HIV Shell Structure Cracked With Help Of Supercomputer

A new study that features on the cover of Nature this week describes how researchers in the US have for the first time cracked the chemical structure of the capsid or protein shell of the human immunodeficiency virus (HIV). The breakthrough, which likely opens the way to powerful new drugs against the virus that causes AIDS, was made possible with the help of a new "petascale" supercomputer.
Scientists have been trying for some time to crack the precise chemical structure of HIV's cone-shaped capsid, a protein shell that protects the virus's genetic material. The capsid is thought to be the key to virulence of HIV and has become an attractive target for new antiretroviral drug development.

As senior author of this new Nature study, Peijun Zhang, an associate professor of structural biology at the University of Pittsburgh School of Medicine, says in a statement:

"The capsid is critically important for HIV replication, so knowing its structure in detail could lead us to new drugs that can treat or prevent the infection."

"This approach has the potential to be a powerful alternative to our current HIV therapies, which work by targeting certain enzymes, but drug resistance is an enormous challenge due to the virus' high mutation rate."

Previous studies have described attempts to chip away at the capsid structure bit by bit. To try and see the atomic-level detail of the shell, made of over 1,300 identical proteins, researchers have used a range of sophisticated lab tools, from nuclear magnetic resonance spectroscopy and X-ray crystallography, to cryo-electron microscopy and cryo-EM tomography.

But it was only when they added the processing power of the new petascale Blue Waters supercomputer at the National Center for Supercomputing Applications at the University of Illinois, to the already impressive array of tools, that Zhang and colleagues were able to fathom the chemical structure of the entire capsid.

A petascale computer has a number-crunching rate measured in "petaflops", or petas (quadrillions, 10¹⁵) of floating point instructions per second. To put this into context, a petascale computer can perform in one second the same number of instructions as it would take everyone on Earth doing one calculation per second for 1.5 days.

The simulations that added the missing pieces to the HIV capsid puzzle were conducted during testing of Blue Waters by co- authors Klaus Schulten, a physics professor, and Juan R. Perilla, a post-doc researcher, both at the University of Illinois.

Commenting on the HIV capsid challenge, Schulten says:

"This is a big structure, one of the biggest structures ever solved."

"It was very clear that it would require a huge amount of simulation - the largest simulation ever published - involving 64 million atoms," he adds.


From previous studies that had found the HIV capsid contains a number of identical proteins, the researchers already knew these proteins are arranged as pentagons and hexagons, and they had a hunch that the pentagons formed the tight round corners of the cone-shaped capsid they could see under an electron microscope.

But exactly how many of these proteins it takes to make the capsid, or how the pentagons and hexagons fit together, remained a mystery.

Zhang and the structural biology team at Pittsburgh found that when exposed to high concentrations of salt, the protein building blocks assemble into tubes made only of hexagons.

From further experiments they found that certain regions of the proteins interact with one another in a way that is "critical for capsid assembly and stability, and for viral infectivity," they note.

They then managed to get a rough idea of the overall shape of the capsid by taking cryo-electron tomographs of it sliced into sections.

From these results, and their own simulations of how the hexamers and pentamers might interact, Schulten and Perilla carried out a series of large-scale computer simulations.

Schulten says that they could only match the 64-million-atom capsid structure to the "diverse" experimental data using a unique approach they developed themselves that they call "molecular dynamic flexible fitting".

"You basically simulate the physical characteristics and behavior of large biological molecules but you also incorporate the data into the simulation so that the model actually drives itself toward agreement with the data," he explains.

With these techniques the researchers found that the HIV protein shell comprises 216 hexagons and 12 pentagons arranged in the way the experimental data suggested.

The proteins in the hexagons and pentagons were identical but the angles through which they attached to each other were different among different regions of the structure.

Schulten says this is what puzzled them: such a protein would have to be inherently flexible to form such a varied structure.

By having pentagons as well as hexagons, the capsid can form a closed structure, explain the researchers, describing the property the pentagons bring as "induced acute surface curvature". (A quick look at the structure of fullerenes, or even soccer balls for that matter, and you get an idea of what they are talking about).

Schulten says that knowing more about the detailed structure of the HIV capsid will help researchers understand how it functions, and this helps drug developers work out how to disrupt those functions.

He explains how the HIV capsid has to perform two opposing functions. It has to remain intact to protect its genetic material, but it also has to be able to release it in a timely manner once inside the host cell so it can replicate.

"That has to happen with really good timing - too quick is not good, too slow is not good. And this is a moment when you can throw a wrench into the system," says Schulten.

"The timing of the opening of the capsid is essential for the degree of virulence of the virus. This is where we could perhaps best interfere with HIV infection," he adds.

Funds for the study came from the National Institute of General Medical Sciences at the National Institutes of Health and the National Science Foundation, which also funds the Blue Waters supercomputer.

Earlier this year, scientists in the UK developed a vaccine against foot and mouth disease that uses a synthetic virus capsid to provoke an immune response.

To determine the structure of that virus shell, and identify mutations that would improve it, they used Diamond Light Source, the UK's national synchrotron facility.

Scaling Up HIV Treatments Worth The Price, South Africa

According to two studies published in this week's Science journal, ramping up HIV antiretroviral treatments in the South African province of KwaZulu-Natal has been worth the extra expense.
According to the findings of the HTPN 052 (HIV Prevention Trials Network 052) trial, people who are HIV positive have a 96% lower chance of transmitting the virus to their partners if they are receiving ART (antiretroviral) medications.

Jacob Bor, from Harvard University, Massachusetts, USA, and team followed up on this trial. They reported that the life expectancy of the average KwaZulu-Natal adult is now 11.3 years longer since ART was expanded in this rural region of the country - life expectancy rose from 49.2 years in 2003 to 60.5 years in 2011.

Scaling up antiretroviral treatments is expensive

By local standards, these treatments are not cheap. Annual ART costs between $500 and $900 per year for each person. Experts and agencies had disagreed on whether scaling up such treatments could be justified.

The authors gathered and analyzed data on the changes in adult life expectancies of about 100,000 people from 2000 to 2011. They focused on the difference in life expectancy four years before ARTs were scaled up in the region, and eight years afterwards, and "determined that the survival benefits of antiretroviral treatments exceeded the cost of the treatments 26 times over."

The longer adult life expectancy in the region was nearly entirely due to changes in HIV-related deaths, they added.

In a related news release from the Harvard School of Public Health, Bor said:

"Many people have been worried that the ART scale-up, which is a massive public health intervention, would negatively affect populations who do not suffer from HIV but need care for other diseases. We do not find any evidence to support this worry."

In an Abstract in Science, the authors concluded "These gains in adult life expectancy signify the social value of ART and have implications for the investment decisions of individuals, governments, and donors."

One of the limitations in the study, the authors explained, was that access to clean water and electricity occurred at the same time the antiretroviral treatments were being scaled up. Even so, they added, in a worst-case scenario, increasing access to retroviral treatments in southern Africa would save lives and money.

In another study published in the same journal, Frank Tanser and team discovered that the risk of becoming infected with HIV in sub-Saharan Africa is reduced considerably when ARTs are scaled up.

They followed up 16,667 people who were not infected with HIV in KwaZulu-Natal for a period of eight years after ARTs were expanded in 2004. They found that HIV-free people had a 38% lower risk of becoming infected when they lived in areas with high ART coverage, compared to areas where coverage was low.

For years, experts have been saying that if the South African government started ART for HIV-positive residents earlier, the country would save money and many deaths would be prevented.

Early HIV Antiretroviral Therapy is Cost-Effective

Researchers from Weill Cornell Medical College and GHESKIO (Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes) showed in PLoS Medicine that early treatment for HIV is not only a life-saving move, but also a cost-effective one.

Before 2009, WHO (World Health Organization) recommended that antiretroviral therapy for HIV-positive patients should only start when their CD4 T cells went below 200 cells per cubic millimeter. Weill Cornell scientists carried out a randomized clinical trial in Haiti which demonstrated that early ART reduced mortality by 75% in HIV-positive adults with a CD4 cell count between 200 and 350 cells/mm³.

After looking at their findings, WHO changed their recommendation to start ART in HIV-positive patients when their CD4 cell count drops below 350 cells/mm³.

'Exhausted' T Cells Lead To Chronic Viral Infection

When you get an acute infection, such as influenza, the body generally responds with a coordinated response of immune-cell proliferation and attack that rapidly clears the pathogen. Then, their mission done, the immune system stands down, leaving a population of sentinel memory cells to rapidly redeploy the immune system in the event of reinfection.

This is why vaccination works, and it's why, in theory at least, people who have had the chicken pox once will never get it again.

But what about chronic infection? In the case of such pathogens as hepatitis C, HIV, and malaria, the body and the pathogen essentially fight to a prolonged stalemate, neither able to gain an advantage. Over time, however, the cells become "exhausted" and the immune system can collapse, giving the pathogen the edge.

Now, a new study by researchers at the Perelman School of Medicine, University of Pennsylvania, is showing just how that happens. The findings also suggest a novel therapeutical approach that might be used to shift the balance of power in chronic infections. The study appears in Science.

The team, led by E. John Wherry, PhD, associate professor of Microbiology and Director of the Institute for Immunology, used a mouse model of chronic viral infection to map the T-cell response that arises when the immune system is on an extended war footing. They found that two distinct classes of virus-specific CD8+ T cells - one expressing high levels of the protein T-bet, the other expressing high levels of the protein Eomes, work together to keep the infection in check.

Specifically, they found that the two cell populations appear to have a progenitor-mature cell relationship. The T-bet-expressing cells appear to function as the progenitor cells - that is, stem cells. These cells divide both to regenerate and maintain the pool of virus-specific T cells. But they also divide and differentiate to form mature, terminally differentiated Eomes-expressing cells. These cells are more effective at fighting the virus itself, but cannot replicate.

"There's a balance, an equilibrium, which allows you to maintain control over the infection but is insufficient to give you complete clearance," Wherry explains.

These two cell subpopulations tend to confine themselves to different anatomic regions in the infected animals, the researchers found. T-bet-positive cells were found in the blood and spleen, whereas Eomes cells were found in the liver, bone marrow, and gut.

Loss of either subpopulation, which the researchers modeled by deleting one or the other protein, reduces the immune system's ability to fight the infection, leading to a shift in favor of the pathogen.

According to Wherry, these data can help explain the gradual loss of virus-specific T cells observed in such chronic infections as hepatitis C.

"Our data suggest the reason for loss of immune control during some chronic infections is that the long-term pressure on this progenitor-mature cell relationship depletes the progenitor pool," he says.

What's more, the study suggests new therapeutic avenues that can be used to fight, or at least better control, chronic infections. For instance, he says, "If we can maintain these progenitor cells longer, or coax the terminal progeny to divide further, we may be able to shift the balance and maintain control of the infection," he says.

Wherry's lab is now studying candidate molecular pathways to determine their efficacy in controlling, and perhaps modulating, these two T-cell populations.