Live data from Hacker News

Cryo-electron microscopy breaks a key barrier

nature.com

91–100 of 110 posts

Re: Cryo-electron microscopy breaks a key barrier

#91
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…

Ok, since at least two of you who know what you're talking about have objected to the title, I've replaced it with the more general subtitle above. Thanks!

(Submitted title was "Cryo-electron microscopy technique sees individual atoms for first time".)

Re: Cryo-electron microscopy breaks a key barrier

#92

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…

Title changed now (see https://news.ycombinator.com/item?id=23423910).

Re: Cryo-electron microscopy breaks a key barrier

#94

Earlier quoted context omitted.

Thank you. > once you're used to it, the simple isosurface mesh is super easy to work with One wouldn't know it from the state of content, or even of much education research, but educational representation is much harder than professional. Students are unable to untangle features reflecting careful correctness, from artistic license. So both seed mis/conceptions. Professionals can downregulate misconceptions... thoug…

All I can offer in response is vague, hand-wavy speculation about human perceptive and cognitive limitations and how this impacts scientific representations. Coming from a biology background, I'm very used to artistic license and gross oversimplifications - and from years of habit, it almost hurts my brain to think about molecules as anything other than chicken-wire! From your complaint about those representations, I…

My own focus is more on science education representations. And on how badly they describe the represented physical systems. Emphasizing that this seems as much a science community failure, as an education community fail.

Consider an illustration of the solar system in some introductory astronomy content. Let say, that not atypically, it misrepresents sizes, positions, orientations, lighting, and Sun color. Thus creating and reinforcing misconceptions known to be a problem in K-12, in undergrad, and even on into astronomy graduate school. In contrast, consider a line representing an Earth-Mars transfer orbit. It seems unlikely that students will say think there's a material long pole there, and worry about it hitting satellites and cities. Students and teachers are both clear on the aphysicality of the line, but not of the Sun color. Hmm, though using a minimum-energy line to represent an energy landscape is a source of misconceptions.

Similarly, common representation of atoms and molecules are known to be causatively associated with the stew of misconceptions that pervade students and teachers of chemistry. Ribbons, perhaps not so much. Hmm, though also similarly, they're often used without indication of regional flexibility, and so perhaps contribute to the underappreciation of configuration landscapes, of the importance of tuned floppiness. Perhaps.

Consider a currently implausible goal, of science education which accessibly describes the physical world, and conveys a transferable understanding of it. Arguably its content would look much more like scientific visualizations than content does at present. But being for education, it faces additional constraints, challenges and tradeoffs, distinct from those of professional scientific visualization. Creating such would require a collaboration of both deep scientific and educational expertise. For which very little incentive exists at present.

I'm trying to come up with an XR-compatible visual representation of electron density, that is physically correct, accessible, and bears in mind patterns of misconceptions in chemistry education. That task should probably be more than one random software dev's lockdown hobby hack. But as far as I know, that's were we're at. The related NSF-funded work I've seen... doing this bit well wasn't their focus. Same with XR ed tech side. Same with chem ed apps. And scientific visualization programs. And chem ed research. There may well be something nice out there, but I've not yet seen it. And big ed side... I was chatting with a leading textbook publisher, which onboards content creators with the indoctrination that their liberal arts background, and complete unfamiliarity with science and tech, is not a problem... because there's "a scientist" on call. Deriving electron density, with current nice python libraries, and GPUs, has surely gotten vastly easier than it was with old fortran messes, but still... it seems something more is needed here. Some societal staffing seems missing. No?

Re: Cryo-electron microscopy breaks a key barrier

#95

While this is a breakthrough within the field of cryo-electron microscopy it is important to appreciate that for many questions in structural biology we also need to understand how protein structure changes over time. With the presented method the structure sampling time seems to be O(10 s) which easily is about 10 orders of magnitudes slower than the dynamics we're interested in seeing. A direct consequence of this…

To add on, another promising technique is ultrafast electron diffraction (UED). You can get atomic space and time resolution (sub-angstrom and 100 fs) already. It's just a matter of scaling up beam quality to the point we can study complex macromolecules. UED will also fit in a single room while the worlds only XFEL is miles long.

(I work on instrumentation improvements for XFELs and UED.)

Re: Cryo-electron microscopy breaks a key barrier

#96
post #88

Earlier quoted context omitted.

Further, atomic resolution is routine in electron microscopy, it's specifically Cryo EM (a sub-technique aimed at imaging proteins, which are extremely fragile compared to, say, chunks of metal or computer chips) where the advance has happened. This is phenomenal! The title still feels a bit sensationalized, but don't they all?

Cryo EM is really cool (not just in temperature! ;-) ) technology! :) Recently I had a chance to go on a tour in the two-part CEITEC research center in Brno, a city with long history of electron microscopy manufacturing and research. One part of the CEITEC research center does "dry" tech - chemistry, robotics, motor and machine control and chips. Of course, they have quite a lot of cutting edge electron microscopes t…

Small world :)

Re: Cryo-electron microscopy breaks a key barrier

#97

While this is a breakthrough within the field of cryo-electron microscopy it is important to appreciate that for many questions in structural biology we also need to understand how protein structure changes over time. With the presented method the structure sampling time seems to be O(10 s) which easily is about 10 orders of magnitudes slower than the dynamics we're interested in seeing. A direct consequence of this…

You're glossing over the advantages specific to cryo-EM though, which is it can give you a good picture of large ensembles of small things at this accuracy, with a lot less computational/interpretation hardship than X-ray crystallography or NMR. So for seeing structures of large protein complexes and how the super structure varies with heteromeric variation this is a really big deal. If you wanted to see what viral capsids in-situ looked like down to the atoms this is what you'd use. There are a lot of places this is going to be useful, there is no one method to rule them all in structural proteomics simply because nothing can offer all of the spatial and temporal scales one might need. Plus cryo would only give you the surface hull of these complexes, you'd still need a different method to fill in all the exact structures inside. Writing up these methods as if there is some competition for "best" is an entirely false impression to a lay person reading. The best is all methods improve and researchers collaborate to provide every possible scoped view. Even mass spectrometry is doing crazy things for investigating the structure of disordered proteins. You'd never use that for something you would use cryo-EM for.

Re: Cryo-electron microscopy breaks a key barrier

#99

While this is a breakthrough within the field of cryo-electron microscopy it is important to appreciate that for many questions in structural biology we also need to understand how protein structure changes over time. With the presented method the structure sampling time seems to be O(10 s) which easily is about 10 orders of magnitudes slower than the dynamics we're interested in seeing. A direct consequence of this…

But don't forget that these methods use class-averaging and each class represents members of a frozen structure. One of the beauties of cryoEM is that if your structure is dynamic, cryoEM will actually capture the ensemble in each class, which if you have enough images of each class you can solve each states' structure. One caveat is that if there are no local minima, you may have a huge number of states which means you won't get high resolution structures of each, but typically you'll have a few conformations that are reasonably stable. The other cool thing is you can throw in literal cell lysate and let the computers "purify" the sample for you. This allows the native environment to participate in the thermodynamic landscape of dynamic proteins, possibly showing more meaningful dynamic states.

Re: Cryo-electron microscopy breaks a key barrier

#100
post #80

Earlier quoted context omitted.

Thank you. Would it be fair to say that crystallized protein is always in one specific confirmation? Compared to that, would vitrification have the chance (however random) to capture protein molecules in different conformations?

Yes, a crystallized protein will always be in a single conformation, or you won't be able to see it because the electron density map will be an average of all possible conformations, and therefore meaningless. Single particle gives you the opportunity to see different conformations, but only if the data is discrete. If there's a continuous amount of conformations (think a molecular motor that's rotating) you would ne…

I hate to be that guy, but your first statement is technically incorrect: you can have discrete alternate conformations superimposed in the electron density (usually 2-3 is the most that can be resolved), and you can have different conformations of multiple copies of the molecule. (I've personally worked with both, although the differences in the second case were small.) That's not even counting ensemble-based approaches to modeling the crystal structure, although that's arguably just a different way of representing the uncertainty.

All that aside, crystallization certainly biases it towards specific conformations, which single-particle EM does not.

Post reply on HN