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    While it is still an ongoing struggle for scientists to find an effective, safe HIV vaccine, a new supercomputer-aided discovery is offering new hope. Researchers from the University of Illinois and the University of Pittsburgh were able to accurately map the four million atoms that make up the HIV capsid (a protein shell that contains the virus’s genetic material), and this new knowledge may help find new ways to battle the virus and stop it from reproducing so rampantly. “The capsid is critically important for HIV replication,” said senior author Peijun Zhang from the University of Pittsburgh School of Medicine. “Knowing its structure in detail could lead us to new drugs that can treat or prevent the infection.”
    At the heart of these findings is the University of Illinois’ Blue Waters petascale supercomputer it broke down the incredibly complex HIV capsid, which is made up of some 1,300 identical proteins arranged into pentagons and hexagons. While researchers knew generally how the proteins were arranged, they didn’t know how the whole structure fit together or how many proteins made up the capsid. But Blue Waters was up to the task of running the many, many simulations needed to fully piece together the HIV capsid’s structure. “This is a big structure, one of the biggest structures ever solved,” said University of Illinois physics professor Klaus Schulten. “It was very clear that it would require a huge amount of simulation the largest simulation ever published — involving 64 million atoms.”
    With the HIV capsid now fully mapped, researchers hope the new knowledge will let them develop more beneficial vaccines and treatment options that take advantage of the capsid’s vulnerabilities. “The capsid is very sensitive to mutation, so if we can disrupt those interfaces, we could interfere with capsid function,” Dr. Zhang said. “The capsid has to remain intact to protect the HIV genome… but once inside it has to come apart to release its content so that the virus can replicate. Developing drugs that cause capsid dysfunction by preventing its assembly or disassembly might stop the virus from reproducing.” Some of the more effective antiviral drugs already target the capsid — with this new information, the HIV virus could be more vulnerable than ever.

    Source: The Verge

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