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V-ATPase: Build-A-Thon Entry

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    googleplx
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    Hi All,

    My entry isn’t so much Sci-Fi as Sci-Non-Fi, but Kao insisted so here it is. This build is a color-coded model of the V-Type ATPase (one of nature’s smallest rotary pumps) from the budding yeast Saccharomyces cerevisiae (beer, bread). The different colors represent different protein chains, in places I have represented two proteins as one due to spacial considerations. The bottom bit spins relative to the top bit.

     photo 2013-03-10_225547_zpsbbae8a3c.png

     photo 2013-03-10_225043_zps4dec19a2.png

     photo 2013-02-26_212002_zps5dd6b9b8.png

    The pic (figure 8) I used for the build can be found here:

    Pubmed:
    http://www.ncbi.nlm.nih.gov/pubmed/18955482

    Link to paper(free):
    http://www.jbc.org/content/283/51/35983.full.pdf+html

    This shape was generated using some cool science that I don’t understand (freeze-fracture cryo-electron microscopy, and a shit-load of math) to generate a 3D rendering of this massive protein complex (~1 megadalton), and Patty Kane “docked” the known structures for individual protein chains (and made guesses for stuff with no known structure). The technique used to determine structures for the individual protein chains was x-ray crystallography which has ~ 10-fold better resolution and is capable of seeing individual atoms. However, there is disagreement between various labs about how the known high-rez structures fit in the larger shape, so ultimately this thing is a “best guess” on a number of levels.

    For those who are still reading and are wondering “but what the fuck does it do?”, it’s simple: This thing breaks down ATP and uses the energy from that reaction to push atoms of elemental hydrogen (protons) across a membrane. Essentially, the V-ATPase acidifies the membrane enclosed space and in doing so changes the properties of the solvent (water) to favor certain chemical reactions. This is hugely important for proper organelle function. In humans, subtle defects lead to a variety of diseases and major defects in V-ATPase function are embryonic lethal.

    I put this build in my backyard to remind me of the time I spent working on the V-ATPase. The lake represents the cytoplasmic-facing surface of a lipid bilayer. Opposed to how I have depicted it here, the bilayer itself is slightly less thick than the lower ring; in reality the bottom of the V-ATPase is exposed to bulk-solute from the lumen of the organelle/vesicle/plasma-membrane.

    http://en.wikipedia.org/wiki/V-ATPase

    It looks like a pile of assymetric shit colored by a blind person firstly, because nature made it that way and secondly, because things that size don’t have color and scientists like things to be obviously different so this is a somewhat standard color scheme.

    Maybe I’ll build a helicase next year.

    Specifics: Kaosubaloo kindly provided the materials. Constructed with scaffolding.

     photo 2013-02-26_212120_zps0f4a01ed.png

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