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Thread: HIV explained in Blender

  1. #1 HIV explained in Blender 
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    Hi,

    I'm a biochemist and for a group meeting presentation I wanted to illustrate the first step of the HIV entry and disassembly.
    So I took the occasion of doing some work with a program which I learned as an hobby (the best organic modeller open source).

    anyway this is the little animation:


    any comment are appreciated and if you spot mistakes please let me know!

    best regards,
    Pella


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  3. #2  
    Forum Professor Zwirko's Avatar
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    Very nice work, Pella. I have two criticisms, however: one very minor and one major.


    The minor first:
    You have the genome of HIV labelled as a negative sense RNA - it should be a positive sense RNA genome, ssRNA(+)
    Also, it's not all that clear if you have one RNA molecule in the capsid or two. There should be two, since retroviruses have dimeric RNA genomes.

    The major:
    You don't really show how the virus binds its receptors and is taken into the cell via the endocytic pathway - it's quite a bit more complicated than simply penetrating the cell and dumping the capsid inside the cytosol. So, the part where you describe the capsid as travelling along the cytoplasm and disassembling at the nuclear pore complex isn't very accurate.


    Other than that, I like it.


    edited to add: the protease should also be in the capsid.


    Last edited by Zwirko; November 29th, 2011 at 06:07 PM.
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    Quote Originally Posted by Zwirko View Post
    Very nice work, Pella. I have two criticisms, however: one very minor and one major.


    The minor first:
    You have the genome of HIV labelled as a negative sense RNA - it should be a positive sense RNA genome, ssRNA(+)
    Also, it's not all that clear if you have one RNA molecule in the capsid or two. There should be two, since retroviruses have dimeric RNA genomes.

    This I will put as a major, thank you! I read fast throught the wikipedia and I don't know why I was convinced it was a negative sesnse... And really I didn't know that it was a dimeric genome...

    Quote Originally Posted by Zwirko View Post
    The major:
    You don't really show how the virus binds its receptors and is taken into the cell via the endocytic pathway - it's quite a bit more complicated than simply penetrating the cell and dumping the capsid inside the cytosol. So, the part where you describe the capsid as travelling along the cytoplasm and disassembling at the nuclear pore complex isn't very accurate.
    It's simplified, and is really difficult to animate a membrane fusion process, so I decided to skip it... The receptor binding is not a major issue in my research, so I don't think it will make a big difference.

    Anyway are you really sure that the virus is taken up by endocytic pathway? and not by direct fusion with the plasma membrane?
    oky found the answer myself after a short google search (A new path for HIV entry - The Scientist - Magazine of the Life Sciences)
    I will read the original article when I get back to the uni... My information about the viral entry were a bit outdated.

    And if you know some review or articles, where is described how the capsid goes from the plasma membrane to the nucleus I will be really thankful!

    Quote Originally Posted by Zwirko View Post
    edited to add: the protease should also be in the capsid.
    wikipedia might be wrong?


    Thanks for the comments, finally something helpful!!
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    Forum Professor Zwirko's Avatar
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    Yeah, you're probably right about the location of the HIV-1 protease; I just assumed everything of value was in the capsid for some reason.

    For endocytosis of HIV you could try:

    Marc Permanyer, Ester Ballana, José A. Esté,
    Endocytosis of HIV: anything goes
    Trends in Microbiology
    Volume 18, Issue 12, December 2010, Pages 543-551



    For amusement you could also have a look at this interactive HIV model (activate labels and click on the thumbnails to peel away the layers). Obviously a bit over the top on the level of detail for your needs, but nice to look at anyway.
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