Breakthrough simulations focus on the HIV-1 virus

When is a container not just a container?

For the HIV-1 virus, a double layer of fatty molecules called lipids not only serves as a container, but also plays a key role in the replication and infectivity of the virus. Scientists have used supercomputers to complete the first-ever biologically authentic computer model of the HIV-1 virus liposome, its complete spherical lipid bilayer.

Furthermore, this study comes directly from a new atomistic model of the HIV-1 capsid that contains its genetic material. The scientists hope this basic research on viral envelopes can support efforts to develop new HIV-1 therapeutics and provide a basis for studying other enveloped viruses such as the novel coronavirus SARS-CoV-2.

“This work represents a full-scale study of the HIV-1 liposome with an unprecedented level of chemical complexity,” said Alex Bryer, a Ph.D. Student in the Perilla Laboratory, Department of Chemistry and Biochemistry, University of Delaware. Bryer is the lead author of the liposome modeling research published in the journal in January 2022 PLOS Computational Biology.

The science team developed a complex chemical model of the HIV-1 liposome that revealed key features of the liposome’s asymmetry. Most of these models assume a geometrically uniform structure and do not capture the asymmetry inherent in such biological containers.

lipid flip-flop

Bryer and his co-authors studied a mechanism colloquially known as “lipid flip-flop,” in which lipids in one of the leaflets of the bilayer are moved or transported to the other leaflet. The leaflets flip the lipids and exchange the molecules for various purposes, such as achieving dynamic equilibrium.

“For the spherical vesicle model of the liposome, our simulations show that even in the absence of embedded proteins, asymmetry occurs spontaneously and the vesicle can flip over to maintain an asymmetric composition within tight tolerances—even over biological timescales greater than five microseconds,” Bryer said.

Interestingly, the science team did not observe any occurrence of flip-flops in a flat-membrane system, suggesting that shell curvature is closely related to this biological process.

“Something like this has never been simulated before.” said study co-author Juan R. Perilla, assistant professor in the Department of Chemistry and Biochemistry, University of Delaware.

“What surprised us is this dynamic equilibrium that the vesicle shows,” added Perilla. “Lipids move in and out, but the overall composition doesn’t change — that was surprising.”

key asymmetryThis key finding demonstrates that the complex, asymmetric membrane composition of the HIV-1 virus can result in macroscopic features such as differential interleaflet shifting and the formation of lipid microdomains.

This formation could affect how membrane proteins, often located within specific lipid microdomains, interact with the membrane and perform functions such as binding to host cells and allowing virus entry into them.

Microdomains are known to form for HIV-1 and serve as targets for the localization of membrane proteins. One protein in particular, gp41, is critical for membrane fusion, where HIV-1 attaches to and eventually infects the host cell membrane.

“It is believed that gp41 is locating these domains,” Bryer said. “What we showed was that these microdomains can form in the vesicle without the help of proteins. They seem to arise spontaneously.”

This finding could also explain the preferential budding behavior in HIV-1 virus replication without the need for embedded proteins to mediate the formation of the microdomains that enable budding.

supercomputer simulations

The computer model developed by Bryer and colleagues has a diameter of 150 nm and consists of 24 different chemical components. There are more than 300,000 lipid molecules in total, dissolved in water and ionized with sodium chloride to represent a biological environment. The science team used a coarse-grained model called MARTINI, which allowed them to reduce the degrees of freedom in the molecular system and achieve simulation sampling over microsecond timescales.

The scientists were awarded supercomputer assignments and training by XSEDE, funded by the National Science Foundation. Through XSEDE, they used the Stampede2 system at the Texas Advanced Computing Center (TACC) and Bridges-2 at the Pittsburgh Supercomputing Center (PSC). Also, they used Grizzly at Los Alamos National Laboratory; Blue Waters at the National Center for Supercomputing Applications; and the Frontera system at TACC.

“Our study would not have been possible without XSEDE resources,” said Bryer. “With Stampede2 Skylake nodes, we can achieve some very high sampling efficiencies, both to run the simulations and to perform analysis.”

“I could do calculations and without having to transfer data, I could set up a visualization session through the TACC portal and analyze and work with my data directly on Stampede2. That’s amazing,” added Bryer. He noted that “in terms of productivity, not having to transfer terabytes of data to a separate visualization computer node was just tremendous.” “We also used quite a bit of the high-memory nodes on PSC’s Bridges-2,” said Perilla. They supported simulations that compared the control, a flat HIV-1 virus membrane, to the curved one in dynamic equilibrium.

In addition, the Perilla Lab has delegated the simulation work to its local cluster, the University of Delaware’s XSEDE-associated DARWIN system.

“It is important to highlight the fact that XSEDE is not only providing resources that are extremely valuable. There are training courses and other opportunities like workshops,” said Perilla.

“When I joined the group, I had never logged on to a supercomputer,” Bryer said. He recalled valuable training in XSEDE workshops on OpenMP, MPI and OpenACC, which support scientists in parallelizing their computer code.

Frontera work

Bryer also highlighted the analytical work done on TACC’s Frontera, the world’s fastest academic supercomputer. “Parallel I/O through Luster enabled many of the analyzes in the manuscript,” said Bryer. “On Frontera we were able to quickly classify the volume around the vesicle and process our data in minutes. We estimated that if we ran the analysis in a serial naïve implementation, it could take about three weeks.”

The Perilla Lab has focused all that computing power and expertise on learning more about the mysteries of what happens to the HIV-1 viral envelope during infection.

“Although this study does not provide the whole answer, it is about what the lipids are doing and what integral membrane proteins are doing or could do; and not just how proteins like gp41 interact with human receptors, but also how they transmit their signals and how that relates to lipid composition,” Perilla said.

“This computational study offers an opportunity for drug development research,” added Perilla.

Since lipid symmetry is maintained by the curvature of the shell, a promising yet unexplored possibility is the design of small molecules that affect symmetry and potentially yield a therapeutic target.

HIV-1 capsid

Immediately prior to liposome research, Perilla and colleagues also broke new ground using supercomputers to build the first-ever atomistic model of the HIV-1 capsid, the envelope for its genetic material, in the presence of the metabolite IP6. The work was published in the journal in November 2021 scientific advances. It also used the Bridges-2 and Stampede2 supercomputers allocated through XSEDE.

The simulations, validated by cryo-electron tomography data, showed that IP6 was able to bind to the capsid at two sites instead of just one as previously thought. This finding is important because during infection the capsid is exposed to the cytoplasm and must pass through the nuclear import mechanism, namely the nuclear pore complex. All of these pieces together indicate that the capsid can ‘sense’ the concentration of IP6 in a way previously unknown.

Perilla said: “Computationally, these are very unique simulations because of the number of degrees of freedom involved. No one has ever walked this path before. We walk through the dark. And we make tools that can help us see beyond our limitations.”