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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

#51

Post by natechols »

benjaminva wrote: post #45

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…

Having worked in X-ray crystallography on synchrotrons and XFELs, I can't take the single-particle XFEL concept seriously any more. Ten years ago it seemed impressive, but the EM technology has advanced so much faster - and it's a fraction of the cost. There are some neat applications of nanocrystallography, but that too seems like a niche application now, not a magic bullet for accelerating protein structure determination.

Re: Cryo-electron microscopy breaks a key barrier

#52

Post by natechols »

l33tman wrote: post #38
TomJansen wrote: post #10

The real breakthrough here is that with this technique you don't have to crystallize the proteins anymore, which is the biggest bottleneck in X-Ray Crystallography. Relevant; they used Cyro-EM to elucidate the structure of the SARS-CoV-2 Spike protein [1], which is a big step towards the development of a vaccine. This is a resolution of 3.5 ångström, but still a very nice feat. [1]: https://science.sciencemag.org/con…

3.5Å cryo-EM structures have existed for some time. The important thing coming down under 2Å or so, is that it drastically improves the quality of the molecular dynamics simulations you build of these structures.

I'm skeptical of molecular dynamics and docking studies... but the ability to clearly resolve bound drug molecules, or host-pathogen interactions, is very valuable indeed.

Re: Cryo-electron microscopy breaks a key barrier

#53

Post by natechols »

COGlory wrote: post #35
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.

What you see with cryo-EM are essentially clouds of electron density. So unfortunately, it doesn't address this.

Confirmed. I've worked with structures at close to sub-atomic resolution (0.8Å), where you can even see the "deformation" of hydrogen bonds and lone pairs in the electron density. But the actual information we have is simply a grid of electron density values averaged over an entire crystal.

Re: Cryo-electron microscopy breaks a key barrier

#55

Post by natechols »

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.

Haven't checked the article, but it's certainly possible the individual particle micrographs are archived somewhere. (But you're right, each will just look like a fuzzy gray blob.)

Re: Cryo-electron microscopy breaks a key barrier

#56

Post by natechols »

twic wrote: post #26
TomJansen wrote: post #18

Earlier quoted context omitted.

Oh please, this philosophical stuff is unnecessary. Cyro-EM is about a decade old and is just an alternative to X-Ray Crystallography for elucidating the structures of proteins. This article describes a way to improve the resolution of Cyro-EM, matching it to X-Ray Crystallography. The biggest bottleneck of X-Ray Crystallography is the production of protein crystals which is not necessary with Cyro-EM.

It's unbelievable how cryo-EM has come on. When i was a student, it was an also-ran behind crystallography and NMR, something that a few weird groups used to study a few special cases. Now you have to wonder if there's any point doing crystallography at all! I still like NMR, because you're looking at proteins in solution. But if the freezing is good in cryo-EM, maybe even that becomes moot.

It's especially shocking how many crystallographers have switched over - when I started, the ribosome crystal structures were the latest heroic achievement, but now nobody would waste time trying to crystallize ribosomes.

Re: Cryo-electron microscopy breaks a key barrier

#57

Post by tom-thistime »

pritovido wrote: post #16
The_rationalist wrote: post #2

What would be the "realistic" potential use cases?

We don't know yet. That is the idea about research. When the microscope was invented, people made the same question: What is the use of it? Just watching things we already know bigger? That is a recurring question. So much that Aristotle created the book MetaPhysics(meta meaning different from the Physics book) with the idea that this particular book did not need to be useful to be created. It was a compilation of no…

I agree about the microscope comments. On metaphysics I'm sorry but I have to disagree. "Metaphysics" was not Aristotle's name for those books, and unfortunately it's not even clear what the word means https://plato.stanford.edu/entries/metaphysics/#WorMetConMet

Re: Cryo-electron microscopy breaks a key barrier

#58

Post by pas »

mysterypie wrote: post #50

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 b…

Very good question. It'd be great to understand how this whole imaging process works. I have no idea, but it seems it involves many photos and rotation, and then DSP. So it's like CT for proteins .. maybe. It's like the x-ray crystallography but instead of repeating the x-ray many times on many-many samples. (edited)

https://kpwulab.wordpress.com/2018/12/13/a-1-96-a-cryoem-map...

https://cryoem.med.ubc.ca/image-gallery/

https://cemas.osu.edu/news/2019/03/exciting-cryo-em-updates

https://elifesciences.org/articles/25648.pdf

Re: Cryo-electron microscopy breaks a key barrier

#59

Post by ryanmt »

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 was doing this in grad school in 2009, we were pulling down to 10 angstroms in our best 3d reconstructions, sampling something around 30k virus particles (which I and some undergrads got to pick from the chromatographs).

Re: Cryo-electron microscopy breaks a key barrier

#60

Post by rezna »

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.

No longer need for hundreds of thousands. The aim is for just few thousands in few hours to reach acceptable resolution.

The development goes real fast with both SW and HW.

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