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Biotech Science

First X-Ray Diffraction Image of a Single Virus 57

Posted by kdawson
from the caught-ya dept.
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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First X-Ray Diffraction Image of a Single Virus

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  • Those that cure HIV.
  • Makes sense (Score:1, Interesting)

    by clonan (64380)

    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: (Score:3, Informative)

      by Anonymous Coward

      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

      • Re: (Score:3, Informative)

        by clonan (64380)

        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 i

        • 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

          • Re: (Score:3, Interesting)

            by clonan (64380)

            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

    • Re: (Score:2, Informative)

      by rnaiguy (1304181)
      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 protei
      • by clonan (64380)

        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: (Score:2, Informative)

          by rnaiguy (1304181)
          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
          • Re: (Score:3, Insightful)

            by clonan (64380)

            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

  • by jschen (1249578) on Friday June 20, 2008 @12:09PM (#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.
    • by damn_registrars (1103043) <damn.registrars@gmail.com> on Friday June 20, 2008 @12:25PM (#23874587) Homepage Journal

      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.
      • 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.

      • by Nimey (114278)

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

        • 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...
      • 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.
      • by comm2k (961394)

        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: (Score:1, Interesting)

        by Anonymous Coward

        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

    • by gbjbaanb (229885)

      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.
  • 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

    • by Cevets (989963) on Friday June 20, 2008 @12:26PM (#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: (Score:3, Interesting)

        by blueg3 (192743)

        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.

        • 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

          • Re: (Score:3, Informative)

            by blueg3 (192743)

            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 s

            • Re: (Score:3, Informative)

              by Steve525 (236741)

              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 us

  • Impressive (Score:4, Insightful)

    by seanellis (302682) on Friday June 20, 2008 @12:11PM (#23874397) Homepage Journal

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

    • by Ferzerp (83619)

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

  • by Headw1nd (829599) on Friday June 20, 2008 @12:11PM (#23874407)
    ...though it seems strange to call it that.

  • looks like one of these [google.com]

    ... :-P

    (burning karma at a rate of ten)

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

  • with electron spectroscopy?

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