Case Western Reserve University Chemist Mary Barkley wants to find out what makes two pieces of a protein in the AIDS virus begin the biochemical processes that lead to AIDS.
A four-year, $ 1.029 million grant from the National Institutes of Health will support Barkley's work in a new area of AIDS research that examines the chemical processes between the two pieces of reverse transcriptase (RT) protein that mobilizes the HIV-1 virus into action.
For the more than 40 million humans suffering worldwide from AIDS, researchers like Barkley, the M. Roger Clapp University Professor in Case's College of Arts and Sciences, offer hope in finding new therapies for their disease by understanding the basic science of how the AIDS virus HIV-1 functions.
But Barkley is finding that the protein in this virus is not acting like other proteins she encounters in her lab. The flexibility of the AIDS virus that robs humans of their immune defenses has stumped her time and again.
A pilot study in 2003-04 from the American Foundation for AIDS Research provided the groundwork that led to her recent award from the NIH's National Institute of General Medical Sciences.
Barkley's lab is taking a new approach to studying the enzyme RT that copies the viral RNA into the virus' DNA that is then inserted into the human host cell's chromosomal DNA by another HIV-1 enzyme called integrase.
Thousands of journal papers over the past decades have mostly examined the catalytic activity of the HIV-1's RT enzyme and its end products.
Barkley said researchers assumed the RT was like a rock where the two pieces or subunits of the RT protein clung together in order for it to be able to copy the RNA into DNA.
Some of the current drugs called nonnucleoside RT inhibitors used by doctors to treat HIV-1 target the enhancement or lessening of the two subunits of proteins coming together.
While it has been known for years that the subunits can come apart, mostly everyone has ignored this fact in research, said Barkley.
She sees the potential of interfering with how the subunits come together as one way of thwarting the spread of the virus.
"We know that the subunits have to be together to catalyze DNA synthesis, and that the second generation RT inhibitors can alter how tightly the two subunits stick together," Barkley explains. "We think the way that the subunits come together play a role in the protein's—and thus the patient's—resistance to drugs and in how the drugs inhibit the DNA synthesis."
"No one has looked at how these pieces come together and how it is related to the catalysis other than they knew it had to happen for the virus to grow. This is where we started working," she said.
Barkley began work on the HIV-1's reverse transcriptase enzyme in 1998 through collaboration with Stuart Le Grice, the former director of the Center for AIDS Research at the Case School of Medicine.
She said researchers have crystallized the RT and then looked its 3-dimensional structure using x-ray diffraction, but according to Barkley, the structure does not tell how it works.
She will collaborate with Patrick Wintrode in the Case School of Medicine's department of physiology and biophysics, who uses a new technique that tracks the fast exchanges of protons for deuterons on the protein's surface. This technique will provide another view of how the protein functions and as well as answers to what happens when the two subunits are apart and then come together.
"It has been difficult," said Barkley. "Everything we have done with this protein is that you try it and think it is going to be a straightforward method that is used on many other proteins and will work on this one, but it doesn't work as expected."
This new approach may be the answer to understanding the protein, she said.
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