HIV-1: 360 degrees, inside and out

Posted by ERV on July 27, 2011
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This has been out for some time, but I was just linked to it by my Facebook friend, Brian– a really cool model of HIV-1, inside and out, based off of “more then 100 latest scientific publications in the fields of virology, X-ray analysis and NMR spectroscopy. The depicted spatial configurations of 17 different viral and cellular proteins found in HIV particle are in strict accordance with known 3D-structures.”

This isnt just an ‘artistic rendition’– its an artistic rendition founded on the best science to date ;)

Human Immunodeficiency Virus model

Now, if that image doesnt mean a whole hellovalot to you, I can fix that!

First, go back and refresh your memory on the basics of ERVs and all retroviruses!

Then, go back to the Human Immunodeficiency Virus model page, and click on the orange button in the upper left ‘Labels’.

Now when you scroll through the layers, you can see what all those components are, and when coupled with my SUPER AWESOME explanations of gag, pol, and env, it might kinda sorta make sense :P “‘MA protein is the product of viral Gag gene.’ Gag=structure, so MA must be a structural core protein!” “‘Integrase is encoded by the viral gene Pol.’ Integrase must be an enzyme!”

If you have any more Qs about what all is going on there– leave em in the comments!

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Comments

  1. #1 Kevin
    July 27, 2011

    I have a question: Why did looking at those pictures make me hungry? And then terrified?

  2. #2 G
    July 27, 2011

    Fantastic work .I really hope you will get to a day when editing genetic code would be as easy as is in software.

    I want to ask you a question . If i was the creator of a static animal world could i used the DNA backup mechanism of the deinococcus radiodurans to make my creation static ?
    Or there are obvious reasons for not using such thing (beside the need to evolve which i recon is vital but let say is not)

  3. #3 Mick
    July 27, 2011

    This is really, really cool. A little spooky, too. I didn’t expect so much internal structure.

    When I look at something like this, and marvel at the fact that it’s an amazing emergent property of an evolutionary system powered by a trickle of solar energy, one of my first thoughts is “Man, Creationists must be bored out of their minds.” Because an omnipotent god is a way less interesting explanation than the bizarre truth.

  4. #4 Antiochus Epiphanes
    July 27, 2011

    Maybe if you referred to HIV as “that fucking bitch” your audience might find this article interesting.

  5. #5 ERV
    July 27, 2011

    There is no point in personifying viruses. They dont ‘want’ to do what they do any more than water ‘wants’ to freeze at the appropriate temperature and pressure. Its just biochemistry.

  6. #6 Antiochus Epiphanes
    July 27, 2011

    Don’t imagine that the chimps over at teh big man thread would get that, though. My point is that maybe you should just stick to throwing poo.

  7. #7 windy
    July 27, 2011

    Maybe if you referred to HIV as “that fucking bitch” your audience might find this article interesting.

    Or, maybe she could attract an even wider audience if she described HIV as a rotting porcupine getting a rusty knife up its arse?

  8. #8 Antiochus Epiphanes
    July 27, 2011

    See? It’s working already. Your comment rate on this thread has increased from three comments in six hours to one in 20 minutes. Not counting yours or mine of course.

  9. #9 ERV
    July 27, 2011

    My point is that maybe you should just stick to throwing poo.

    Indeed– Ive been blogging about HIV-1 (politics, treatments, vaccines, immunology, etc), cancers (of all kinds), gene therapy, vaccines, evolution, any/all viruses, etc etc etc for almost six years now, and you have never commented on any of that until I caught your attention by throwing poo.

    So, either Im not the one that needs to get my priorities straight (Twatson=infinitely less important than using gene therapy to restore blind kids sight), or poo was indeed a functional means to get more peoples attention.

  10. #10 Antiochus Epiphanes
    July 27, 2011

    [meta]
    All this other junk aside, how have you been, windy? I laughed at your Lebowski reference the other day. FWIW.
    [/meta]

    Indeed– Ive been blogging about HIV-1 (politics, treatments, vaccines, immunology, etc), cancers (of all kinds), gene therapy, vaccines, evolution, any/all viruses, etc etc etc for almost six years now, and you have never commented on any of that until I caught your attention by throwing poo.

    Which is why I guess you ought to stick to it.

    So, either Im not the one that needs to get my priorities straight (Twatson=infinitely less important than using gene therapy to restore blind kids sight), or poo was indeed a functional means to get more peoples attention.

    You are completely right. Everyone who isn’t using gene therapy to cure blind kids is a complete cunt. It’s what my mama always said, anyway.

    Oh. That’s not what you meant. You meant that if someone isn’t doing something that you regard as important, you are completely justified in attacking them with sexist language.

    Or, what is it you were getting at?

  11. #11 nsib
    July 28, 2011

    Antiochus Epimanes,

    What the hell? Seriously, what the hell? Normally trolls say “stick to science” or something when a blogger posts an opinion piece they disagree with, but you do the opposite. Do you realize how completely insane you sound?

    Also, the last half of your post was complete argleblargle. Just a heads-up.

  12. #12 Antiochus Epiphanes
    July 28, 2011

    Do you realize how completely insane you sound?

    Sorry to be oblique, but of course I do. My point didn’t so much sail over your head, as right upside it.

    This place has turned into a complete asylum. I admit that ERVs writing in this blog has by and large been terrific. Many of the commenters over on the Mysogyny Thread don’t know that though, do they? This will be ERVs audience for awhile. She may want to keep them. I just offered advice on how to do that.

    Also, the last half of your post was complete argleblargle. Just a heads-up.

    I suppose it might be to the dimwitted. Again, I apologize for being oblique.

    My comment refers to the opinion that the discussion of “Twatson*” is of lesser concern than teaching people about using gene therapy to cure blindness. I didn’t address ERV’s fallacy that the poo flinging is the bait and the gene therapy discussion is the switch because it is patently ridiculous. I mean, look how fast this thread is filling up**. Rebecca Watson being unimportant doesn’t justify her having been called Rebecca Twatson. For that matter, even if Rebecca Watson were egregiously wrong, “Twatson” is just sexist. I wouldn’t call Anne Coulter that, and she makes my skin crawl. I recognize that ERV has the right to do this, because she has the right to use mysogynist language. However, having the right to use mysogynist language doesn’t make it any less mysogynist.

    *Jesus. I’m the troll here.
    **Although I bet that changes if we keep talking about elevatorgate rather than 3D HIV.

  13. #13 TylerD
    July 28, 2011

    You’re a low-quality threadjacking troll, AE.

  14. #14 mary
    July 28, 2011

    One of the many things I love about this blog is that you encourage questions..

    that pic is beyond cool and yup, as others have said..terrifying

  15. #15 dustbubble
    July 28, 2011

    That graphic you linked to is sublime. And a much less eye-jabbingly horrid colour scheme than the run-of-the-mill, aesthetically-challenged boffin’s diagram. Which goes a long way to helping know-nothings like me just keep on staring in wonder, and desperate to find out ‘WTF is going on there, then, eh?.
    Maybe I should rip it and have it printed up as a poster for the bedroom. Just to remind people.

    Oh, and get yer coat, I think you’ve pulled.
    On behalf of your trade, that is.
    Kid was scratching about behind me, so I said, seeing as you’re off to do Chem. in Sept., have a squint at this.
    Had to crowbar the lad off the machine, big smiles.
    I think he’s hooked.

    (They only teach a bit of Org. Chem. at High School, just enough to fail the exam, unless they can be persuaded to dig a bit deeper.
    Feckin’ internets, eh? If’n it had been around when I were a lad, I’d be unemployed and living in a skip.
    It’s absolutely marvellous. My second favourite waste of time.)

  16. #16 The Chimp's Raging Id
    July 28, 2011

    Antiochus Epiphanes | July 28, 2011 1:33 AM:

    *Jesus. I’m the troll here.

    Yes, your attempted thread derailment makes you exactly that. One look at that other thread will tell anyone who hasn’t lost their sanity to SIWOTI is that there is nothing that can be salvaged from it. All the disputants are now doing is spraying kerosene on a house fire. What on earth did you think you were going achieve by bringing the Rebeccapocalypse onto a perfectly good science thread beyond furthering the shitstorm?

    (FWIW My opinion of the arseholes on that other thread is in line with the majority opinion of Pharyngulites, but even with that in mind, I am left scratching my head at what you are trying to do here.)

  17. #17 Antiochus Epiphanes
    July 28, 2011

    What on earth did you think you were going achieve by bringing the Rebeccapocalypse onto a perfectly good science thread beyond furthering the shitstorm?

    I hadn’t thought about it that carefully.

  18. #18 ErkLR
    July 28, 2011

    I was shocked when ICAM showed up on the HIV-1 labels (I use it as a marker sometimes). I was thinking “WTF? How does HIV have an ICAM gene?” Then I saw that it steals the ICAM from the surface of infected cells (and apparently steals actin during budding). I had no idea viruses did this.

  19. #19 Phyraxus
    July 28, 2011

    I always HATED genetics just because geneticists always liked to name their genes the most elaborate name then give them an acronym with some numbers till eventually the original name is lost (textbooks rarely tell you the original name). Or, they find closely related genes that produce proteins of completely different function but keep with the acronym to signify their relatedness and not their function. That’s why I prefer biochemistry, they name their enzymes based on what they DO and tend to have some from of standardization. The naming of genes are just too random and seems to be like astronomy, whomever discovers it gets to name it whatever the hell they want.

    Anyway, nice picture, it’s shit like that that makes me realize that I have actually learned something in college.

  20. #20 JohnV
    July 28, 2011

    Good news phyraxus, with the amount of sequencing that’s done now, we get locus tags which are unique to each strain or each sequencing center (in the case of multiple centers sequencing the same strain) (or worse, one place sequences it and 2 places annotate it and you have multiple locus tags for the same gene). So by good news I mean it’s getting worse.

    And @Antiochus Epiphanes

    Who the fuck are you exactly? And why are you such a misogynistic shit bucket to come here and tell a woman what she should be blogging about. Go back to your echo chamber of female enlightenment where that sort of patriarchal behavior is acceptable.

    Also way to go dehumanizing people with whom you disagree. yeah yeah we’re all chimps. Of course some of us are scientists with real degrees in pertinent fields, but “OMG THEY’RE INHUMAN BECAUSE THEY’RE NOT ONE OF US”.

  21. #21 Mick
    July 28, 2011

    Yeah, just don’t feed the troll trolling about trolling, please. Shit’s getting dangerously recursive here.

  22. #22 JohnV
    July 28, 2011

    That’s why I included some science first :p

  23. #23 Mick
    July 28, 2011

    Sure, I wasn’t trying to bag on you.

    And… I didn’t realize gene naming was such a nightmare. Makes me feel a little blessed to be in another field. A quick search reveals that BioThesaurus might be an attempt to bring some order to things?

  24. #24 Phyraxus
    July 28, 2011

    For example, CYP450 genes encode CYtochrome P450 enzymes. They are typically found in the mitochondria, notably the electron transport chain (oxidative phosphorylation), detoxification of ROS (Reactive Oxygen Species), lipid biosynthesis, cholesterol biosynthesis, and initiate (or propagate the signal of) apoptosis (regulated cell death [cell suicide, if you will]).

    Thankfully, those guys aren’t all that messed up when it comes to nomenclature. Oh, they are called cytochromes because they absorb visible light due to their association with heme, a cytochrome, and the 450# because they absorb light of 450nm wavelength when they are conjugated/associated with carbon monoxide. They are not to be confused with hemoglobin, the protein oxygen carrier in red blood cells and also associated with heme, as it is not part of the CYP450 family.

    http://en.wikipedia.org/wiki/Cyp450

  25. #25 JohnV
    July 28, 2011

    Oh wow, I didn’t know about biothesaurus, that looks like it could be really helpful.

  26. #26 Antiochus Epiphanes
    July 28, 2011

    And why are you such a misogynistic shit bucket to come here and tell a woman what she should be blogging about. Go back to your echo chamber of female enlightenment where that sort of patriarchal behavior is acceptable. Also way to go dehumanizing people with whom you disagree. yeah yeah we’re all chimps. Of course some of us are scientists with real degrees in pertinent fields, but “OMG THEY’RE INHUMAN BECAUSE THEY’RE NOT ONE OF US”.

    How Orwellian.

    For the record I wasn’t dehumanizing people with whom I disagree. I was dehumanizing people who were behaving as if they weren’t human. That doesn’t apply to all of the people who were commenting over there, naturally. FWIW, while you didn’t say anything that was very meaningful, you didn’t come off as a complete slime-bucket either. From what I read anyway.

    Also, am I supposed to be very impressed that some of you are scientists with degrees in “pertinent”* fields? I suppose those degrees confer on you immunity from awful behavior. In that case, I guess I am impressed. Carry on with your shit-slinging.

    Maybe something on-topic: The real nomenclatural nightmare isn’t with organellar, prokaryotic, and certainly not with viral loci. The level of paralogy among eukaryotic nuclear genes that has surfaced with next-gen type technology is stupifying, and will continue to be problematic because it is very difficult to make names of copies parallel in different species without lots of phylogenetic analysis, so in the meantime, phyA1 in taxon Z may actually not be orthologous with phyA1 in closely related taxon Y. It is a nightmare of annotation that advanced bionformatics will not easily solve.

    *What that means in the context of the current slimo-apocalypse, I’ll never know.

  27. #27 Dwayne L
    July 29, 2011

    There is no point in personifying viruses. They dont ‘want’ …

    Ahem: “But the HIV-1 monster DO NOT WANT!” ;-P

    Love your writing, ERV.

  28. #28 Woden
    July 29, 2011

    I don’t typically comment on the science-y entries like this one, because they tend to be far enough past my knowledge level that I don’t feel I have much to contribute (this is not a bad thing, though; I’ve learned a lot about viruses from reading your blog, and that is an area I was quite uneducated on), but I just felt the need to chime in after reading A.E.’s first comment here:

    No need to change anything. This is a wonderful and very informative site you’ve got going, Abbie. While I’ll freely admit that I only started visiting here in the aftermath of the Elevatorgate stuff, that’s only because I’d never come across this blog before then.

  29. #29 Rin
    July 31, 2011

    Because I was bored that’s why! And Antiochus Epiphanes is getting on my tits…
    I noted down all the tags used in the last 50 entries of both ERV’s blog and pharyngula and seperated them into science and non-science tags. Here are the results…
    ERV’s posts contained 51 science tags and 24 non-science tags. The most popular science tags were – HIV/Aids (9), Vaccines (9) and XMRV (8). The most popular non-science tags were – Atheism (5), Douchebaggery (4) and Skepticism/Critical Thinking (3).
    Pharyngula had 16(!) science tags and 61(!) non-science tags. The most popular science tags were Organisms (5), Cephalopods (3) and Technology (2). I can’t be bothered going back to see how many of these posts were either “squee! baby octopus!” or “Mary’s Monday Metazoan” my guess is more than half. The most popular non-science tags were Open Thread (8), Godlessness (8) and Religion (8).
    So yes, ERV’s blog may soon see a rapid reduction in comments once this shit storm has all blown over but then, science is hard. I’ve thought about commenting here on a number of occasions but all I could ever sensibly write would be ‘Wha?’ The same goes with Starts With a Bang, that blog absolutely blows my mind, truly the best thing on the internet. Being a fearless culture warrior like PZ on the other hand is, quite frankly, a piece of piss, but certainly doesn’t do anything to increase anybody’s understanding of science. Finally, want to know how often the evolution tag appeared over the last 50 entries at pharyngula? Once.

  30. #30 fnxtr
    August 4, 2011

    Awesomepants. And it steals bits of membrane from the host to help it attach to the next host. Creeeeeepy.

  31. #31 Science Realist
    August 14, 2011

    Wow! Now THAT really scared me. The imaginary HIV boogeyman muppet you showed us is undoubtedly sure to be found in your head, Erv, even though it has never been found in the blood of even a single of those diagnosed as poz.

    The HIV-Muppet-Monster you shared with us foolish followers of false beliefs, is obviously made out of Russian carpet, pre-chewed multi-colored bubblegum, and is all mixed with clumps of silly string. How absolutely terrifying!!!

    Amazing that after 350 billion has been given to researchers such as Erv, that we still have no cure for stopping those who continue to project these imaginary Muppet Monsters that keep on sprouting up in the heads of those on the $$HIV-research-bandwagon$$.

    Nonetheless, I look forward to the day when there is a cure for illusionary monster muppets, or at least earmuffs given out for protection from those such as Erv, who continue projecting and spouting and promoting illusions of killer sex muppets into the minds of those naive and ignorant enough of reality who would believe her. But do keep in mind that ultimately she too, is the product of those who filled her own head with beliefs in such.

    Do you think that if we just throw more money at her and the rest of the HIV research megalopoly, they will just go away and stop harrassing the public with their fear-filled projections and illusions.

    Naaaah. That is what we have been doing wrong for the last 30 years, and the more we feed the fearfilled HIV scaremongerers, the more they want. The more they want, the more they try to scare us into giving them ever more money with more false data. They would have us believe that every gay and every African who has ever died has died of AIDS. They would have us falsely continue to believe for another 30 years that it is a threat to all of us, as in: “AAAAAGGGGHHHH, we are all gonna die of AIDS!”

    Perhaps the only workable solution for all mankind is to understand that the irrational sexually based fears and beliefs in and of HIV and AIDS that we as a society have, for the last 30 years, projected upon every self destructive drug-addled and eventually ill gay man, or every time we noticed another starving black person in Africa who gets ill, is to understand that these issues are really just that simple.

    They are no more than fear based illusions. No need for our current generation to continue our grandparents error of misperceiving reality, and inserting our own fear filled paranoiac delusions and illusions of sexually transmitted killer muppets. The cure for any insanity is to simply quit believing in it. Poof, HIV sex muppets and AIDS will be gone, humanity can get to working on the real underlying issues, the sick will be treated for actual illnesses presented, and Erv can get a real job flipping burgers and working at a dog kennel, or doing something else more constructive than what she is currently wasting her life and breath on.

  32. #32 SR
    August 14, 2011

    Nevermind,

    I realize it is a bit too much to expect the magical Harry Potter generation, which Erv exemplifies, to do much of anything other than continue to project illusions of magical and terrifying sex-muppet monsters.

    To understand her overactive imagination that got sucked into the hiv-aids boogeyman belief did not take much effort at all:

    To quote Erv: “I am Abbie, the cunning leader of an elite team of hackers. Born and raised in the fiery hell of Arrakis, we now relentlessly stalk our victims using our 31337 h4x0r skills like “Looking someone up on LinkedIn”, “Google”, and “Flickr”. FEAR OUR POWER!

    You are very powerful Abbie. Quite the magical female warrior-conquerer of all your imaginary demons, other than HIV.

    Good Grief