Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Molecular animations of ATP synthase

mrc-mbu.cam.ac.uk

Post reply on HN
Print view View original

1–10 of 11 posts

Re: Molecular animations of ATP synthase

#2

Post by jballanc »

To be more specific, this is the F0F1 Mitochondrial ATP Synthase. This protein is the reason that I decided to study biochemistry, but I have to say that this animation doesn't nearly do it justice. For one thing, the entire rotor/stator mechanism of the F0 unit is woefully glossed over. The rotor itself is composed of a number of alpha-helices that have a single location for a motile hydrogen to attach. In doing so, it causes a rotation of the lower half of the helix, generating a mechanical motion that turns the rotor.

In fact, probably the most amazing aspect of this protein is that it is, in every sense of the term, a nano-machine. ATP is generated not by chemical reaction, but rather by mechanical force. The 3 active sites in the F1 unit have residues which hold the ADP and Pi in a favorable arrangement, but it is the spring action, triggered by the crankshaft, that causes a vice-like movement that literally squeezes the two together to form ATP.

Very cool...if you ask me.

Re: Molecular animations of ATP synthase

#3

Post by kens »

This molecule is an amazing machine, powered by electricity. One thing I didn't realize until recently is how fast real molecules are compared to the animations. The molecular motor in the animation spins in real life at about 40,000 RPM - jet engine fast. The small molecules drifting around are actually moving at about 250 miles per hour. And instead of a few molecules drifting around, there are billions of molecules slamming into it every second.

I wrote a blog post a while back about how fast and crowded things are inside cells, that goes into more detail on this very protein: http://www.arcfn.com/2011/07/cells-are-very-fast-and-crowded...

Re: Molecular animations of ATP synthase

#4

Post by backprojection »

kens wrote: post #3

This molecule is an amazing machine, powered by electricity. One thing I didn't realize until recently is how fast real molecules are compared to the animations. The molecular motor in the animation spins in real life at about 40,000 RPM - jet engine fast. The small molecules drifting around are actually moving at about 250 miles per hour. And instead of a few molecules drifting around, there are billions of molecule…

Very cool. It seems fortunate that all these biological processes happen on a timescale comparable to the timescales of other processes around us - we're able to sense and think and respond about as fast as we would fall a couple of feet, so that we can land on our feet, for instance.

Re: Molecular animations of ATP synthase

#5

Post by robbiep »

kens wrote: post #3

This molecule is an amazing machine, powered by electricity. One thing I didn't realize until recently is how fast real molecules are compared to the animations. The molecular motor in the animation spins in real life at about 40,000 RPM - jet engine fast. The small molecules drifting around are actually moving at about 250 miles per hour. And instead of a few molecules drifting around, there are billions of molecule…

Hi kens, This is actually not powered by electricity but by the gradient of hydrogen ions between the inside and outside of the mitochondrial matrix... As jballanc says, and you say, this is awesomely cool though. I use this video http://www.youtube.com/watch?v=zOSyGTYCRFw to teach my future medical students the function of the ATPase - jballanc, I agree the mechanical aspect of ATP synthesis is awesome.

Re: Molecular animations of ATP synthase

#7

Post by vecter »

jballanc wrote: post #2

To be more specific, this is the F0F1 Mitochondrial ATP Synthase. This protein is the reason that I decided to study biochemistry, but I have to say that this animation doesn't nearly do it justice. For one thing, the entire rotor/stator mechanism of the F0 unit is woefully glossed over. The rotor itself is composed of a number of alpha-helices that have a single location for a motile hydrogen to attach. In doing so,…

I have a residual background in biochemistry from some high school science fair work, and what you described is absolutely amazing to hear! The fact that ATP is made by a "mechanical" force is pretty mind-blowing (although I suppose everything is "chemical" in the end at this scale).

Re: Molecular animations of ATP synthase

#9

Post by pygy_ »

jballanc wrote: post #2

To be more specific, this is the F0F1 Mitochondrial ATP Synthase. This protein is the reason that I decided to study biochemistry, but I have to say that this animation doesn't nearly do it justice. For one thing, the entire rotor/stator mechanism of the F0 unit is woefully glossed over. The rotor itself is composed of a number of alpha-helices that have a single location for a motile hydrogen to attach. In doing so,…

The video is part of a series.

http://www.mrc-mbu.cam.ac.uk/category/slideshows/atpmovies

The second one illustrates your description.

Post reply on HN