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Cryo-electron microscopy breaks a key barrier

nature.com

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Re: Cryo-electron microscopy breaks a key barrier

#41

Post by petermcneeley »

COGlory wrote: post #39

I'm a structural biologist that uses CryoEM to study archeal viruses. I'd be happy to answer any questions about CryoEM. I did want to point out though that this title is misleading. The researchers didn't get an image of an atom. Instead, they reconstructed hundreds of thousands of images of the protein to determine where the atoms are almost exactly. So there's no actual image that shows an atom, as cool as that wo…

Are there any observations that are surprising with respect to the predictions from quantum chemistry? (More specifically computational chemistry)

Re: Cryo-electron microscopy breaks a key barrier

#42

Post by criddell »

ckocagil wrote: post #30
criddell wrote: post #17

Earlier quoted context omitted.

I hope somebody weighs in because ever since I read that matter is just quantum field excitations I've lost all intuition about what reality is. Everything seems to be nothing.

Learn about the quantum eraser experiments and your jaw will drop. https://youtu.be/8ORLN_KwAgs

Oh wow. It's weirder than I thought.

Re: Cryo-electron microscopy breaks a key barrier

#43

Post by gewa »

mynegation wrote: post #40
COGlory wrote: post #39

I'm a structural biologist that uses CryoEM to study archeal viruses. I'd be happy to answer any questions about CryoEM. I did want to point out though that this title is misleading. The researchers didn't get an image of an atom. Instead, they reconstructed hundreds of thousands of images of the protein to determine where the atoms are almost exactly. So there's no actual image that shows an atom, as cool as that wo…

What are the limitations of this technique in determining spatial structure of the proteins? Do they get denaturated when cooled?

No, the proteins are vitrified very rapidly in liquid ethane at approx. -200°C, so that the structure ist conserved.

Re: Cryo-electron microscopy breaks a key barrier

#44

Post by diegoperini »

COGlory wrote: post #36
diegoperini wrote: post #33

Where can I find the pictures?

There aren't any. The way cryo-EM works is it images hundreds of thousands of copies of the molecule and uses those to construct a 3D model, in this case, with atomic resolution. However, a single micrograph doesn't necessarily contain atomic resolution.

Thanks for the explanation.

Re: Cryo-electron microscopy breaks a key barrier

#45

Post by benjaminva »

I had the privilege to ocasionally work with Holger Stark on similar structure determination challanges and can confirm that they really pushed the limits here thanks to very smart statistical methods. The resolution heavily depends on correctly sorting/classifying the large amount (> 10k for sure) images of these small particles.

There exists a race in the structural biology community about the next big method that allows to determine structures of proteins that were hard to crystalize and it seems that CryoEM is becoming the winner in this race.

As an alternative approach, people are building large X-ray lasers that have extremly high intensity and short pulse lengths which they plan to shoot at single particles and resolve individual scattering images. This method can very likely also achieve atomic resolution of non-crystaline particles, even without the need to freeze them down.

It will be exciting times for the whole bio-chemical physics community. Congrats to Holger and the team for another great publication in Nature.

Re: Cryo-electron microscopy breaks a key barrier

#46

Post by AtHeartEngineer »

marcosdumay wrote: post #24
iagovar wrote: post #9

So, pardon my ignorance, but can we finally say that atoms are particles with concrete dimensions? Last time I checked the whole field seemed measuring everything into probabilistic and statistical terms.

You can resolve atoms despite all the uncertainty just like you can resolve a tree at distance despite it not having a clear surface. The electron distribution falls with an exponential function on large distances, what is much cleaner than a tree surface anyway.

This is a good analogy

Re: Cryo-electron microscopy breaks a key barrier

#47

Post by candiodari »

gewa wrote: post #43
mynegation wrote: post #40

Earlier quoted context omitted.

What are the limitations of this technique in determining spatial structure of the proteins? Do they get denaturated when cooled?

No, the proteins are vitrified very rapidly in liquid ethane at approx. -200°C, so that the structure ist conserved.

"Vitrification" is a way to freeze water so that it forms a glassy solid instead of ice crystals, locking the proteins in place and so that the "ice" reflects electrons randomly like water does, and so the only large structure redirecting electrons is the protein particles.

Re: Cryo-electron microscopy breaks a key barrier

#48

Post by natechols »

fabian2k wrote: post #11

The headline is potentially confusing, it doesn't mean that this is the first time individual atoms were measured, but the first time this particular method has been pushed to such a high resolution that individual atoms could be distinguished. Cryo EM is a very hot method right now to determine the three-dimensional structure of large molecules like e.g. proteins or protein complexes. Something like 10-15 years ago…

When I started grad school in 2003 there were a handful of structures approaching 0.4 nm, which is the point where you might be able to build most of the sequence into the map de novo. But those were exceptional cases.

Re: Cryo-electron microscopy breaks a key barrier

#50

Post by mysterypie »

Could someone confirm what we’re looking at in that picture please? In that spider web of blue points joined by blue line segments: Those tiny blue points are atoms? The blue line segments are covalent bonds? And what’s the difference between the blue and purple areas?

If those line segments are probability distributions of shared electrons, that means our high school mental model of a covalent bond (drawing a line between two atoms) is not too bad.

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