Imaging of HIV protein may lead to new treatments against the virus, Salk scientists say

Dario Passos (left) and Dmitry Lyumkis are co-authors of a study on how HIV replicates within cells.
(Courtesy of Salk Institute)

Understanding how HIV replicates within cells is key for developing new therapies that could help nearly 40 million people around the world who are living with HIV, the immune system virus that causes AIDS.

Now, a team of scientists from the Salk Institute for Biological Studies in La Jolla and Rutgers University in New Jersey have for the first time determined the molecular structure of HIV Pol, a protein that plays a key role in the late stages of HIV replication, or the process through which the virus propagates itself and spreads through the body.

Determining the molecule’s structure helps answer long-standing questions about how the protein breaks itself apart to advance the replication process. The discovery, published July 6 in Science Advances, reveals a new vulnerability in the virus that could be targeted with drugs.

“Structure informs function, and the insights we gained from visualizing the molecular architecture of Pol give us a new understanding of the mechanism by which HIV replicates,” said study co-senior author Dmitry Lyumkis, an assistant professor in the Laboratory of Genetics and the Hearst Foundation Developmental Chair at Salk.

Scientists previously knew that HIV Pol, a polyprotein, breaks into three enzymes — protease, reverse transcriptase and integrase — that work together to assemble the mature form of the virus.

“It was known, but not understood, that there is a coupling between these enzymes before HIV Pol breaks apart. Visualizing the HIV Pol structure explains the basis for this complex mechanism,” said co-senior author Eddy Arnold of the Center for Advanced Biotechnology and Medicine at Rutgers.

“The first challenge was producing a stable version of HIV Pol so the structure could be analyzed, which had never previously been reported,” said co-author Jerry Joe Harrison, a senior lecturer at the University of Ghana.

“This was a key missing piece of the HIV structural puzzle,” Arnold said.

The team used cryogenic electron microscopy, an imaging technique to which Lyumkis has made important contributions, to reveal the three-dimensional structure of the HIV Pol protein molecule. This led to the discovery that Pol is a dimer, meaning it’s formed by two proteins bound together. The finding was a surprise because other similar viral proteins are single-protein assemblies.

The group showed that in this two-sided structure, the protease enzyme is “loosely tethered” to the reverse transcriptase enzyme in a binding configuration that keeps the protease slightly flexible.

“It’s holding the protease at arm’s length, loosely, and we believe that gives the protease a little bit of movement, which in turn allows it to initiate the cutting of polyproteins that is a prerequisite for viral maturation,” said co-author Dario Passos, a former researcher in Lyumkis’ lab at Salk.

“Current HIV treatments include multiple classes of inhibitors for all three enzymes, and the discovery also reveals a new vulnerability that could be targeted with drugs,” Passos said.

The authors say the discovery opens the door for important follow-up research, including studies of the structure of the larger and more complex polyprotein Gag-Pol, which also is involved in viral assembly, as well as taking a closer look at the role of the integrase enzyme in assembling the mature form of HIV during replication. ◆