Researchers Determine Chemical Structure of HIV Capsid 90
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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Yeah, it's amazing how the evil bad guys had technology that was sixty years ahead of everybody else. Lemme guess, their cold-blooded space rulers gave them an R&D lab?
Mutations of the HIV virus (Score:4, Informative)
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
Since the "discovery" of the HIV virus in the late 1980's scientists have discovered that the HIV virus has undergone several mutations
Even if there are drugs which can successfully targets the HIV capsid that have been decoded in this experiment, it does not mean that the HIV virus won't mutate again, and change their capsid sequence (or chemical formula) to foil those drugs
But all in all, the effort in sequencing the capsid is indeed a breakthrough, a step forward in understanding the nature of the bug, even if it's one type, amongst the many varieties
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The thing is, the capsid's only 'function' is to keep the contents safe and prevent the immune system from recognising it as a threat. Because of this, it can mutate very quickly while still being viable, because it doesn't contain any essential machinery for the virus's infection vectors. There is more genetic variance in the HIV population of a single person after a year of infection than there is in all mammals. Trying to create a drug which targets a non-essential, rapidly changing component, like the c
Re: Mutations of the HIV virus (Score:1)
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Indeed. The AC was wrong. HIV is a blood-borne disease, not an STD. It didn't get to humans through sex, but from butchering monkeys for food - get a little infected blood on a cut and you'll catch it.
The GP is obviously an anti-government tin foil hat wearer and racist to boot. I can't figure out why so many anti-intellectuals like him are spouting off in a nerd site.
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50% is not good enough for medical science, they want guaranteed cures with well understood results. But if the WHITE PAPERS were fucking available to us we should be able to sell it as a non-medical treatment without guaranteed results.
Fat chance advertising it though and getting any credibility in our crazy ass fascist SCIENCE ONLY PLEASE culture.
There's also sound waves that break up and disturb pathogens as well. But no sonic waves can't do that... without harming the rest of the host. Bullshit.
-not pos
3,000 Nvidia Tesla K20X GPU (Score:5, Insightful)
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.
The picture suggests ... (Score:5, Insightful)
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?)
Re:The picture suggests ... (Score:5, Informative)
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
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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.
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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.
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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
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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
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Thanks for the awesome illustration of how the process works =)
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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].
It's repeated by the data (Score:1)
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
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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.
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Of course smartphones and tablet are not capable of curing disease. That is a good 4 or 5 years off.
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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
Re:3,000 Nvidia Tesla K20X GPU (Score:4, Funny)
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.
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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.
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So that's why they never released the third one.
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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.
this was with 0.011 exaFLOPS (Score:2)
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
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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!
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Much like there's no point building weather prediction computers, since all we do is put data we already have from weather stations into them, and no point building FEM simulators for structural engineering since we already know how a single girder acts under st
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breakthroughs in AIDS research have in fact come from supercomputer modeling.
Strange we have the simple equations of gravitation, but can't solve them for even the simple general case of three interacting bodies. But we can use numerical methods on supercomputer good enough for modeling interactions of millions of gravitational bodies. Something must be wrong about your assumptions.
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the simple general case of three interacting bodies.
You scientist types are all perverts, aren't you?
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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!
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"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.
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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....
Expected (Score:1)
Amazing, because that's exactly how I envisioned the HIV capsid would look, except in red and blue.
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Re:Expected (Score:4, Funny)
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Re:its a tesselated icosohedron (Score:5, Funny)
just like a geodesic dome, thats kind of interesting
Oh, cool, we can kill AIDS with zoning ordinances.
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just like a geodesic dome, thats kind of interesting
Oh, cool, we can kill AIDS with zoning ordinances.
HIV is no match for an HOA!
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If you don't want to live by the rules of an HOA, don't buy a house that is subject to them. It's not as if you don't have a choice.
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I've wondered along these lines in the past.
It's almost certain that the drug industry isn't deliberately withholding cures. Competition still exists between companies, and thanks to patents any novel cure would print money for the company that controlled it. It's not like they're in danger of running out of diseases to treat if they manage to cure a couple, is it?
But I think you're on to something with the pursuit of profit not being the best driving force for medical innovation. The cost of each dead e
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Yeah, greed is totally a modern invention brought about by The Evil Corporations. I think my eyes just rolled a full 360*.
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The supercomputer was the point of that (Score:1)
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
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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
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For various reasons NVIDIA's architecture is not optimal for bitcoin mining. But as you can see, it is quite powerful in other problem spaces.
Capsid Inhibitors Already Being Developed (Score:3, Interesting)
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