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First X-Ray Diffraction Image of a Single Virus

kdawson posted more than 6 years ago | from the caught-ya dept.

Biotech 57

KentuckyFC writes "X-ray crystallography has been a workhorse for chemists since the 1940s and 50s, revealing the 3D structure of complex biological molecules such as haemoglobin, DNA and insulin. But the technique has a severe limitation: it only works with molecules that form into crystals and that turns out to be a tiny fraction of the proteins that make up living things. But today, a team of US researchers say they have created the first image of a single uncrystallized virus using x-ray diffraction. The trick is to take a diffraction pattern of the virus and then subtract the diffraction pattern of its surroundings (abstract). The breakthrough paves the way for scientists to start teasing apart the 3D structures of the many proteins that have eluded biologists to date."

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The nobel prize goes to :D (1, Offtopic)

networkconsultant (1224452) | more than 6 years ago | (#23874325)

Those that cure HIV.

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23875585)

Those that cure HIV.

The girl with the biggest tits!

There, fixed that for you.

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23875687)

It's not that hard, really. All you need to do is inject yourself with a large dose of money... And then your AIDS will be gone!

Then again, Why give up your AIDS when they helped Jared of Subway fame lose so much weight?

I'm not just sure, I'm HIV positive

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23875819)

Prevention is the best cure. Free (abstinence), cheap (condoms), single partner who is also HIV free (cheap until you have a kid of course). Not saying to stop research into curing HIV, but I'll donate my money toward things that are not a behavioral problem.

Mij

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23876133)

So the best way to not die of aids, is to not get aids?

BRILLIANT!

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23876315)

His point is that it's not the same thing as, say polio, which you get just by walking down the street.

Re:The nobel prize goes to :D (-1, Troll)

Anonymous Coward | more than 6 years ago | (#23877231)

I dunno; My mother's cousin's best friend got aid by tripping onto a nigger's dick

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23878757)

Thank you. That was my point exactly. HIV is not a birth defect or similar issue. HIV is more akin to smoking related cancer, both avoidable.

Mij

Re:The nobel prize goes to :D (1)

palegray.net (1195047) | more than 6 years ago | (#23882243)

HIV is more akin to smoking related cancer, both avoidable.
Sure, right up to the point that your spouse decides to have an extramarital affair and doesn't bother to inform you. Does the uninformed party deserve to die?

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23903749)

I am not saying to stop research, just that when it comes down to it, the money would be better spent elsewhere first. If a spouse has an extramarital affair, isn't that a behavioral issue that should be avoided? The extramarital affair is similar to a rape by a HIV person. Yes it is sad and would definitely benefit by the research. On the other hand, if people didn't spread HIV by sleeping with numerous partners, wouldn't the disease eventually disappear? How many sexually transmitted diseases would disappear if one generation simply had one partner? What if those who had HIV (or other diseases) simply did the greater good for society by not reproducing? Wouldn't future society benefit?

Mij

Re:The nobel prize goes to :D (2, Insightful)

UncleTogie (1004853) | more than 6 years ago | (#23877273)

Not saying to stop research into curing HIV, but I'll donate my money toward things that are not a behavioral problem.

...because all those that contracted HIV from a bunk blood transfusion had a behavioral problem. Same with rape victims too, huh?

HIV is not necessarily a behavioral problem.

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23878689)

What are the statistics for HIV infections? How many are related to unsafe sex versus rape versus blood transfusion? Rape is still a behavioral problem (not on the victim, but the raper did choose to rape a person). Blood transfusion infections should be picked up in screening and testing (I know this was a concern in the early days of HIV but I haven't heard much on it of late).

True then that HIV is not necessarily a behavioral problem, but if you fix the behavioral side, the non-behavioral side eventually disappears too.

Mij

oh fuck off (2, Informative)

afxgrin (208686) | more than 6 years ago | (#23879959)

You are so deluded with this belief that it's a behavioral issue.

I think there's a bunch of Libyan kids [google.ca] who'd like to crack you across the head with a crowbar.

Re:oh fuck off (0)

Anonymous Coward | more than 6 years ago | (#23904047)

You prove my point exactly. The kids are a victim of the behavior of either a conspiracy or poor hygene on the part of the hospital administrators. They didn't develop the disease as a mutation, birth defect, etc..., rather it was something imposed on them by the behavior of others.

Mij

Re:The nobel prize goes to :D (1)

palegray.net (1195047) | more than 6 years ago | (#23882265)

There's an old saying that if a law harms one innocent man, it's a bad law. The same could be said for ignoring research that might cure any given terminal illness or disease. I take it you're not married, but I may be mistaken. If you're not, imagine your spouse contracting HIV from unprotected sex while having an affair. Let's say you've been, to the best of your ability, a devoted partner and have upheld "your end of the deal" faithfully. Someone comes along and says AIDS is a behavioral problem, and you're shit out of luck.

Here, let me load that pistol for you, it won't take that long with only one round...

Re:The nobel prize goes to :D (0)

Anonymous Coward | more than 6 years ago | (#23903901)

First, I'm not saying to stop research. I'm only saying that it shouldn't be the darling research project when money could be better spent elsewhere. Plain and simple, if you don't spread the disease, the disease will disappear. Based on some of the challenges to my statement should I gather that everyone would prefer to continue spreading and hope for a miracle cure? Wouldn't it be best to change behaviors to stop the spread of the disease? I for one will donate my money toward other causes.

I am actually married and have two children. As to my spouse having an affair, I'll still contend that it would be a behavioral issue that she should avoid (not just because it would be unfair to me but because of the risk it would present for health).

It will always be sad for those who are victims of other peoples behavioral actions that cause AIDs. For these people, research is probably the main reason to continue research. But just for a moment, consider that if everyone else would change their behavior, the victims of rape, birth, and blood transfusions wouldn't be in that situation.

Mij

Re:The nobel prize goes to :D (1)

palegray.net (1195047) | more than 6 years ago | (#23882235)

What happens when your partner in a monogamous relationship decides to alter the terms without informing you?

Makes sense (1, Interesting)

clonan (64380) | more than 6 years ago | (#23874353)

If you look at the density of a protein (which is pretty much all of a virus) it looks like a crystal. The common high school idea of a protein as a drop of fatty amino acids surrounded but wet amino acids is very false.

I wonder when they will start imaging other proteins?

This could be a boon to proteinomics!

Re:Makes sense (3, Informative)

Anonymous Coward | more than 6 years ago | (#23875417)

I think you are confusing terms. Fatty acids don't refer to amino acids. While it is true that there are certain amino acids that are hydrophobic and hydrophilic (among other properties) like many fatty acids, this doesn't mean they are fatty acids themselves.

As far as the rest of your comment, it is confusing. I assume you are talking about the primary structure of the protein when you talk about 'fatty' and 'wet' amino acids (which I'm guessing you are trying to say that the side chains of the primary structure are hydrophobic and hydrophilic). But then you jump to the tertiary structure by talking about 'fatty' amino acids being surrounded by 'wet' amino acids. I really don't follow what you are trying to say. Many proteins have surfaces designed for certain conditions (like transmembrane proteins that have both hydrophilic and hydrophobic surfaces to anchor them in a phospholipid bilayer), and indeed, their surfaces in the tertiary structure do cover over parts that may not be desirable on the surface. Are you trying to argue that this is wrong?

Re:Makes sense (2, Informative)

clonan (64380) | more than 6 years ago | (#23875833)

That is exactly what I am arguing is wrong.

The internal consistency of a protein more closley matches a very tight crystal than a hydrophobic amalgum.

It is absolutly true that hydrophilic amino acids are often on the surface except for specific circumstances like you mentioned. However these amino acids tend to adopt the most energetically efficient form possible which is usually crystaline.

What I was refering to is that for most of modern biology there was an assumption that since the consistency of the individual hydrophobic amino acids was very much like a oil that therefore the internal consistency of the protein should be similar. A more detailed analysis of densities, x-ray diffraction, fNMR and computer modeling proved that the internal structure of a protein is actually a very hard crystal with very little mobility of the individual atoms.

The older assumption is still often taught up through undergraduate level. When I was in High school proteins were described as a drop of oil surronded by hydrophilic amino acids.

Which high school was that? (1)

bill_mcgonigle (4333) | more than 6 years ago | (#23876549)

What I was refering to is that for most of modern biology there was an assumption that since the consistency of the individual hydrophobic amino acids was very much like a oil that therefore the internal consistency of the protein should be similar.

That's weird, I never heard anything like that in high school biochemistry or college biology.

A more detailed analysis of densities, x-ray diffraction, fNMR and computer modeling proved that the internal structure of a protein is actually a very hard crystal with very little mobility of the individual atoms.

Hrm? How do you explain proteins getting re-folded in that model? I mean, maybe when they're dry, but proteins are getting folded all the time in vivo.

Re:Which high school was that? (2, Interesting)

clonan (64380) | more than 6 years ago | (#23877675)

Actually refolding is fairly rare and almost always results from an environmental change (the protein get shoved into a membrane or it is surrounded by chaperon proteins). There are hinges and the like which affect functionality but thoes are very specific domains typically including a proline which isn't really an amino acid. Whole sale spontaneous refolding is essentially unheard of.

I went to a public high school and an engineering college. I heard the oil-drop model of proteins until I took biochem as a junior in college. The Biochem I took was actually a graduate level course.

Re:Makes sense (2, Informative)

rnaiguy (1304181) | more than 6 years ago | (#23877409)

While the interior of a protein resembles a crystal in terms of atomic packing density, it is certainly not crystalline, as it lacks the crucial requirement of being arranged in a regular pattern. You need a regular crystal lattice in order to amplify x-ray diffraction signals to detect them. That's why the resolution on this is so bad compared to x-ray crystallography studies. However, since you don't need crystals, this can be very useful for larger complexes and stuff, though probably not single proteins (unless the resolutions comes up 2 orders of magnitude).

Re:Makes sense (1)

clonan (64380) | more than 6 years ago | (#23877707)

Conceded. Protein's primary amino acid structure is too random (in most cases) to trully form a crystal.

But it is still cystaline. The local environment of most atoms resembles a cyrstal even if the more macro level does not.

Re:Makes sense (2, Informative)

rnaiguy (1304181) | more than 6 years ago | (#23878629)

What you say is correct to a point, but i don't understand the point you're trying to make. As you correctly alluded, the local environment of atoms in the protein interior has a packing density resembling that of a salt crystal, BUT they lack the regular lattice structure that allows for constructive interference to occur between X-ray photons to produce detectable diffraction patterns. That repetitiveness is the essential component of a crystal! There are crystals with low packing densities (solid water is less densely packed than liquid, and protein crystals can have huge holes in between protein molecules), but what they all have in common is a regular repeating lattice. So, in short, the protein interior is densely packed, but NOT crystalline.

Re:Makes sense (2, Insightful)

clonan (64380) | more than 6 years ago | (#23884423)

The reason X-ray diffraction needed a regular crystal not because it was impossible to get information but because there are limits on sensitivity and computation.

The first protein that X-ray crystallography was successfully used on was myoglobin. The processing included housewives recording the position of small,medium and large dots.

Now the sensitivity is much higher and the processing ability is astounding. This article is saying that they have figured out how to isolate the x-ray signal from a single protein. There is no reason that you can't get a high enough resolution to see the domains of a protein which often do have a regular crystal structure even if the whole protein doesn't.

overreaching /. summary (3, Informative)

jschen (1249578) | more than 6 years ago | (#23874379)

This work is really cool, and it's interesting to muse about what else might be imaged this way. But while 22 nanometer resolution may give insight into the structure of a virus, that would be awfully lousy resolution for a macromolecule (say, a protein) or even a macromolecular complex.

Re:overreaching /. summary (3, Informative)

damn_registrars (1103043) | more than 6 years ago | (#23874587)

while 22 nanometer resolution may give insight into the structure of a virus, that would be awfully lousy resolution for a macromolecule (say, a protein)

You hit the nail on the head, there. Indeed, protein structures generally need to be solved at a resolution of 8 angstroms or less to be taken seriously. And of course there are 10 Angstroms to a nanometer, so 22 nanometer resolution is equal to 220 Angstroms.

Useful for a virus superstructure, but with a protein you wouldn't be able to distinguish one end from another.

Not necessarily a overreaching /. summary (1)

clonan (64380) | more than 6 years ago | (#23874853)

There are a lot of protein superstructures in the body. Many of them are larger than viruses. I am thinking immune cell communications, mitrocondrial kreb cycle, ribosomes etc.

This system can be used to eveluate the actual difference a point mutation makes. That will allow better models of protein folding and therefore more accurate predictions of final protein function.

Re:overreaching /. summary (1)

Nimey (114278) | more than 6 years ago | (#23875989)

Could they get better resolution by using gamma rays, or (besides the radiation hazard) is there a technical problem with using higher-frequency photons?

Re:overreaching /. summary (1)

VeNoM0619 (1058216) | more than 6 years ago | (#23877127)

Are you trying to say the circle [arxivblog.com] photographs they took aren't high res enough? I thought I could tell plenty about the virus. It's circular and its composed of mostly 1 color...

Re:overreaching /. summary (1)

Nimey (114278) | more than 6 years ago | (#23878131)

No, dipshit, I asked if resolution could be improved with higher-freq light. Learn to read.

Re:overreaching /. summary (0)

Anonymous Coward | more than 6 years ago | (#23879059)

The joke obviously went over your head, now you look like an ass. Hand in your geek badge and may Robin Williams have mercy on your soul.

Re:overreaching /. summary (1)

Schraegstrichpunkt (931443) | more than 6 years ago | (#23886097)

Since when is Robin Williams a requirement for geek cred? Yeesh.

Re:overreaching /. summary (0)

Anonymous Coward | more than 6 years ago | (#23887767)

It's hard to generate that a beam of that frequency. They already have to use cyclotrons to get X rays of the desired frequencies for crystallography.

Re:overreaching /. summary (1)

mavi_yelken (801565) | more than 6 years ago | (#23876359)

Even that resolution can be beneficial. I am thingking they are aiming for big complexes in functional interactions with other proteins. Say observing a nucleosome in actin? or what exactly is going on during exocytosis? You might distinguish familiar players by their rough shape and this might be enough to say your protein complex of interest is involved in exocytosis.Couple this with transmission electron microscopy (which has 2nm resolution) it might be powerful indeed.

Re:overreaching /. summary (1)

comm2k (961394) | more than 6 years ago | (#23877403)

Indeed, protein structures generally need to be solved at a resolution of 8 angstroms or less to be taken seriously.
More like 2-4A. 8 Angstroms isn't much either and at 22A you may as well try single-particle EM. They have similar or slightly better resolution and don't depend on diffracting crystals.
Not to dismiss their work, in fact this may be very helpful for all these huge complexes where you're not even close to get nicely diffracting crystals.

Re:overreaching /. summary (1, Interesting)

Anonymous Coward | more than 6 years ago | (#23882195)

This is actually a very important point. The limiting factor in pretty much any coherent diffractive imaging (CDI) experiment is the angle to which one can measure scattering. This angle depends strongly on the wavelength of the light and the size of the detector: shorter wavelengths and larger detectors get you better potential resolution.

Whether or not you can measure scattering to the highest possible angle is often another question entirely. In particular, for biological specimens, there appears to be a pretty fundamental limit on how much energy you can deposit in the sample before it, for lack of a better term, blows up. That's why papers of this ilk usually rely on the supposition that one can measure 100,000 or more such patterns and combine them to form a very high resolution data set (or at least a reconstruction that's consistent with all the data).

CDI's a pretty new field and some of us think it has a lot of promise; however, it should be pointed out that for something like a virus, one might well be better off with a TEM. There you could probably get better than 1 nm resolution on a 100 nm thick sample. Of course, with TEM the resolution becomes poorer as the sample thickness increases, so like traditional X-ray microscopy, CDI probably has a more credible application in cellular imaging.

Re:overreaching /. summary (0)

Anonymous Coward | more than 6 years ago | (#23887637)

Actually, you need a structure resolution of about 2 to 2.5 angstroms to have a good idea of the side chains. About 4 angstroms will get you the backbone but anything more than that, protein size measurements are what you should be happy with.

Personally, I think this makes imaging of molecular superstructures possible, like collagen and myosin assemblies. Those things just don't crystallize.

Re:overreaching /. summary (1)

gbjbaanb (229885) | more than 6 years ago | (#23874953)

from TFA:

If confirmed, that's an extraordinary breakthrough. With brighter x-ray sources, the team says higher resolution images will be possible and that it's just a matter of time before they start teasing apart the 3D structures of the many proteins that have eluded biologists to date.

Re:overreaching /. summary (-1, Troll)

Anonymous Coward | more than 6 years ago | (#23876101)

On top of that, evolution is a THEORY at this point, not a solid, ironclad FACT. (My pastor has a good explanation of this.) So theres another problem.

WHy do I have to type in letters to post on this internet?

First step towards X-ray microscopy (1, Informative)

vossman77 (300689) | more than 6 years ago | (#23874391)

This is very exciting, I remember during my Biophysics training that "blah, blah, blah you cannot focus X-rays like you can visible light with lenses, so we'll never have an X-ray microscope." Well, this looks promi

Re:First step towards X-ray microscopy (4, Informative)

Cevets (989963) | more than 6 years ago | (#23874609)

Sorry, but people have been focusing x-rays for decades. As for x-ray microscopes, search up scanning transmission x-ray microscopy (STXM) or X-ray Photoelectron emission microscopy (X-PEEM), you should find them an interesting read.

Re:First step towards X-ray microscopy (2, Interesting)

blueg3 (192743) | more than 6 years ago | (#23875081)

While the statement "you cannot focus X-rays like you can visible light with lenses" is misleading, it's true. You can't focus X-rays like you can focus visible light, and you can't do it (effectively) with lenses. However, you can focus X-rays.

Re:First step towards X-ray microscopy (1)

Colonel Korn (1258968) | more than 6 years ago | (#23875215)

While the statement "you cannot focus X-rays like you can visible light with lenses" is misleading, it's true. You can't focus X-rays like you can focus visible light, and you can't do it (effectively) with lenses. However, you can focus X-rays.

Yeah, you just use zone plates.

Anyway, the GP is correct in saying that x-ray microscopy is nothing new. The technique in TFA is not microscopy. My understanding (just from skimming the abstract, mind you) is that this is x-ray scattering, which is physically equivalent to taking a fourier transform of the sample, followed by subtraction of the scattering image from a black sample cell, and then an inverse fourier transform to get back to a position-space image of the virus.

Maybe I'm being dim, but I can't currently think of a reason this is better than SEM/TEM of the virus. Maybe sample prep for normal microscopy isn't feasible, or maybe there's x-ray contrast but no electron contrast. I'm sure there are some compelling reasons to do this.

Re:First step towards X-ray microscopy (2, Informative)

blueg3 (192743) | more than 6 years ago | (#23876959)

Yes, neither x-ray microscopy nor x-ray diffraction are new. This appears to be essentially small-sample x-ray diffraction, as you describe.

TEM of biological materials (like a virus or protein) is tricky because the TEM can destroy the structure of the protein and can't adequately discern its internal structure. I'm less familiar with SEM, so I couldn't say, but diffraction is usually interesting not for obtaining an image of the sample, but determining its structure.

And yeah, you use zone plates. Or, for some applications, optical fiber (which is what we use to do confocal X-ray fluorescence).

Re:First step towards X-ray microscopy (2, Informative)

Steve525 (236741) | more than 6 years ago | (#23877597)

SEM imaging is not going to offer much improvement over TEM. The main advantage of a SEM is that you (usually) look at the electrons scattered from the surface instead of having to transmit the electrons through the sample. This does have some important advantages - you don't need to thin samples, and you can use lower electron energies. Lower electron energies might lead to less damage, but all that energy is deposited right at the surface. Plus, you only end up imaging the surface, which is why it's useful for images, but not for looking at internal structure. The resolution of a SEM tops (bottoms?) out at 1-2 nm.

This is interesting work, but as others have pointed out it'll need to achieve better resolution to really be useful. (22 nm is similar to what can be achieved with an x-ray microscope). I'm not sure what's limiting the resolution right now, but I'm guessing it's a signal to noise problem. One exciting thing this work has to potential to do is 3-D reconstructions. Think of this technique as crystallography without needing the ordered crystal to produce the data. That's (perhaps) the potential of the technique. The reality is, however, that radiation damage might be too much of a problem no matter how many advances they make.

Impressive (3, Insightful)

seanellis (302682) | more than 6 years ago | (#23874397)

What I find impressive is that they were able to get detectable amounts of x-rays diffracted off a single virus, with no staining.

Re:Impressive (1)

Ferzerp (83619) | more than 6 years ago | (#23878053)

I think you're a little confused at how light at xray wavelengths work and diffraction in general.

This is huge development (2, Funny)

Headw1nd (829599) | more than 6 years ago | (#23874407)

...though it seems strange to call it that.

Re:This is huge development (0)

Anonymous Coward | more than 6 years ago | (#23875113)

It should more aptly be called a Microscopic development

Re:This is huge development (1)

TornCityVenz (1123185) | more than 6 years ago | (#23881853)

Ohhh wait.....ehhh it was just something on the film. *rubs it off* /. "errmm Nevermind"

Rape? (-1, Offtopic)

Anonymous Coward | more than 6 years ago | (#23874451)

Rape rape rapE RaEp reap RAYYEP

Re:Rape? (-1, Offtopic)

Anonymous Coward | more than 6 years ago | (#23875169)

Holy shit, that guy was posting from prison, and apparently one of the larger guys is offended (or, strangely, aroused) by slashdot.

Nothin like the intertubes to bring you live (rectum) breaking news.

ring nebula (1)

johnrpenner (40054) | more than 6 years ago | (#23876657)


looks like one of these [google.com]

... :-P

(burning karma at a rate of ten)

Teasing apart the viruses (1)

denzacar (181829) | more than 6 years ago | (#23878743)

And you thought you had it hard back in high school.

Could you get a better image (1)

LuxMaker (996734) | more than 6 years ago | (#23888835)

with electron spectroscopy?
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