PSC, TACC Support HIV Replication Discovery

By Oliver Peckham

April 3, 2021

Like any virus, HIV requires host cells to reproduce: however, key steps in HIV’s reproductive process have eluded scientists for decades. Now, a team of researchers from the University of Pittsburgh, Ben-Gurion University of Negev, the University of Delaware and Cornell University have used a pair of supercomputers to uncover one of those mysteries, illuminating a key mechanism that enables the deadly virus to spread.

“For our part, we used MD [molecular dynamics] simulations,” said Chaoyi Xu, a graduate student at the University of Delaware and lead author on the paper, who explained that the research focused on HIV’s viral capsid – the envelope that holds the virus’ genetic material. “We studied how the HIV capsid allows permeability to small molecules, including nucleotides, IP6 [a metabolite that stabilizes the capsid] and others.”

Key to this: the observation of nucleotide translocation, where nucleotides (the building blocks of DNA and RNA) move in or out of the virus. To make the nucleotide translocation MD simulations computationally feasible at meaningful timescales, the researchers employed a modified form of umbrella sampling. “The advantage of using this technique is that we can separate the whole translocation process into small windows,” Xu explained.

Those small windows, of course, were then run in parallel on supercomputers: specifically, Bridges at the Pittsburgh Supercomputing Center (PSC) and Stampede2 at the Texas Advanced Computing Center (TACC), on which time was awarded to the project via XSEDE. 

“Without supercomputers, the computational part of the study would have been impossible,” Xu said. “By using the resources provided from XSEDE, we were able to run and not only test the translocation processes, but also the effects of small molecules binding on the translocation process by comparing the free energy differences calculated from our results.”

The molecular mechanism for nucleotide transmission. Image courtesy of Xu et al.

Co-author Juan R. Perilla, who leads the Perilla Lab at the University of Delaware, praised the unique capabilities of the systems. “On Bridges, we took advantage of the high memory nodes. They have these massive memory machines with 3 and 12 terabytes of inline memory. They’re really good for analysis,” he said, adding: “When I transferred from Stampede1 to Stampede2, the hardware was a big improvement. At the time, we were fascinated with the Intel Xeon Skylake nodes. They were fantastic.”

When the simulations were said and done, the researchers found that HIV would make use of its permeable capsids to “import” nucleotides from surrounding cells into its core for its replication process. The results were validated using both atomic force and transmission electron microscopy.

“To my knowledge, it’s the first piece of work that comprehensively shows an active role of the capsids in regulating a very specific lifecycle of the virus, not only computationally, but also in vitro assays and ultimately in the cells,” Perilla said.

To read Jorge Salazar’s reporting on this research, click here.

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