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Biotech Medicine Supercomputing

Researchers Determine Chemical Structure of HIV Capsid 90

Posted by timothy
from the new-line-of-attack dept.
adeelarshad82 writes "Researchers at the University of Illinois at Urbana-Champaign (UIUC) have determined the precise chemical structure of the HIV 'capsid,' a protein shell that protects the virus's genetic material and is a key to its virulence. The experiment involved mapping an incredible 64 million atoms to simulate the HIV capsid, pictured here. Interestingly no current HIV drugs target the HIV capsid and researchers believe that understanding the structure of the HIV capsid may hold the key to the development of new and more effective antiretroviral drugs. What makes this whole experiment even more fascinating is the use of Blue Waters, a Cray XK7 supercomputer with 3,000 Nvidia Tesla K20X GPU accelerators."
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Researchers Determine Chemical Structure of HIV Capsid

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  • by flayzernax (1060680) on Saturday June 01, 2013 @08:09PM (#43886195)

    I guess all those gamers aren't useless after all. You can thank me later for my donations to Nvidia's profits. So they could research and develop this technology.

    • by ColdWetDog (752185) on Saturday June 01, 2013 @08:32PM (#43886269) Homepage

      That there are numerous repeating elements in the capsid. Seems like this would be a perfect target for antibody formation. But obviously, that hasn't worked out. Be interesting to know why.

      (Armchair biology is wonderfully simple, isn't it?)

      • by Anonymous Coward on Saturday June 01, 2013 @08:39PM (#43886301)

        That there are numerous repeating elements in the capsid. Seems like this would be a perfect target for antibody formation. But obviously, that hasn't worked out. Be interesting to know why.

        (Armchair biology is wonderfully simple, isn't it?)

        The capsid is not exposed to the blood and therefore subject to interaction with antibodies. It's the layer beneath the viral capsule, and it is the capsule that is the most external layer which is exposed to the blood. Drug design will be likely to try and interact with the capsid once it is inside the cell and before it releases its payload

        • by X0563511 (793323)

          So, aggressive drugs that could enter the virus could then be targeted to act on the capsid, sparing other cells/bacteria/viruses in the body.

          I know nothing about this though, really.

          • I am not a biologist or very knowledgeable. However it seems according to this quote from the article:

            While no current HIV drugs target the HIV capsid, it is seen as "an attractive target for the development of new antiretroviral drugs" because scientists have discovered that the disruption of capsid functioning via a protein produced by Rhesus monkeys has given them an immunity to HIV.

            Perhaps some how managing to introduce something like you said into our biology that would damage the capsid once it was in a cell would allow nature to do the rest. And we would not even need further drugs.

            • by Ubi_NL (313657)

              the capsid doe not enter the cell. You need to administer that resus protein into the bloodstream where it will be a foreign substance and will induce an immune response

              • Re: (Score:3, Informative)

                by Vesvvi (1501135)

                The capsid doesn't enter the cell, but it is produced there.

                There are many possible lines of defense against viruses. Ignoring natural innate/adaptive immunity, you can block viral binding to cells (target receptors). You can interfere with replication of viral genomes (reverse transcription inhibitors, a big one for HIV). You can prevent assembly of new viruses (capsid inhibitors: http://jvi.asm.org/content/82/20/10262.full [asm.org], note the way they used structure to guide their work). Or you can prevent vir

      • Re: (Score:2, Interesting)

        by game kid (805301)

        What really catches my eye, irrelevant as it may be to its biology, is the capsid's vague resemblance to a monarch chrysalis [wikipedia.org].

      • by Anonymous Coward

        They didn't take a capsid. measure 64 million atoms and then simulate those atoms. They know what the capsid is made from, and they duplicated it up to the capacity of their supercomputer. The repeats are just a consequence of the small data they modeled from.

        Next year, when they get an upgrade, they'll be modelling the same data into 128 million atoms, or 200 million atoms, to no extra benefit.

        It reminds me of a Feyman story. How he used to make paints that could coat plastic. The competing company spend a

      • by Ubi_NL (313657)

        the repetitiveness of the capsid actually functions against antibodies, because the structure is immuno-dominant (so it attracts antibody targeting). However, binding of antibodies to the capsid does not inhibit the virus from infecting, as antibodies against virusses work via physical blockage of a molecular mechanism (like HA hexamerization) rather than act as a flag for termination by white blood cells.

    • by wjcofkc (964165)
      Talk about perspective. I doubt many people have ever bothered to stop and thing about it that way. I never did, but you are right. A vague analogy might along the lines: If Apple had not developed the first iPhone and functional tablet, none of our wonderful Android toys would be half as advanced as they are now, if they would even exits at all...

      Of course smartphones and tablet are not capable of curing disease. That is a good 4 or 5 years off.
      • I must admit that my assumptions are partially untrue in a logical sense. As we cannot predict alternative time lines. But thank you for the praise =) I suppose in a sense all things we do like this as a society can lead to potentially good (and bad) things. I would like to think that we are all somehow capable of doing this unintentional good however =)

        It is just as possible those GPUs could be used to make a weapon.

        I suppose like you say it is entirely a matter of perspective. And in this case a good pers

    • by K. S. Kyosuke (729550) on Saturday June 01, 2013 @09:05PM (#43886415)

      So they could research and develop this technology.

      ...and so that the future-formerly-sick people would be able to enjoy full life and not only Half Life.

      • by c0lo (1497653)

        So they could research and develop this technology.

        ...and so that the future-formerly-sick people would be able to enjoy full life and not only Half Life.

        Doh... take a HalfLife and a HalfLife2 license and you have a full life cheaper than the treatment will cost.

    • Re: (Score:1, Funny)

      by formfeed (703859)

      I guess all those gamers aren't useless after all. You can thank me later for my donations to Nvidia's profits.

      Of course. People buying a Nvidia Tesla have a significantly lower risk of contracting HIV.

      But who knew, they're also helping to fund research.

  • We'll have +100 exaFLOP systems in five years, 100 times the performance. Major structures in cells, and complete viruses, will be modelled to the atomic level

    • by inflamed (1156277)

      We'll have +100 exaFLOP systems in five years, 100 times the performance. Major structures in cells, and complete viruses, will be modelled to the atomic level

      Waiting for faster interconnects!

    • We'll have +100 exaFLOP systems in five years, 100 times the performance

      Exaflops?! And those suckers are electrical? Great Scott! We'll need a Nuclear Reaction to produce the 1.21 Jiggawahts of electricity required to power such things!

    • by Raul654 (453029)

      "We'll have +100 exaFLOP systems in five years" - that's totally untrue. There's an active debate going on in the field whether or not we'll be at 1 exaflop by 2020. We absolutely will not get to 100 before then.

      • by iggymanz (596061)

        oh really. so Intel's promise to deliver such a system by 2018 to DOE and NNSA is nonsense. or the Indian government's 2017 system by the ISRO and ISRC? see you in five years....

  • Amazing, because that's exactly how I envisioned the HIV capsid would look, except in red and blue.

    • Re: (Score:2, Funny)

      by K. S. Kyosuke (729550)
      It looks like a potato with a few buds sprouting. I wonder if they tried homeopathy. Perhaps the potato blight could be efficient against the virus, if you dilute it sufficiently.
      • Re:Expected (Score:4, Funny)

        by K. S. Kyosuke (729550) on Saturday June 01, 2013 @09:12PM (#43886449)
        Oh, sorry, my bad. That was supposed to be sympathetic magic, not homeopathy. Ever since the discovery of phlogiston, I have had hard time trying to keep pace with these modern scientific developments.
        • by dbIII (701233)
          Actually phlogiston makes a lot of sense until you consider the oxidation of iron. Phlogiston is how science is supposed to work - put up a theory, test it to destruction then work on what that tells you, such as the existence of oxygen and not just a single type of gas.
  • by Anonymous Coward

    They didn't need to simulate the *whole* capsid, it's homogeneous and any variations in it are unknowns, its like simulating 64 million atoms of carbon to understand graphene... completely pointless when a small number will do.

    Illinois only just got its supercomputer finished, courtesy of a gift from the National Science Foundation, and now needs to justify that budget:
    http://www.engadget.com/2013/03/29/blue-waters-supercomputer-now-online-24-7/

    And Aids research is the 'cute puppies' justificaton, it's like

    • by mcgrew (92797) *

      From wikipedia:

      The National Center for Supercomputing Applications (NCSA) is an American state-federal partnership to develop and deploy national-scale cyberinfrastructure that advances science and engineering. NCSA operates as a unit of the University of Illinois at Urbana-Champaign, although it provides high-performance computing resources to researchers across the country. Support for NCSA comes from the National Science Foundation, the state of Illinois, the University of Illinois, business and industry

  • by dplentini (1334979) on Sunday June 02, 2013 @06:51AM (#43887899)
    Check out U.S. Patent Publication Nos. 20130053267 and 20120302556 (among others from the same assignee). Capsid structures, like protein structures, can be useful starting points for drug development. Ultimately, however, the goal is to find a substance that will kill the disease without killing the patient. So far, no computer graphics package has replaced the grunt work of medicinal chemistry---methyl, ethyl, butyl, futile.

Murphy's Law, that brash proletarian restatement of Godel's Theorem. -- Thomas Pynchon, "Gravity's Rainbow"

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