THE HOLY GRAIL: Structure of a Nanomachine If seeing is believing, how do scientists see cellular nanomachines,…

THE HOLY GRAIL: Structure of a Nanomachine If seeing is believing, how do scientists see cellular nanomachines, smaller than the wavelength of visible light? One way is to use a beam of electrons 100,000 times smaller than ordinary light to peer at individual atoms. But the energy of the powerful 200,000 volt electron beam can destroy the protein being imaged: imagine the radiation damage if you stood 20 m away from a thermonuclear device.

Take a Chill Pill: To cut down on damage to delicate chemical bonds, scientists use a variation known as Cryo EM. First, they place the purified sample on to a microfabricated carbon grid. Then they plunge it into a bath of liquid ethane that instantly vitrifies water, not allowing it to form crystals. This preserves the molecules in its native state. Using only a small puff of electrons, they image the sample in liquid nitrogen in a vacuum.  The resulting underexposed and overdeveloped image is disappointingly grainy. So they average many images of the same view to sharpen the resolution and cut down on noise. The 3D image is made from a series of tilted 2D images.

Tripping on Acid: The image seen in gray scale is at an unprecedented 9.7 angstroms resolution (or 0.97 nm) of a nanomachine from an ancient bacteria, Thermus thermophilus.  Although it functions as a rotary ATP synthase, it resembles the V-ATPase found in our cells- another rotary machine that works in reverse: breaking down ATP to acidify compartments. The V-ATPase and the ATP synthase share a common evolutionary origin seen in ancient archaebacteria like Thermus.

Intel Inside: Inside the gray outline seen by cryo-EM are the individual proteins that make up this nanomachine, observed by X-ray imaging. Compared to the ATP synthase (, the V-ATPase is even more complex and sophisticated.


Many thanks to expert gif-fer and science enthusiast Kevin Staff  who converted the original movie for your viewing pleasure! Check out Kevin’s original style and wit on his profile.

♫  Konstantin Lamanov saw the HOLY GRAIL and suggested the mystical melody of “The Holy Grail” Composed by Laurence Galian

Thank you for the musical pairing, Konstantin Lamanov as always 🙂

REF: Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.Lau WC, Rubinstein JL. Nature. 2011 Dec 18;481(7380):214-8. doi: 10.1038/nature10699

John Rubinstein:

ScienceSunday #sciencesunday  

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31 Responses to THE HOLY GRAIL: Structure of a Nanomachine If seeing is believing, how do scientists see cellular nanomachines,…

  1. “…they plunge it into a bath of liquid ethane that instantly vitrifies water…”

    Does the water still expand even though it doesn’t form crystals? I’m guessing that it does expand but the expansion doesn’t affect the sample.

  2. Rajini Rao says:

    Richard Healy , my understanding is that there is minimal physical alteration. I’ll have to look into volume changes. But here is a cool link that explains vitrification is a simplistic way:

  3. Mahesh K says:

    so.. vitrification is done for storing human donated organs.. is it??

  4. Rajini Rao says:

    Yes, that’s right Mahesh Kumar . Ice crystals are very damaging to living tissue.

  5. Mahesh K says:

    nice.. but i don’t think that chemical enters easily so that we can get uniform concentration

  6. Rajini Rao says:

    What chemical, Mahesh Kumar ?

  7. Mahesh K says:

    “Adding chemicals called cryoprotectants”   as mentioned in the link you gave

  8. Rajini Rao says:

    Prabat Parmal , the gif is large (8 Mb), so it probably does not load if the connection/band width is slow. Apologies..Kevin did give me smaller options but I did not like either the size or resolution. Thanks for that insight on electrical conductors! Good to know. These EM machines are power intensive.

  9. Sally Morem says:

    Totally awesome.  Nanotech is that much closer.

  10. Rajini Rao says:

    Mahesh Kumar , the cryoprotectants don’t enter cells. They fill the spaces between cells and protect cell membranes from cracking. Something as simple as glycerol (called glycerin, non scientifically) can work.

  11. Mahesh K says:

    ok.. thanks Rajini…

  12. Mahesh K says:

    Rajini Rao  And thanks for posting useful stuff among the dirty stuff in my profile..

  13. Jim Carver says:

    I don’t see how there could be a volume change if no crystals are formed. If there was, it would be slight as water has max density at 4C. But in any case the expansion of water as it freezes is not what causes most of the cell damage. It’s the change of osmotic pressure within the cell as the water comes out of solution as it crystallizes.

  14. Jim Carver says:

    hope I understood what you guys were talking about. 🙂 Having a bad hand day and had to take drugs.

  15. James Pearn says:

    Great post, fascinating stuff! I don’t mean to nitpick, but I think the size units are mixed up here: “9.7 angstroms resolution (or 97 nm)”. Surely 9.7 Å is equal to 0.97 nm?

  16. Thank you Rajini Rao for helping me learn info in an area that I know little about….very interesting!

  17. Rajini Rao says:

    James Pearn , edited..thanks. Back to grad high school for me. Sheesh 😛

  18. Rajini Rao says:

    Sorry that you are not feeling well, Jim Carver . You are quite right about the osmotic damage from freezing. I understand that the volume change should be slight, but I can’t figure out which direction it would be (slight expansion?). Thanks.

  19. Jim Carver says:

    Thanks Rajini Rao I think I typed too much yesterday.

    I’m thinking a slight expansion also. Wish I could give a good reason for thinking that. I guess just the fact that it decreases in density from 4C down to 0C under normal circumstances . But the effect is small (but important), only about 1 part in 10 000. Very important for life when we talk about lakes freezing.

  20. Rajini Rao says:

    We’ve made them already..they are in every cell you have, Feisal Kamil . Re. dad’s day..they are critical for becoming a dad too 😉

  21. Rajini Rao says:

    Haha, that would be cool too!

  22. Rajini Rao says:

    Feisal Kamil , they are likely just beads of some sort, coated with stuff. These nanomachines are ridiculously sophisticated. Unfortunately, there is no way we can replicate them as they are, but we could certainly design a simple rotary motor of sorts. I recall seeing some cool designs- I’ll share them if I find them.

  23. Nice!! post but tell me why its moving round..

  24. Raj Verma says:

    nice one dudeeeeee 

  25. … and we still need to visualize the result of such amazing science by using the gif image format.

  26. Rajini Rao says:

    Unfortunately, G+ technology and journal paywalls (not to mention copyright, oops!) don’t allow me to post the original 22 Mb movie here 🙂

  27. Rajini Rao says:

    We do in the lab, Feisal Kamil. Just not accessible on G+. It’s time G+ started to roll out some more innovations. It’s been a while since they did anything new here.

  28. ya its a nanomachine.. Feisal Kamil

  29. It’s fun how we have always dreamed to make nanomachines, just to find later that we are, in fact, a group of nanomachines working together, 

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