The human immunodeficiency virus (HIV) is a formidable pathogen. It mutates rapidly; in fact, it has been estimated that at a given point in time, the genetic diversity of HIV in a single person is equivalent to the global diversity of influenza viruses in a year. In addition, HIV produces structures that protect itself from being recognized and attacked by antibodies and drugs. All of these factors contribute to making HIV a dangerous, difficult-to-treat virus.
The more scientists learn about the biological process of how HIV infects host cells, the better treatments can be designed to penetrate the virus' defenses and destroy it. Now, in a new study, researchers from the California Institute of Technology have imaged the structure of an elusive HIV protein at the atomic scale. The findings were published online Nov. 22, 2023, in the journal Nature under the title "Intermediate conformations of CD4-bound HIV-1 Env heterotrimers.
The new study was conducted in the lab of Dr. Pamela Björkman, professor of biology and bioengineering at Caltech. The first authors of the paper are Caltech postdoctoral scholars Kim-Marie Dam and Chengcheng Fan.
HIV primarily attacks immune cells called T cells, disabling them so they cannot protect other cells in the body from infection. When HIV is ready to enter a T cell, it undergoes a number of shape-shifting changes. These changes occur in what is called the envelope protein of this virus - that is, the protein on the surface of this virus that allows HIV to enter the host cell. Because the envelope proteins are so important to the virus' infection process, they are good targets for drug or vaccine development.
The HIV envelope protein is a "trimer", similar to a tripod-shaped flower: it has three "stem" sections, each called gp41, and three "petal "To initiate infection, each of the three gp120 proteins grabs a receptor called CD4 on the surface of the T cell. Once the three CD4 receptors have been seized by the three gp120 proteins, they expose sites that are recognized by host co-receptors, and a needle-like structure appears on the stem of the envelope protein, allowing the virus to infect and enter human cells.
But what if the gp120 "petals" of the HIV envelope protein could only grab one or two CD4 receptors? Would the envelope still be fully open to allow the virus to infect the cell? Understanding this process could have a major impact on drug design. If one or two CD4 receptors could be prevented from being seized by gp120, would that be enough to stop the infection? To answer this unanswered question, these authors attempted to image HIV envelope proteins in the presence of only one or two CD4 receptors bound by gp120.
Dam says, "Structurally characterizing the conformation of HIV envelope proteins located in the intermediate state is valuable for a fundamental understanding of how HIV proteins work."
But imaging these structures is a challenge: for biochemical reasons, it's not easy to create "heterotrimers," or envelope proteins that bind to only one or two CD4 receptors, in the test tube. Through an innovative engineering approach, these authors devised a scheme to construct stable heterotrimers. They then utilized Fan's expertise in cryo-electron microscopy, a delicate experimental process, to take structural images of heterotrimers of fragile HIV envelope proteins bound to CD4 receptors.
These structures show that if only one or two CD4 receptors are bound by the HIV envelope protein, the envelope protein is unable to fully open and undergo the shape-changing process associated with infection.Dam says, "One of the main questions raised by this new study is: can envelope proteins that cannot fully open still promote infection?"
Image from Nature, 2023, doi:10.1038/s41586-023-06639-8.
Björkman's team then shared the results with the Walther Mothes lab at Yale University, which was conducting similar attempts to image heterotrimers. The sharing of information between the two labs showed that the free-floating behavior of the engineered heterotrimer in a test tube was remarkably similar to the behavior of the envelope proteins on the surface of the HIV virus in a more "realistic" infection scenario.
This is an important finding because soluble heterotrimers of HIV envelope proteins are being used as the basis for developing new therapeutics, and it is critical to understand whether they accurately mimic natural processes.
Structural biology studies such as these are important not only for the study of HIV, but also for the study of many different kinds of viruses," says Dam, "We've learned a lot from HIV. When the COVID-19 pandemic started, we applied what we learned from HIV to SARS-CoV-2."
Björkman says, "These previously unknown structures of HIV envelope protein conformations in an intermediate state provide fascinating new insights into the structural changes driven by receptor interactions prior to fusion of host and viral membranes. Our study not only opens new avenues for exploring the complexity of HIV infection, but also provides valuable insights not limited to therapeutic design and enhances our overall understanding of the changing dynamics of HIV."
