysis — 20,000 samples. Proteins present so many more complications than genes that the technology has yet to catch up.

Some researchers believe that combining genomics and proteomics will yield the best results. Scientists at UNC's Center for Genomic Sciences are beginning to collaborate with scientists using proteomics tools such as crystallography and protein modeling to help guide their work, says Terry Magnuson, director of the center. The classic way of learning about genes' functions is to make a sequence variation — commonly called a mutation — in a particular gene and then observe the effect on say, a mouse or a fly. Magnuson says, "We'd like to get to the point where if we make a mutation in a gene, we can ask the question ahead of time, 'what do we think that mutation is going to do to that protein structure, and do we even want to make a mouse out of it?'"

Tropsha and John Sondek, assistant professor of pharmacology, help Magnuson answer that question using two different approaches to studying protein structure. The way that proteins fold in on themselves, the shapes and patterns they make, often determines protein function, and learning more about how folding happens can help scientists find proteins that would make good targets for drugs. Tropsha uses computer modeling to predict protein structure. Sondek takes the experimental route, using crystallography to actually examine and see a protein's structure.

Charles Perou, assistant professor of genetics, is also beginning to combine genetics with proteomics. In studying breast cancer tumors, Perou uses microscopy and mRNA to create images known as microarrays, which show 20,000 fluorescent spots representing the expression of as many as 19,000 genes. Perou uses the microarrays to help him classify tumors into various groups. "We had twenty patients with tumors that were all lumped into one group, and the microarray information has helped us divide those tumors into five different groups," he says. Perou knows, for example, that one group of tumors is resistant to treatment and presents a poor prognosis, while another group responds well to treatment.

Now Perou is beginning to work with Borchers to get similar information about proteins involved in these tumors to help define the groups even further, with the hope of developing specific treatments for each group. Marzluff says, "There aren't too many places that can say they can do both microarrays and proteomics real well right now."

Another area that may benefit from proteomics: mouse genetics. Marzluff says, "With all the mouse genetics we have here, as the mouse proteome becomes available for analysis we would be in a real position to become even more of a leader in mouse biology." And if Carolina stays in the lead of the high-throughput race, he adds, "I think we could easily become one of the leading proteomics centers in the country."

Angela Spivey is the associate editor of Endeavors magazine.
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