For the HIV-1 virus, a double layer of fatty molecules referred to as lipids not solely serves as its container, but additionally performs a key position within the virus’s replication and infectivity. Scientists have used supercomputers to finish the first-ever biologically genuine pc mannequin of the HIV-1 virus liposome, its full spherical lipid bilayer.
What’s extra, this research comes contemporary off the heels of a brand new atomistic mannequin of the HIV-1 capsid, which incorporates its genetic materials. The scientists are hopeful this fundamental analysis into viral envelopes can assist efforts to develop new HIV-1 therapeutics, in addition to laying a basis for research of different enveloped viruses such because the novel coronavirus, SARS-CoV-2.
“This work represents an investigation of the HIV-1 liposome at full-scale, and with an unprecedented stage of chemical complexity,” mentioned Alex Bryer, a PhD scholar within the Perilla Laboratory, Division of Chemistry and Biochemistry, College of Delaware. Bryer is the lead writer of the liposome-modeling analysis, revealed January 2022 within the journal PLOS Computational Biology.
The science group developed a posh chemical mannequin of the HIV-1 liposome that exposed key traits of the liposome’s asymmetry. Most such fashions assume a geometrically uniform construction and do not seize the asymmetry inherent in such organic containers.
Bryer and his co-authors investigated a mechanism that is recognized colloquially as “lipid flip-flop,” which is when lipids in one of many leaflets of the bilayer are moved or transported to the opposite leaflet. The leaflets flip-flop the lipids and change the molecules for varied functions akin to attaining a dynamic equilibrium.
“For the spherical vesicle mannequin of the liposome, our simulations present that asymmetry happens spontaneously even with out embedded proteins, and the vesicle can flip-flop to take care of an uneven composition inside tight tolerances — even over organic timescales in extra of 5 microseconds,” Bryer mentioned.
Curiously, the science group didn’t observe incidence of flip-flop in a flat membrane system, which means that curvature of the envelope is intimately associated to this organic course of.
“Nothing like this has ever been simulated earlier than.” mentioned research co-author Juan R. Perilla, an assistant professor within the Division of Chemistry and Biochemistry, College of Delaware.
“What was stunning for us is that this dynamic equilibrium that the vesicle exhibits,” Perilla added. “Lipids are shifting out and in, however the total composition shouldn’t be altering — that was stunning.”
This key discovering exhibits that the complicated, uneven membrane composition of the HIV-1 virus can result in macroscopic properties such because the differential displacement between leaflets and lipid microdomain formation.
That formation may need implications in how membrane proteins, which frequently localize inside particular lipid microdomains, work together with the membrane and perform features akin to binding to host cells and permitting the virus to enter them.
For HIV-1, it is recognized that microdomains kind and act as a goal for the localization of membrane proteins. One protein specifically, gp41, is vital for membrane fusion, which is the method of HIV-1 becoming a member of with the host cell membrane and finally infecting it.
“It is thought that gp41 localizes to those domains,” Bryer mentioned. “What we confirmed was that these microdomains can kind within the vesicle with out assistance from proteins. They appear to emerge spontaneously.”
This discovering may additionally clarify the preferential budding habits in HIV-1 viral replication, with out the necessity of embedded proteins in mediating the formation of the microdomains that allow budding.
The pc mannequin Bryer and colleagues developed is 150 nm in diameter and consists of 24 completely different chemical constituents. There are greater than 300,000 complete lipid molecules, solvated in water and ionized with sodium chloride, to signify a organic atmosphere. The science group employed a coarse-grained mannequin often known as MARTINI, which allowed them to cut back the levels of freedom within the molecular system and obtain simulation sampling over microsecond timescales.
The scientists have been awarded supercomputer allocations and coaching by XSEDE funded by the Nationwide Science Basis. Via XSEDE, they used the Stampede2 system on the Texas Superior Computing Middle (TACC) and Bridges-2 on the Pittsburgh Supercomputing Middle (PSC). Moreover, they used Grizzly on the Los Alamos Nationwide Laboratory; Blue Waters on the Nationwide Middle for Supercomputing Functions; and the Frontera system at TACC.
“Our research would not have been potential with out XSEDE assets,” Bryer mentioned. “We are able to obtain some very excessive sampling efficiencies utilizing Stampede2 Skylake nodes, each to run the simulations and carry out analyses.”
“I used to be in a position to carry out calculations, and without having to switch knowledge, I may arrange a visualization session by the TACC portal and analyze and work with my knowledge instantly on Stampede2. That is wonderful,” added Bryer. He discovered that not having to switch terabytes of information right into a separate visualization pc node was “simply enormous by way of productiveness.” “We additionally used fairly a little bit of the excessive reminiscence nodes on Bridges-2 of PSC,” Perilla mentioned. They helped energy simulations that in contrast the management, a flat HIV-1 viral membrane, to the curved one in dynamic equilibrium.
What’s extra, the Perilla Lab has transferred the simulation work to their native cluster, the XSEDE-allocated DARWIN system of the College of Delaware.
“It is essential to spotlight the truth that XSEDE doesn’t simply present assets, that are extraordinarily helpful. There’s coaching and different alternatives akin to workshops,” Perilla mentioned.
“After I joined the group, I had by no means logged right into a supercomputer,” Bryer mentioned. He recalled helpful coaching in XSEDE workshops on OpenMP, MPI, and OpenACC, which help scientists in parallelizing their pc code.
Bryer additionally highlighted the evaluation work run on TACC’s Frontera, the quickest tutorial supercomputer on the planet. “Parallel I/O through Luster is what made loads of the analyses potential within the manuscript,” Bryer mentioned. “On Frontera we have been in a position to classify the amount surrounding the vesicle shortly and course of our knowledge in minutes. We estimated it would take about three weeks if we have been to run the evaluation in a serial naive implementation.”
The Perilla Lab has targeted all of this computing energy and experience into studying extra concerning the mysteries of what occurs to the HIV-1 viral envelope throughout an infection.
“Whereas this research doesn’t present the entire reply, it is getting there in what the lipids are doing and what integral membrane proteins are doing or may very well be doing; and never solely how proteins like gp41 work together with human receptors but additionally how they transmit their alerts and the way that’s associated to lipid composition,” Perilla mentioned.
“This computational research gives a possibility for drug growth analysis,” Perilla added.
Since lipid symmetry is maintained by the curvature of the envelope, a promising risk but unexplored is growth of small molecules that have an effect on the symmetry and doubtlessly yield a therapeutic goal.
Simply previous to the liposome analysis, Perilla and colleagues additionally broke new floor in utilizing supercomputers to construct the first-ever atomistic mannequin of the HIV-1 capsid, the envelope for its genetic materials, within the presence of the metabolite IP6. The work was revealed November 2021 within the journal Science Advances. It additionally used the Bridges-2 and Stampede2 supercomputers allotted by XSEDE.
The simulations, validated by cryo-electron tomography knowledge, confirmed that IP6 was in a position to bind in two areas to the capsid, as an alternative of only one as beforehand thought. This discovering is essential as a result of throughout an infection, the capsid is uncovered to the cytoplasm and has to undergo the nuclear import mechanism, particularly the nuclear pore complicated. All these items collectively level to the capsid having the ability to “sense” in an as but unknown approach the focus of IP6.
Mentioned Perilla: “Computationally, these are very distinctive simulations due to the variety of levels of freedom concerned. No person’s ever walked this path earlier than. We’re strolling by the darkish. And we’re making instruments that may assist us see past the place we’re.”